Starting phenix.real_space_refine on Thu Feb 5 20:25:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4n_70108/02_2026/9o4n_70108.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4n_70108/02_2026/9o4n_70108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o4n_70108/02_2026/9o4n_70108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4n_70108/02_2026/9o4n_70108.map" model { file = "/net/cci-nas-00/data/ceres_data/9o4n_70108/02_2026/9o4n_70108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4n_70108/02_2026/9o4n_70108.cif" } resolution = 2.48 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= 0.009 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 116 5.16 5 C 12256 2.51 5 N 3288 2.21 5 O 3896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-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: 28 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: "H" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} 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: "E" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "I" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} 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: "F" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "J" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} 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: "G" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "K" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.91, per 1000 atoms: 0.25 Number of scatterers: 19565 At special positions: 0 Unit cell: (144.275, 144.275, 99.325, 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 116 16.00 O 3896 8.00 N 3288 7.00 C 12256 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 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 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG O 1 " - " FUC O 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 3 " " NAG U 1 " - " FUC U 3 " " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 146 " " NAG P 1 " - " ASN B 88 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 146 " " NAG S 1 " - " ASN C 88 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 146 " " NAG V 1 " - " ASN D 88 " " NAG W 1 " - " ASN D 234 " " NAG X 1 " - " ASN D 146 " Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 852.2 milliseconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 48 sheets defined 4.5% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 412A through 414 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 412A through 414 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 412A through 414 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 412A through 414 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.532A pdb=" N SER A 445 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS A 102 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.174A 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: 4.667A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER A 160 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE A 173 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.582A pdb=" N VAL A 202 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR A 207 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 5.495A 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: 3.610A pdb=" N LYS A 264 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.497A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.390A pdb=" N ASN A 372 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY A 399 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 392 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.634A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.521A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.532A pdb=" N SER B 445 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS B 102 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.667A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER B 160 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE B 173 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.582A pdb=" N VAL B 202 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR B 207 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AB8, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.610A pdb=" N LYS B 264 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.497A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 353 through 356 removed outlier: 6.390A pdb=" N ASN B 372 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 399 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 392 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.634A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.521A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU I 46 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.532A pdb=" N SER C 445 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS C 102 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.667A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER C 160 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE C 173 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.582A pdb=" N VAL C 202 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR C 207 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AD2, first strand: chain 'C' and resid 223 through 224 removed outlier: 3.610A pdb=" N LYS C 264 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.497A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 353 through 356 removed outlier: 6.390A pdb=" N ASN C 372 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY C 399 " --> pdb=" O ASN C 372 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 392 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.634A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.521A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU J 46 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.532A pdb=" N SER D 445 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS D 102 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.667A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER D 160 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE D 173 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.582A pdb=" N VAL D 202 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR D 207 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 223 through 224 Processing sheet with id=AE5, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.610A pdb=" N LYS D 264 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.497A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 353 through 356 removed outlier: 6.390A pdb=" N ASN D 372 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY D 399 " --> pdb=" O ASN D 372 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 392 " --> pdb=" O TRP D 378 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.634A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.521A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU K 46 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.570A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 1812 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: 4.00 Time building geometry restraints manager: 2.36 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: 6296 1.34 - 1.47: 5184 1.47 - 1.59: 8412 1.59 - 1.71: 0 1.71 - 1.83: 152 Bond restraints: 20044 Sorted by residual: bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" N GLU J 1 " pdb=" CA GLU J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 20039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26264 2.08 - 4.17: 848 4.17 - 6.25: 128 6.25 - 8.33: 20 8.33 - 10.41: 8 Bond angle restraints: 27268 Sorted by residual: angle pdb=" N LEU D 464 " pdb=" CA LEU D 464 " pdb=" C LEU D 464 " ideal model delta sigma weight residual 109.81 120.22 -10.41 2.21e+00 2.05e-01 2.22e+01 angle pdb=" N LEU B 464 " pdb=" CA LEU B 464 " pdb=" C LEU B 464 " ideal model delta sigma weight residual 109.81 120.22 -10.41 2.21e+00 2.05e-01 2.22e+01 angle pdb=" N LEU C 464 " pdb=" CA LEU C 464 " pdb=" C LEU C 464 " ideal model delta sigma weight residual 109.81 120.22 -10.41 2.21e+00 2.05e-01 2.22e+01 angle pdb=" N LEU A 464 " pdb=" CA LEU A 464 " pdb=" C LEU A 464 " ideal model delta sigma weight residual 109.81 120.22 -10.41 2.21e+00 2.05e-01 2.22e+01 angle pdb=" N GLY A 339 " pdb=" CA GLY A 339 " pdb=" C GLY A 339 " ideal model delta sigma weight residual 112.34 103.97 8.37 2.04e+00 2.40e-01 1.68e+01 ... (remaining 27263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 11204 17.69 - 35.38: 776 35.38 - 53.07: 164 53.07 - 70.76: 36 70.76 - 88.45: 20 Dihedral angle restraints: 12200 sinusoidal: 5132 harmonic: 7068 Sorted by residual: dihedral pdb=" CD ARG D 256 " pdb=" NE ARG D 256 " pdb=" CZ ARG D 256 " pdb=" NH1 ARG D 256 " ideal model delta sinusoidal sigma weight residual 0.00 50.05 -50.05 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CD ARG B 256 " pdb=" NE ARG B 256 " pdb=" CZ ARG B 256 " pdb=" NH1 ARG B 256 " ideal model delta sinusoidal sigma weight residual 0.00 50.05 -50.05 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CD ARG A 256 " pdb=" NE ARG A 256 " pdb=" CZ ARG A 256 " pdb=" NH1 ARG A 256 " ideal model delta sinusoidal sigma weight residual 0.00 50.05 -50.05 1 1.00e+01 1.00e-02 3.44e+01 ... (remaining 12197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2536 0.074 - 0.148: 460 0.148 - 0.222: 16 0.222 - 0.296: 0 0.296 - 0.370: 4 Chirality restraints: 3016 Sorted by residual: chirality pdb=" CA LEU A 464 " pdb=" N LEU A 464 " pdb=" C LEU A 464 " pdb=" CB LEU A 464 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA LEU D 464 " pdb=" N LEU D 464 " pdb=" C LEU D 464 " pdb=" CB LEU D 464 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA LEU B 464 " pdb=" N LEU B 464 " pdb=" C LEU B 464 " pdb=" CB LEU B 464 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 3013 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 256 " -0.690 9.50e-02 1.11e+02 3.11e-01 6.71e+01 pdb=" NE ARG B 256 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG B 256 " -0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG B 256 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG B 256 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 256 " -0.690 9.50e-02 1.11e+02 3.11e-01 6.71e+01 pdb=" NE ARG C 256 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG C 256 " -0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG C 256 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG C 256 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 256 " 0.690 9.50e-02 1.11e+02 3.11e-01 6.71e+01 pdb=" NE ARG D 256 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG D 256 " 0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG D 256 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG D 256 " 0.004 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4240 2.79 - 3.32: 18040 3.32 - 3.84: 34404 3.84 - 4.37: 43668 4.37 - 4.90: 74128 Nonbonded interactions: 174480 Sorted by model distance: nonbonded pdb=" OG SER F 31 " pdb=" OD1 ASN F 98 " model vdw 2.260 3.040 nonbonded pdb=" OG SER E 31 " pdb=" OD1 ASN E 98 " model vdw 2.260 3.040 nonbonded pdb=" OG SER H 31 " pdb=" OD1 ASN H 98 " model vdw 2.260 3.040 nonbonded pdb=" OG SER G 31 " pdb=" OD1 ASN G 98 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASP C 379 " pdb="CA CA C 502 " model vdw 2.270 2.510 ... (remaining 174475 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 502) 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 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } 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: 11.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.750 Find NCS groups from input model: 0.440 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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 0.063 20112 Z= 0.213 Angle : 0.887 10.413 27432 Z= 0.457 Chirality : 0.056 0.370 3016 Planarity : 0.013 0.311 3508 Dihedral : 13.099 88.447 7592 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.38 % Allowed : 1.13 % Favored : 98.50 % 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: 0.55 (0.16), residues: 2472 helix: -1.70 (1.03), residues: 24 sheet: 1.07 (0.16), residues: 988 loop : -0.05 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.003 ARG A 256 TYR 0.035 0.002 TYR C 252 PHE 0.030 0.004 PHE C 410 TRP 0.009 0.001 TRP B 302 HIS 0.007 0.002 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00502 (20044) covalent geometry : angle 0.87298 (27268) SS BOND : bond 0.00550 ( 40) SS BOND : angle 1.93438 ( 80) hydrogen bonds : bond 0.20487 ( 688) hydrogen bonds : angle 9.45657 ( 1812) link_BETA1-4 : bond 0.00216 ( 12) link_BETA1-4 : angle 2.55673 ( 36) link_BETA1-6 : bond 0.00274 ( 4) link_BETA1-6 : angle 1.41520 ( 12) link_NAG-ASN : bond 0.00290 ( 12) link_NAG-ASN : angle 2.56429 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 336 time to evaluate : 0.829 Fit side-chains REVERT: H 10 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8056 (mm-30) REVERT: H 72 ASP cc_start: 0.7262 (t0) cc_final: 0.6807 (t0) REVERT: L 103 LYS cc_start: 0.8690 (tttp) cc_final: 0.8483 (tttp) REVERT: E 10 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8055 (mm-30) REVERT: E 72 ASP cc_start: 0.7262 (t0) cc_final: 0.6807 (t0) REVERT: I 103 LYS cc_start: 0.8690 (tttp) cc_final: 0.8483 (tttp) REVERT: F 10 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8055 (mm-30) REVERT: F 72 ASP cc_start: 0.7261 (t0) cc_final: 0.6807 (t0) REVERT: J 103 LYS cc_start: 0.8692 (tttp) cc_final: 0.8484 (tttp) REVERT: G 10 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8054 (mm-30) REVERT: G 72 ASP cc_start: 0.7261 (t0) cc_final: 0.6807 (t0) REVERT: K 103 LYS cc_start: 0.8691 (tttp) cc_final: 0.8484 (tttp) outliers start: 8 outliers final: 4 residues processed: 344 average time/residue: 0.6612 time to fit residues: 255.4368 Evaluate side-chains 280 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 276 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain D residue 324 ASP 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: 0.9980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 296 HIS H 61 GLN B 226 GLN B 296 HIS E 61 GLN C 226 GLN C 296 HIS F 61 GLN D 226 GLN D 296 HIS D 372 ASN G 61 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.069944 restraints weight = 32635.554| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.25 r_work: 0.2770 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20112 Z= 0.160 Angle : 0.635 7.578 27432 Z= 0.331 Chirality : 0.048 0.210 3016 Planarity : 0.005 0.047 3508 Dihedral : 6.824 52.893 3276 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.50 % Allowed : 7.88 % Favored : 90.62 % 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: 0.67 (0.17), residues: 2472 helix: -0.72 (0.88), residues: 24 sheet: 0.98 (0.16), residues: 980 loop : 0.17 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 24 TYR 0.015 0.001 TYR D 252 PHE 0.022 0.002 PHE A 410 TRP 0.016 0.001 TRP D 178 HIS 0.002 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00358 (20044) covalent geometry : angle 0.62001 (27268) SS BOND : bond 0.00273 ( 40) SS BOND : angle 1.83651 ( 80) hydrogen bonds : bond 0.04686 ( 688) hydrogen bonds : angle 6.74938 ( 1812) link_BETA1-4 : bond 0.00416 ( 12) link_BETA1-4 : angle 1.79749 ( 36) link_BETA1-6 : bond 0.00249 ( 4) link_BETA1-6 : angle 1.32074 ( 12) link_NAG-ASN : bond 0.00192 ( 12) link_NAG-ASN : angle 2.23747 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 0.973 Fit side-chains REVERT: H 61 GLN cc_start: 0.9006 (tp40) cc_final: 0.8786 (tp-100) REVERT: L 24 ARG cc_start: 0.8272 (ttm110) cc_final: 0.8002 (ttm-80) REVERT: E 61 GLN cc_start: 0.9009 (tp40) cc_final: 0.8789 (tp-100) REVERT: I 24 ARG cc_start: 0.8275 (ttm110) cc_final: 0.8006 (ttm-80) REVERT: F 61 GLN cc_start: 0.9009 (tp40) cc_final: 0.8789 (tp-100) REVERT: J 24 ARG cc_start: 0.8274 (ttm110) cc_final: 0.8005 (ttm-80) REVERT: G 61 GLN cc_start: 0.9014 (tp40) cc_final: 0.8794 (tp-100) REVERT: K 24 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7991 (ttm-80) outliers start: 32 outliers final: 12 residues processed: 280 average time/residue: 0.6645 time to fit residues: 208.4733 Evaluate side-chains 252 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain G residue 19 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 53 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 208 optimal weight: 0.0770 chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.063268 restraints weight = 32629.346| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.34 r_work: 0.2666 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 20112 Z= 0.280 Angle : 0.655 12.854 27432 Z= 0.337 Chirality : 0.049 0.208 3016 Planarity : 0.005 0.039 3508 Dihedral : 6.719 54.811 3276 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.25 % Allowed : 8.44 % Favored : 89.31 % 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: 0.47 (0.17), residues: 2472 helix: -0.20 (0.90), residues: 24 sheet: 0.69 (0.16), residues: 960 loop : 0.15 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 118 TYR 0.015 0.002 TYR D 252 PHE 0.021 0.002 PHE D 121 TRP 0.018 0.002 TRP D 178 HIS 0.012 0.002 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00643 (20044) covalent geometry : angle 0.64059 (27268) SS BOND : bond 0.00428 ( 40) SS BOND : angle 1.71224 ( 80) hydrogen bonds : bond 0.04466 ( 688) hydrogen bonds : angle 6.43519 ( 1812) link_BETA1-4 : bond 0.00459 ( 12) link_BETA1-4 : angle 1.84514 ( 36) link_BETA1-6 : bond 0.00020 ( 4) link_BETA1-6 : angle 1.37680 ( 12) link_NAG-ASN : bond 0.00284 ( 12) link_NAG-ASN : angle 2.36120 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.765 Fit side-chains REVERT: H 72 ASP cc_start: 0.7517 (t0) cc_final: 0.7154 (t0) REVERT: H 81 ASP cc_start: 0.9076 (t70) cc_final: 0.8661 (t70) REVERT: L 17 GLU cc_start: 0.8022 (pm20) cc_final: 0.7796 (pm20) REVERT: L 24 ARG cc_start: 0.8314 (ttm110) cc_final: 0.7973 (ttm-80) REVERT: L 70 ASP cc_start: 0.8115 (m-30) cc_final: 0.7577 (m-30) REVERT: E 72 ASP cc_start: 0.7524 (t0) cc_final: 0.7164 (t0) REVERT: E 81 ASP cc_start: 0.9075 (t70) cc_final: 0.8660 (t70) REVERT: I 17 GLU cc_start: 0.8019 (pm20) cc_final: 0.7792 (pm20) REVERT: I 24 ARG cc_start: 0.8328 (ttm110) cc_final: 0.7987 (ttm-80) REVERT: I 70 ASP cc_start: 0.8129 (m-30) cc_final: 0.7605 (m-30) REVERT: F 72 ASP cc_start: 0.7522 (t0) cc_final: 0.7161 (t0) REVERT: F 81 ASP cc_start: 0.9077 (t70) cc_final: 0.8662 (t70) REVERT: J 17 GLU cc_start: 0.8024 (pm20) cc_final: 0.7794 (pm20) REVERT: J 24 ARG cc_start: 0.8323 (ttm110) cc_final: 0.7984 (ttm-80) REVERT: J 70 ASP cc_start: 0.8126 (m-30) cc_final: 0.7600 (m-30) REVERT: G 72 ASP cc_start: 0.7529 (t0) cc_final: 0.7166 (t0) REVERT: G 81 ASP cc_start: 0.9076 (t70) cc_final: 0.8661 (t70) REVERT: K 17 GLU cc_start: 0.8016 (pm20) cc_final: 0.7786 (pm20) REVERT: K 24 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7971 (ttm-80) REVERT: K 70 ASP cc_start: 0.8128 (m-30) cc_final: 0.7598 (m-30) outliers start: 48 outliers final: 8 residues processed: 260 average time/residue: 0.7384 time to fit residues: 212.1509 Evaluate side-chains 244 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 236 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain G residue 19 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 148 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 226 GLN H 61 GLN B 184 HIS B 226 GLN E 61 GLN C 184 HIS C 226 GLN F 61 GLN D 184 HIS D 226 GLN G 61 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.083751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.064239 restraints weight = 32642.842| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.33 r_work: 0.2640 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20112 Z= 0.247 Angle : 0.643 13.195 27432 Z= 0.328 Chirality : 0.049 0.249 3016 Planarity : 0.005 0.040 3508 Dihedral : 6.602 53.780 3276 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.25 % Allowed : 8.82 % Favored : 88.93 % 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: 0.31 (0.16), residues: 2472 helix: -1.02 (0.70), residues: 24 sheet: 0.58 (0.16), residues: 952 loop : 0.06 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 77 TYR 0.013 0.001 TYR B 252 PHE 0.019 0.002 PHE D 121 TRP 0.017 0.001 TRP B 178 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00566 (20044) covalent geometry : angle 0.62762 (27268) SS BOND : bond 0.00349 ( 40) SS BOND : angle 1.72359 ( 80) hydrogen bonds : bond 0.04070 ( 688) hydrogen bonds : angle 6.27715 ( 1812) link_BETA1-4 : bond 0.00405 ( 12) link_BETA1-4 : angle 1.85854 ( 36) link_BETA1-6 : bond 0.00011 ( 4) link_BETA1-6 : angle 1.37592 ( 12) link_NAG-ASN : bond 0.00301 ( 12) link_NAG-ASN : angle 2.35020 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 0.605 Fit side-chains REVERT: H 81 ASP cc_start: 0.9065 (t70) cc_final: 0.8669 (t70) REVERT: L 17 GLU cc_start: 0.8070 (pm20) cc_final: 0.7814 (pm20) REVERT: L 24 ARG cc_start: 0.8324 (ttm110) cc_final: 0.7976 (ttm-80) REVERT: L 70 ASP cc_start: 0.8123 (m-30) cc_final: 0.7573 (m-30) REVERT: E 81 ASP cc_start: 0.9062 (t70) cc_final: 0.8666 (t70) REVERT: I 17 GLU cc_start: 0.8073 (pm20) cc_final: 0.7816 (pm20) REVERT: I 24 ARG cc_start: 0.8332 (ttm110) cc_final: 0.7987 (ttm-80) REVERT: I 70 ASP cc_start: 0.8121 (m-30) cc_final: 0.7581 (m-30) REVERT: F 81 ASP cc_start: 0.9070 (t70) cc_final: 0.8676 (t70) REVERT: J 17 GLU cc_start: 0.8085 (pm20) cc_final: 0.7828 (pm20) REVERT: J 24 ARG cc_start: 0.8323 (ttm110) cc_final: 0.7976 (ttm-80) REVERT: J 70 ASP cc_start: 0.8119 (m-30) cc_final: 0.7574 (m-30) REVERT: G 81 ASP cc_start: 0.9060 (t70) cc_final: 0.8667 (t70) REVERT: K 17 GLU cc_start: 0.8080 (pm20) cc_final: 0.7822 (pm20) REVERT: K 24 ARG cc_start: 0.8316 (ttm110) cc_final: 0.7968 (ttm-80) REVERT: K 70 ASP cc_start: 0.8128 (m-30) cc_final: 0.7580 (m-30) outliers start: 48 outliers final: 8 residues processed: 260 average time/residue: 0.6734 time to fit residues: 194.4832 Evaluate side-chains 232 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 224 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain K residue 45 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: 0.8980 chunk 60 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 39 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS A 450 ASN B 296 HIS B 450 ASN C 296 HIS C 450 ASN D 296 HIS D 450 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.065525 restraints weight = 32375.232| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.36 r_work: 0.2668 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20112 Z= 0.160 Angle : 0.599 11.974 27432 Z= 0.304 Chirality : 0.046 0.182 3016 Planarity : 0.004 0.040 3508 Dihedral : 6.045 49.184 3268 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.88 % Allowed : 10.32 % Favored : 87.80 % 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: 0.29 (0.16), residues: 2472 helix: -1.30 (0.66), residues: 24 sheet: 0.61 (0.16), residues: 968 loop : 0.02 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 61 TYR 0.012 0.001 TYR D 252 PHE 0.015 0.002 PHE C 121 TRP 0.014 0.001 TRP B 178 HIS 0.002 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00360 (20044) covalent geometry : angle 0.58495 (27268) SS BOND : bond 0.00271 ( 40) SS BOND : angle 1.51736 ( 80) hydrogen bonds : bond 0.03606 ( 688) hydrogen bonds : angle 6.10877 ( 1812) link_BETA1-4 : bond 0.00375 ( 12) link_BETA1-4 : angle 1.88265 ( 36) link_BETA1-6 : bond 0.00106 ( 4) link_BETA1-6 : angle 1.35056 ( 12) link_NAG-ASN : bond 0.00240 ( 12) link_NAG-ASN : angle 2.24666 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.771 Fit side-chains REVERT: H 81 ASP cc_start: 0.9053 (t70) cc_final: 0.8649 (t70) REVERT: L 17 GLU cc_start: 0.8124 (pm20) cc_final: 0.7857 (pm20) REVERT: L 24 ARG cc_start: 0.8310 (ttm110) cc_final: 0.8008 (ttm-80) REVERT: L 70 ASP cc_start: 0.8117 (m-30) cc_final: 0.7588 (m-30) REVERT: L 93 GLN cc_start: 0.8749 (mt0) cc_final: 0.8504 (mt0) REVERT: E 81 ASP cc_start: 0.9050 (t70) cc_final: 0.8638 (t70) REVERT: I 17 GLU cc_start: 0.8125 (pm20) cc_final: 0.7858 (pm20) REVERT: I 24 ARG cc_start: 0.8312 (ttm110) cc_final: 0.8012 (ttm-80) REVERT: I 70 ASP cc_start: 0.8118 (m-30) cc_final: 0.7603 (m-30) REVERT: I 93 GLN cc_start: 0.8752 (mt0) cc_final: 0.8509 (mt0) REVERT: F 81 ASP cc_start: 0.9054 (t70) cc_final: 0.8651 (t70) REVERT: J 17 GLU cc_start: 0.8133 (pm20) cc_final: 0.7864 (pm20) REVERT: J 24 ARG cc_start: 0.8314 (ttm110) cc_final: 0.8011 (ttm-80) REVERT: J 70 ASP cc_start: 0.8113 (m-30) cc_final: 0.7594 (m-30) REVERT: J 93 GLN cc_start: 0.8760 (mt0) cc_final: 0.8518 (mt0) REVERT: G 81 ASP cc_start: 0.9045 (t70) cc_final: 0.8636 (t70) REVERT: K 17 GLU cc_start: 0.8131 (pm20) cc_final: 0.7863 (pm20) REVERT: K 24 ARG cc_start: 0.8310 (ttm110) cc_final: 0.8008 (ttm-80) REVERT: K 70 ASP cc_start: 0.8129 (m-30) cc_final: 0.7604 (m-30) REVERT: K 93 GLN cc_start: 0.8754 (mt0) cc_final: 0.8511 (mt0) outliers start: 40 outliers final: 4 residues processed: 258 average time/residue: 0.6465 time to fit residues: 186.4941 Evaluate side-chains 232 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain D residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 112 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 chunk 210 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 296 HIS A 450 ASN H 61 GLN B 226 GLN B 296 HIS B 450 ASN E 61 GLN C 226 GLN C 296 HIS C 450 ASN F 61 GLN D 226 GLN D 296 HIS D 450 ASN G 61 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.085834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.066527 restraints weight = 32385.922| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.37 r_work: 0.2690 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20112 Z= 0.146 Angle : 0.590 11.702 27432 Z= 0.299 Chirality : 0.046 0.183 3016 Planarity : 0.004 0.041 3508 Dihedral : 5.915 49.703 3268 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.69 % Allowed : 10.88 % Favored : 87.43 % 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: 0.32 (0.16), residues: 2472 helix: -1.38 (0.67), residues: 24 sheet: 0.59 (0.16), residues: 936 loop : 0.08 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 118 TYR 0.011 0.001 TYR A 252 PHE 0.014 0.001 PHE C 121 TRP 0.014 0.001 TRP A 178 HIS 0.011 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00329 (20044) covalent geometry : angle 0.57595 (27268) SS BOND : bond 0.00277 ( 40) SS BOND : angle 1.47013 ( 80) hydrogen bonds : bond 0.03468 ( 688) hydrogen bonds : angle 6.00082 ( 1812) link_BETA1-4 : bond 0.00368 ( 12) link_BETA1-4 : angle 1.88795 ( 36) link_BETA1-6 : bond 0.00145 ( 4) link_BETA1-6 : angle 1.34848 ( 12) link_NAG-ASN : bond 0.00217 ( 12) link_NAG-ASN : angle 2.22126 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.743 Fit side-chains REVERT: H 81 ASP cc_start: 0.9044 (t70) cc_final: 0.8642 (t70) REVERT: L 5 THR cc_start: 0.9010 (m) cc_final: 0.8757 (p) REVERT: L 17 GLU cc_start: 0.8129 (pm20) cc_final: 0.7842 (pm20) REVERT: L 24 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7917 (ttm-80) REVERT: L 70 ASP cc_start: 0.8112 (m-30) cc_final: 0.7593 (m-30) REVERT: E 81 ASP cc_start: 0.9039 (t70) cc_final: 0.8635 (t70) REVERT: I 5 THR cc_start: 0.9010 (m) cc_final: 0.8759 (p) REVERT: I 17 GLU cc_start: 0.8129 (pm20) cc_final: 0.7839 (pm20) REVERT: I 24 ARG cc_start: 0.8309 (ttm110) cc_final: 0.7913 (ttm-80) REVERT: I 70 ASP cc_start: 0.8115 (m-30) cc_final: 0.7603 (m-30) REVERT: F 81 ASP cc_start: 0.9044 (t70) cc_final: 0.8642 (t70) REVERT: J 5 THR cc_start: 0.9010 (m) cc_final: 0.8757 (p) REVERT: J 17 GLU cc_start: 0.8136 (pm20) cc_final: 0.7844 (pm20) REVERT: J 24 ARG cc_start: 0.8311 (ttm110) cc_final: 0.7911 (ttm-80) REVERT: J 70 ASP cc_start: 0.8118 (m-30) cc_final: 0.7603 (m-30) REVERT: G 81 ASP cc_start: 0.9033 (t70) cc_final: 0.8632 (t70) REVERT: K 5 THR cc_start: 0.9015 (m) cc_final: 0.8764 (p) REVERT: K 17 GLU cc_start: 0.8140 (pm20) cc_final: 0.7851 (pm20) REVERT: K 24 ARG cc_start: 0.8309 (ttm110) cc_final: 0.7914 (ttm-80) REVERT: K 70 ASP cc_start: 0.8132 (m-30) cc_final: 0.7620 (m-30) outliers start: 36 outliers final: 4 residues processed: 260 average time/residue: 0.5741 time to fit residues: 166.8541 Evaluate side-chains 244 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 240 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 215 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 242 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS H 61 GLN B 296 HIS E 61 GLN C 296 HIS F 61 GLN D 296 HIS G 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.065985 restraints weight = 32611.550| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.33 r_work: 0.2674 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20112 Z= 0.178 Angle : 0.604 12.260 27432 Z= 0.305 Chirality : 0.046 0.198 3016 Planarity : 0.004 0.040 3508 Dihedral : 5.866 49.537 3268 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.31 % Allowed : 11.26 % Favored : 87.43 % 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: 0.29 (0.16), residues: 2472 helix: -1.37 (0.67), residues: 24 sheet: 0.58 (0.16), residues: 936 loop : 0.04 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 83 TYR 0.011 0.001 TYR C 252 PHE 0.015 0.002 PHE C 121 TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00407 (20044) covalent geometry : angle 0.58788 (27268) SS BOND : bond 0.00332 ( 40) SS BOND : angle 1.82214 ( 80) hydrogen bonds : bond 0.03560 ( 688) hydrogen bonds : angle 5.97901 ( 1812) link_BETA1-4 : bond 0.00380 ( 12) link_BETA1-4 : angle 1.89445 ( 36) link_BETA1-6 : bond 0.00096 ( 4) link_BETA1-6 : angle 1.34862 ( 12) link_NAG-ASN : bond 0.00243 ( 12) link_NAG-ASN : angle 2.21477 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.696 Fit side-chains REVERT: A 313 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8255 (mp10) REVERT: H 81 ASP cc_start: 0.9038 (t70) cc_final: 0.8607 (t70) REVERT: L 5 THR cc_start: 0.9009 (m) cc_final: 0.8767 (p) REVERT: L 17 GLU cc_start: 0.8129 (pm20) cc_final: 0.7570 (pm20) REVERT: L 24 ARG cc_start: 0.8329 (ttm110) cc_final: 0.7971 (ttm-80) REVERT: L 70 ASP cc_start: 0.8092 (m-30) cc_final: 0.7559 (m-30) REVERT: L 93 GLN cc_start: 0.8775 (mt0) cc_final: 0.8471 (mt0) REVERT: B 313 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: E 81 ASP cc_start: 0.9038 (t70) cc_final: 0.8602 (t70) REVERT: I 5 THR cc_start: 0.9007 (m) cc_final: 0.8764 (p) REVERT: I 17 GLU cc_start: 0.8134 (pm20) cc_final: 0.7572 (pm20) REVERT: I 24 ARG cc_start: 0.8324 (ttm110) cc_final: 0.7963 (ttm-80) REVERT: I 70 ASP cc_start: 0.8096 (m-30) cc_final: 0.7572 (m-30) REVERT: I 93 GLN cc_start: 0.8767 (mt0) cc_final: 0.8461 (mt0) REVERT: C 313 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: F 81 ASP cc_start: 0.9045 (t70) cc_final: 0.8610 (t70) REVERT: J 5 THR cc_start: 0.9009 (m) cc_final: 0.8766 (p) REVERT: J 17 GLU cc_start: 0.8138 (pm20) cc_final: 0.7573 (pm20) REVERT: J 24 ARG cc_start: 0.8320 (ttm110) cc_final: 0.7958 (ttm-80) REVERT: J 70 ASP cc_start: 0.8090 (m-30) cc_final: 0.7564 (m-30) REVERT: J 93 GLN cc_start: 0.8775 (mt0) cc_final: 0.8471 (mt0) REVERT: D 313 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8255 (mp10) REVERT: G 81 ASP cc_start: 0.9030 (t70) cc_final: 0.8602 (t70) REVERT: K 5 THR cc_start: 0.9008 (m) cc_final: 0.8767 (p) REVERT: K 17 GLU cc_start: 0.8142 (pm20) cc_final: 0.7578 (pm20) REVERT: K 24 ARG cc_start: 0.8326 (ttm110) cc_final: 0.7968 (ttm-80) REVERT: K 70 ASP cc_start: 0.8104 (m-30) cc_final: 0.7576 (m-30) REVERT: K 93 GLN cc_start: 0.8770 (mt0) cc_final: 0.8464 (mt0) outliers start: 28 outliers final: 8 residues processed: 264 average time/residue: 0.7071 time to fit residues: 207.4887 Evaluate side-chains 252 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 313 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: 0.9980 chunk 25 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 54 optimal weight: 0.1980 chunk 195 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 296 HIS A 450 ASN H 61 GLN B 226 GLN B 296 HIS B 450 ASN E 61 GLN C 226 GLN C 296 HIS C 450 ASN F 61 GLN D 226 GLN D 296 HIS D 450 ASN G 61 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.086117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.066838 restraints weight = 32482.573| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.38 r_work: 0.2705 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20112 Z= 0.134 Angle : 0.591 11.489 27432 Z= 0.299 Chirality : 0.046 0.184 3016 Planarity : 0.004 0.040 3508 Dihedral : 5.771 49.922 3268 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.56 % Allowed : 12.38 % Favored : 87.05 % 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: 0.35 (0.16), residues: 2472 helix: -1.38 (0.69), residues: 24 sheet: 0.64 (0.16), residues: 932 loop : 0.08 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 118 TYR 0.011 0.001 TYR A 252 PHE 0.013 0.002 PHE D 121 TRP 0.014 0.001 TRP D 178 HIS 0.011 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00302 (20044) covalent geometry : angle 0.57436 (27268) SS BOND : bond 0.00280 ( 40) SS BOND : angle 1.84887 ( 80) hydrogen bonds : bond 0.03337 ( 688) hydrogen bonds : angle 5.90805 ( 1812) link_BETA1-4 : bond 0.00357 ( 12) link_BETA1-4 : angle 1.89649 ( 36) link_BETA1-6 : bond 0.00151 ( 4) link_BETA1-6 : angle 1.34135 ( 12) link_NAG-ASN : bond 0.00210 ( 12) link_NAG-ASN : angle 2.18276 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 246 time to evaluate : 0.683 Fit side-chains REVERT: A 313 GLN cc_start: 0.8516 (mt0) cc_final: 0.8237 (mp10) REVERT: H 81 ASP cc_start: 0.9021 (t70) cc_final: 0.8597 (t70) REVERT: L 5 THR cc_start: 0.8991 (m) cc_final: 0.8771 (p) REVERT: L 17 GLU cc_start: 0.8144 (pm20) cc_final: 0.7853 (pm20) REVERT: L 24 ARG cc_start: 0.8328 (ttm110) cc_final: 0.7989 (ttm-80) REVERT: L 70 ASP cc_start: 0.8082 (m-30) cc_final: 0.7560 (m-30) REVERT: L 93 GLN cc_start: 0.8764 (mt0) cc_final: 0.8462 (mt0) REVERT: B 313 GLN cc_start: 0.8515 (mt0) cc_final: 0.8236 (mp10) REVERT: E 81 ASP cc_start: 0.9023 (t70) cc_final: 0.8603 (t70) REVERT: I 5 THR cc_start: 0.8984 (m) cc_final: 0.8762 (p) REVERT: I 17 GLU cc_start: 0.8142 (pm20) cc_final: 0.7850 (pm20) REVERT: I 24 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7974 (ttm-80) REVERT: I 70 ASP cc_start: 0.8098 (m-30) cc_final: 0.7587 (m-30) REVERT: I 93 GLN cc_start: 0.8755 (mt0) cc_final: 0.8452 (mt0) REVERT: C 313 GLN cc_start: 0.8516 (mt0) cc_final: 0.8238 (mp10) REVERT: F 81 ASP cc_start: 0.9025 (t70) cc_final: 0.8604 (t70) REVERT: J 5 THR cc_start: 0.8987 (m) cc_final: 0.8767 (p) REVERT: J 17 GLU cc_start: 0.8152 (pm20) cc_final: 0.7858 (pm20) REVERT: J 24 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7973 (ttm-80) REVERT: J 70 ASP cc_start: 0.8092 (m-30) cc_final: 0.7575 (m-30) REVERT: J 93 GLN cc_start: 0.8762 (mt0) cc_final: 0.8460 (mt0) REVERT: D 313 GLN cc_start: 0.8504 (mt0) cc_final: 0.8223 (mp10) REVERT: G 81 ASP cc_start: 0.9017 (t70) cc_final: 0.8594 (t70) REVERT: K 5 THR cc_start: 0.8988 (m) cc_final: 0.8769 (p) REVERT: K 17 GLU cc_start: 0.8147 (pm20) cc_final: 0.7854 (pm20) REVERT: K 24 ARG cc_start: 0.8323 (ttm110) cc_final: 0.7982 (ttm-80) REVERT: K 70 ASP cc_start: 0.8104 (m-30) cc_final: 0.7592 (m-30) REVERT: K 93 GLN cc_start: 0.8759 (mt0) cc_final: 0.8455 (mt0) outliers start: 12 outliers final: 8 residues processed: 254 average time/residue: 0.7310 time to fit residues: 206.9562 Evaluate side-chains 244 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 236 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 192 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 226 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 190 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 131 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS A 450 ASN B 296 HIS B 450 ASN C 296 HIS D 296 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.067528 restraints weight = 32037.537| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.33 r_work: 0.2724 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20112 Z= 0.138 Angle : 0.597 11.259 27432 Z= 0.301 Chirality : 0.045 0.177 3016 Planarity : 0.004 0.040 3508 Dihedral : 5.740 50.205 3268 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.75 % Allowed : 12.29 % Favored : 86.96 % 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: 0.32 (0.16), residues: 2472 helix: -1.40 (0.69), residues: 24 sheet: 0.68 (0.17), residues: 908 loop : 0.02 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 83 TYR 0.011 0.001 TYR A 252 PHE 0.013 0.001 PHE C 410 TRP 0.013 0.001 TRP D 178 HIS 0.002 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00316 (20044) covalent geometry : angle 0.57609 (27268) SS BOND : bond 0.00337 ( 40) SS BOND : angle 2.21101 ( 80) hydrogen bonds : bond 0.03287 ( 688) hydrogen bonds : angle 5.86244 ( 1812) link_BETA1-4 : bond 0.00371 ( 12) link_BETA1-4 : angle 1.90602 ( 36) link_BETA1-6 : bond 0.00205 ( 4) link_BETA1-6 : angle 1.33974 ( 12) link_NAG-ASN : bond 0.00193 ( 12) link_NAG-ASN : angle 2.17645 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 0.820 Fit side-chains REVERT: A 313 GLN cc_start: 0.8481 (mt0) cc_final: 0.8195 (mp10) REVERT: H 81 ASP cc_start: 0.9021 (t70) cc_final: 0.8607 (t70) REVERT: L 5 THR cc_start: 0.8977 (m) cc_final: 0.8765 (p) REVERT: L 17 GLU cc_start: 0.8146 (pm20) cc_final: 0.7855 (pm20) REVERT: L 24 ARG cc_start: 0.8309 (ttm110) cc_final: 0.7971 (ttm-80) REVERT: L 70 ASP cc_start: 0.8072 (m-30) cc_final: 0.7542 (m-30) REVERT: L 93 GLN cc_start: 0.8757 (mt0) cc_final: 0.8453 (mt0) REVERT: B 313 GLN cc_start: 0.8480 (mt0) cc_final: 0.8192 (mp10) REVERT: E 81 ASP cc_start: 0.9021 (t70) cc_final: 0.8609 (t70) REVERT: I 5 THR cc_start: 0.8973 (m) cc_final: 0.8758 (p) REVERT: I 17 GLU cc_start: 0.8147 (pm20) cc_final: 0.7857 (pm20) REVERT: I 24 ARG cc_start: 0.8297 (ttm110) cc_final: 0.7956 (ttm-80) REVERT: I 70 ASP cc_start: 0.8088 (m-30) cc_final: 0.7569 (m-30) REVERT: I 93 GLN cc_start: 0.8756 (mt0) cc_final: 0.8454 (mt0) REVERT: C 313 GLN cc_start: 0.8485 (mt0) cc_final: 0.8197 (mp10) REVERT: F 81 ASP cc_start: 0.9020 (t70) cc_final: 0.8608 (t70) REVERT: J 5 THR cc_start: 0.8974 (m) cc_final: 0.8761 (p) REVERT: J 17 GLU cc_start: 0.8155 (pm20) cc_final: 0.7858 (pm20) REVERT: J 24 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7951 (ttm-80) REVERT: J 70 ASP cc_start: 0.8074 (m-30) cc_final: 0.7551 (m-30) REVERT: J 93 GLN cc_start: 0.8762 (mt0) cc_final: 0.8462 (mt0) REVERT: D 313 GLN cc_start: 0.8473 (mt0) cc_final: 0.8184 (mp10) REVERT: G 81 ASP cc_start: 0.9016 (t70) cc_final: 0.8601 (t70) REVERT: K 5 THR cc_start: 0.8977 (m) cc_final: 0.8765 (p) REVERT: K 17 GLU cc_start: 0.8155 (pm20) cc_final: 0.7859 (pm20) REVERT: K 24 ARG cc_start: 0.8302 (ttm110) cc_final: 0.7963 (ttm-80) REVERT: K 70 ASP cc_start: 0.8097 (m-30) cc_final: 0.7578 (m-30) REVERT: K 93 GLN cc_start: 0.8757 (mt0) cc_final: 0.8453 (mt0) outliers start: 16 outliers final: 12 residues processed: 248 average time/residue: 0.7990 time to fit residues: 218.8501 Evaluate side-chains 252 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain G residue 83 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 25 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 243 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 240 optimal weight: 0.0570 chunk 118 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 222 optimal weight: 0.0000 chunk 150 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.1506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 296 HIS H 61 GLN B 226 GLN B 296 HIS E 61 GLN C 226 GLN C 296 HIS C 450 ASN F 61 GLN D 226 GLN D 296 HIS D 450 ASN G 61 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.085659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.066302 restraints weight = 32507.899| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.37 r_work: 0.2689 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20112 Z= 0.194 Angle : 0.611 12.187 27432 Z= 0.309 Chirality : 0.046 0.188 3016 Planarity : 0.004 0.040 3508 Dihedral : 5.821 49.700 3268 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.94 % Allowed : 12.01 % Favored : 87.05 % 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 (0.16), residues: 2472 helix: -1.35 (0.69), residues: 24 sheet: 0.64 (0.17), residues: 932 loop : 0.02 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.010 0.001 TYR B 252 PHE 0.015 0.002 PHE C 121 TRP 0.013 0.001 TRP C 178 HIS 0.010 0.002 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00449 (20044) covalent geometry : angle 0.59223 (27268) SS BOND : bond 0.00321 ( 40) SS BOND : angle 2.15813 ( 80) hydrogen bonds : bond 0.03525 ( 688) hydrogen bonds : angle 5.91273 ( 1812) link_BETA1-4 : bond 0.00372 ( 12) link_BETA1-4 : angle 1.88647 ( 36) link_BETA1-6 : bond 0.00079 ( 4) link_BETA1-6 : angle 1.34259 ( 12) link_NAG-ASN : bond 0.00244 ( 12) link_NAG-ASN : angle 2.17751 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: H 81 ASP cc_start: 0.9040 (t70) cc_final: 0.8640 (t70) REVERT: L 5 THR cc_start: 0.8979 (m) cc_final: 0.8757 (p) REVERT: L 17 GLU cc_start: 0.8135 (pm20) cc_final: 0.7833 (pm20) REVERT: L 24 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7993 (ttm-80) REVERT: L 70 ASP cc_start: 0.8105 (m-30) cc_final: 0.7569 (m-30) REVERT: B 313 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: E 81 ASP cc_start: 0.9037 (t70) cc_final: 0.8638 (t70) REVERT: I 5 THR cc_start: 0.8976 (m) cc_final: 0.8752 (p) REVERT: I 17 GLU cc_start: 0.8137 (pm20) cc_final: 0.7833 (pm20) REVERT: I 24 ARG cc_start: 0.8327 (ttm110) cc_final: 0.7979 (ttm-80) REVERT: I 70 ASP cc_start: 0.8108 (m-30) cc_final: 0.7578 (m-30) REVERT: C 313 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8270 (mp10) REVERT: F 81 ASP cc_start: 0.9037 (t70) cc_final: 0.8638 (t70) REVERT: J 5 THR cc_start: 0.8982 (m) cc_final: 0.8761 (p) REVERT: J 17 GLU cc_start: 0.8147 (pm20) cc_final: 0.7843 (pm20) REVERT: J 24 ARG cc_start: 0.8329 (ttm110) cc_final: 0.7981 (ttm-80) REVERT: J 70 ASP cc_start: 0.8106 (m-30) cc_final: 0.7573 (m-30) REVERT: D 313 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: G 81 ASP cc_start: 0.9033 (t70) cc_final: 0.8633 (t70) REVERT: K 5 THR cc_start: 0.8983 (m) cc_final: 0.8762 (p) REVERT: K 17 GLU cc_start: 0.8139 (pm20) cc_final: 0.7835 (pm20) REVERT: K 24 ARG cc_start: 0.8338 (ttm110) cc_final: 0.7992 (ttm-80) REVERT: K 70 ASP cc_start: 0.8116 (m-30) cc_final: 0.7585 (m-30) outliers start: 20 outliers final: 8 residues processed: 244 average time/residue: 0.7795 time to fit residues: 210.8723 Evaluate side-chains 248 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain F residue 83 ARG Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain G residue 83 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 142 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 194 optimal weight: 0.3980 chunk 147 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 33 optimal weight: 0.0040 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 296 HIS C 296 HIS D 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.087643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.068823 restraints weight = 32797.745| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.33 r_work: 0.2728 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20112 Z= 0.122 Angle : 0.582 10.804 27432 Z= 0.294 Chirality : 0.045 0.165 3016 Planarity : 0.004 0.041 3508 Dihedral : 5.645 50.337 3268 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.75 % Allowed : 12.01 % Favored : 87.24 % 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: 0.35 (0.16), residues: 2472 helix: -1.44 (0.70), residues: 24 sheet: 0.70 (0.17), residues: 908 loop : 0.04 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.010 0.001 TYR D 252 PHE 0.012 0.001 PHE C 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 0.00276 (20044) covalent geometry : angle 0.56331 (27268) SS BOND : bond 0.00343 ( 40) SS BOND : angle 1.99105 ( 80) hydrogen bonds : bond 0.03200 ( 688) hydrogen bonds : angle 5.78541 ( 1812) link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 1.90595 ( 36) link_BETA1-6 : bond 0.00191 ( 4) link_BETA1-6 : angle 1.30317 ( 12) link_NAG-ASN : bond 0.00204 ( 12) link_NAG-ASN : angle 2.12306 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7728.21 seconds wall clock time: 132 minutes 28.85 seconds (7948.85 seconds total)