Starting phenix.real_space_refine on Tue Sep 15 01:39:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7znj_14803/09_2026/7znj_14803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7znj_14803/09_2026/7znj_14803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7znj_14803/09_2026/7znj_14803.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7znj_14803/09_2026/7znj_14803.cif" model { file = "/net/cci-nas-00/data/ceres_data/7znj_14803/09_2026/7znj_14803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7znj_14803/09_2026/7znj_14803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7znj_14803/09_2026/7znj_14803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7znj_14803/09_2026/7znj_14803.map" } resolution = 2.4 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= 0.003 sd= 0.079 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 6 5.21 5 S 156 5.16 5 C 22086 2.51 5 N 5994 2.21 5 O 6798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 163 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35088 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "B" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "C" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "D" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNAv2': 6} Modifications used: {'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "b" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "c" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "d" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "e" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNAv2': 6} Modifications used: {'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "G" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "I" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNAv2': 6} Modifications used: {'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "g" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "h" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "i" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNAv2': 6} Modifications used: {'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "L" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "M" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "N" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNAv2': 6} Modifications used: {'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "l" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "m" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "n" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "o" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNAv2': 6} Modifications used: {'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.27, per 1000 atoms: 0.24 Number of scatterers: 35088 At special positions: 0 Unit cell: (176.715, 166.32, 117.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 156 16.00 P 48 15.00 Mg 6 11.99 O 6798 8.00 N 5994 7.00 C 22086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.4 seconds 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7884 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 42 sheets defined 40.1% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.826A pdb=" N THR A 42 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.507A pdb=" N TYR A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.940A pdb=" N ILE A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LYS A 70 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.628A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.521A pdb=" N ASP A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 197 through 207 removed outlier: 4.181A pdb=" N TYR A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 removed outlier: 3.557A pdb=" N MET A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 263 through 271 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 312 through 325 Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.617A pdb=" N TYR A 361 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'B' and resid 53 through 68 removed outlier: 3.505A pdb=" N MET B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.751A pdb=" N VAL B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 142 removed outlier: 3.519A pdb=" N GLN B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 94 removed outlier: 3.586A pdb=" N LYS C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 155 through 167 removed outlier: 3.670A pdb=" N ALA D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 39 through 43 removed outlier: 3.576A pdb=" N THR a 42 " --> pdb=" O THR a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 57 Processing helix chain 'a' and resid 64 through 74 removed outlier: 3.989A pdb=" N ILE a 69 " --> pdb=" O GLN a 65 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN a 71 " --> pdb=" O ARG a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 99 removed outlier: 3.604A pdb=" N PHE a 92 " --> pdb=" O LYS a 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU a 97 " --> pdb=" O SER a 93 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS a 99 " --> pdb=" O SER a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 115 through 130 Processing helix chain 'a' and resid 145 through 156 removed outlier: 3.549A pdb=" N ASP a 149 " --> pdb=" O ASN a 145 " (cutoff:3.500A) Processing helix chain 'a' and resid 163 through 173 Processing helix chain 'a' and resid 188 through 193 Processing helix chain 'a' and resid 197 through 207 removed outlier: 4.168A pdb=" N TYR a 207 " --> pdb=" O ASP a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 222 through 229 removed outlier: 3.623A pdb=" N MET a 228 " --> pdb=" O GLU a 224 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 232 No H-bonds generated for 'chain 'a' and resid 230 through 232' Processing helix chain 'a' and resid 242 through 246 removed outlier: 3.619A pdb=" N LEU a 246 " --> pdb=" O ARG a 243 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 262 No H-bonds generated for 'chain 'a' and resid 260 through 262' Processing helix chain 'a' and resid 263 through 271 removed outlier: 3.555A pdb=" N ASP a 270 " --> pdb=" O ASP a 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 271 through 276 Processing helix chain 'a' and resid 286 through 300 Processing helix chain 'a' and resid 312 through 325 Processing helix chain 'a' and resid 335 through 338 Processing helix chain 'a' and resid 357 through 366 removed outlier: 3.693A pdb=" N TYR a 361 " --> pdb=" O ASN a 357 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE a 362 " --> pdb=" O ARG a 358 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS a 363 " --> pdb=" O GLU a 359 " (cutoff:3.500A) Processing helix chain 'a' and resid 385 through 397 Processing helix chain 'b' and resid 53 through 68 Processing helix chain 'b' and resid 69 through 72 Processing helix chain 'b' and resid 106 through 112 removed outlier: 3.677A pdb=" N VAL b 110 " --> pdb=" O SER b 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 115 through 142 removed outlier: 3.524A pdb=" N GLN b 127 " --> pdb=" O TYR b 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 94 Processing helix chain 'c' and resid 123 through 135 Processing helix chain 'd' and resid 118 through 127 Processing helix chain 'd' and resid 155 through 167 removed outlier: 3.708A pdb=" N ALA d 159 " --> pdb=" O ARG d 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 43 removed outlier: 3.823A pdb=" N THR F 42 " --> pdb=" O THR F 39 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET F 43 " --> pdb=" O PHE F 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 39 through 43' Processing helix chain 'F' and resid 46 through 57 Processing helix chain 'F' and resid 64 through 74 removed outlier: 3.965A pdb=" N ILE F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS F 70 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 99 removed outlier: 3.598A pdb=" N PHE F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 130 Processing helix chain 'F' and resid 145 through 156 removed outlier: 3.866A pdb=" N ASP F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 173 Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'F' and resid 197 through 207 removed outlier: 4.170A pdb=" N TYR F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 229 removed outlier: 3.589A pdb=" N MET F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR F 229 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 242 through 246 removed outlier: 3.620A pdb=" N LEU F 246 " --> pdb=" O ARG F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 263 through 271 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 286 through 300 removed outlier: 3.525A pdb=" N ARG F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 325 Processing helix chain 'F' and resid 335 through 338 Processing helix chain 'F' and resid 357 through 366 removed outlier: 3.618A pdb=" N TYR F 361 " --> pdb=" O ASN F 357 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 362 " --> pdb=" O ARG F 358 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 397 Processing helix chain 'G' and resid 53 through 68 Processing helix chain 'G' and resid 69 through 72 Processing helix chain 'G' and resid 106 through 112 removed outlier: 3.759A pdb=" N VAL G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 142 removed outlier: 3.503A pdb=" N VAL G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN G 127 " --> pdb=" O TYR G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 Processing helix chain 'H' and resid 123 through 135 Processing helix chain 'I' and resid 118 through 127 Processing helix chain 'I' and resid 155 through 167 removed outlier: 3.711A pdb=" N ALA I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 39 through 43 removed outlier: 3.554A pdb=" N THR f 42 " --> pdb=" O THR f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 46 through 57 Processing helix chain 'f' and resid 64 through 74 removed outlier: 3.968A pdb=" N ILE f 69 " --> pdb=" O GLN f 65 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS f 70 " --> pdb=" O GLN f 66 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN f 71 " --> pdb=" O ARG f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 87 through 99 removed outlier: 3.640A pdb=" N PHE f 92 " --> pdb=" O LYS f 88 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS f 99 " --> pdb=" O SER f 95 " (cutoff:3.500A) Processing helix chain 'f' and resid 115 through 130 Processing helix chain 'f' and resid 145 through 156 removed outlier: 3.562A pdb=" N ASP f 149 " --> pdb=" O ASN f 145 " (cutoff:3.500A) Processing helix chain 'f' and resid 163 through 173 Processing helix chain 'f' and resid 188 through 193 Processing helix chain 'f' and resid 197 through 207 removed outlier: 4.242A pdb=" N TYR f 207 " --> pdb=" O ASP f 203 " (cutoff:3.500A) Processing helix chain 'f' and resid 222 through 229 removed outlier: 3.514A pdb=" N MET f 228 " --> pdb=" O GLU f 224 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR f 229 " --> pdb=" O ILE f 225 " (cutoff:3.500A) Processing helix chain 'f' and resid 230 through 232 No H-bonds generated for 'chain 'f' and resid 230 through 232' Processing helix chain 'f' and resid 260 through 262 No H-bonds generated for 'chain 'f' and resid 260 through 262' Processing helix chain 'f' and resid 263 through 271 Processing helix chain 'f' and resid 271 through 277 removed outlier: 3.845A pdb=" N ILE f 277 " --> pdb=" O ASP f 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 286 through 300 Processing helix chain 'f' and resid 312 through 325 Processing helix chain 'f' and resid 335 through 338 Processing helix chain 'f' and resid 357 through 366 removed outlier: 3.706A pdb=" N TYR f 361 " --> pdb=" O ASN f 357 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE f 362 " --> pdb=" O ARG f 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS f 363 " --> pdb=" O GLU f 359 " (cutoff:3.500A) Processing helix chain 'f' and resid 385 through 397 Processing helix chain 'g' and resid 53 through 68 removed outlier: 3.570A pdb=" N MET g 57 " --> pdb=" O HIS g 53 " (cutoff:3.500A) Processing helix chain 'g' and resid 69 through 72 Processing helix chain 'g' and resid 106 through 112 removed outlier: 3.669A pdb=" N VAL g 110 " --> pdb=" O SER g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 142 removed outlier: 3.536A pdb=" N GLN g 127 " --> pdb=" O TYR g 123 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 94 Processing helix chain 'h' and resid 123 through 135 Processing helix chain 'i' and resid 118 through 127 Processing helix chain 'i' and resid 155 through 167 removed outlier: 3.640A pdb=" N ALA i 159 " --> pdb=" O ARG i 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 57 Processing helix chain 'K' and resid 64 through 74 removed outlier: 3.974A pdb=" N ILE K 69 " --> pdb=" O GLN K 65 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS K 70 " --> pdb=" O GLN K 66 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 99 removed outlier: 3.604A pdb=" N PHE K 92 " --> pdb=" O LYS K 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS K 99 " --> pdb=" O SER K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 130 Processing helix chain 'K' and resid 145 through 156 Processing helix chain 'K' and resid 163 through 173 Processing helix chain 'K' and resid 188 through 193 Processing helix chain 'K' and resid 197 through 207 removed outlier: 4.187A pdb=" N TYR K 207 " --> pdb=" O ASP K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 229 removed outlier: 3.720A pdb=" N MET K 228 " --> pdb=" O GLU K 224 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR K 229 " --> pdb=" O ILE K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 230 through 232 No H-bonds generated for 'chain 'K' and resid 230 through 232' Processing helix chain 'K' and resid 242 through 246 removed outlier: 3.644A pdb=" N LEU K 246 " --> pdb=" O ARG K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 262 No H-bonds generated for 'chain 'K' and resid 260 through 262' Processing helix chain 'K' and resid 263 through 271 Processing helix chain 'K' and resid 271 through 276 Processing helix chain 'K' and resid 286 through 300 Processing helix chain 'K' and resid 312 through 325 Processing helix chain 'K' and resid 335 through 338 Processing helix chain 'K' and resid 357 through 366 removed outlier: 3.607A pdb=" N TYR K 361 " --> pdb=" O ASN K 357 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE K 362 " --> pdb=" O ARG K 358 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS K 363 " --> pdb=" O GLU K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 397 Processing helix chain 'L' and resid 53 through 68 Processing helix chain 'L' and resid 69 through 72 Processing helix chain 'L' and resid 106 through 112 removed outlier: 3.726A pdb=" N VAL L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 142 removed outlier: 3.527A pdb=" N GLN L 127 " --> pdb=" O TYR L 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 123 through 135 removed outlier: 3.510A pdb=" N ALA M 127 " --> pdb=" O THR M 123 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 127 Processing helix chain 'N' and resid 155 through 167 removed outlier: 3.691A pdb=" N ALA N 159 " --> pdb=" O ARG N 155 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 43 Processing helix chain 'k' and resid 46 through 57 Processing helix chain 'k' and resid 64 through 74 removed outlier: 3.983A pdb=" N ILE k 69 " --> pdb=" O GLN k 65 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS k 70 " --> pdb=" O GLN k 66 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN k 71 " --> pdb=" O ARG k 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 99 removed outlier: 3.609A pdb=" N PHE k 92 " --> pdb=" O LYS k 88 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS k 99 " --> pdb=" O SER k 95 " (cutoff:3.500A) Processing helix chain 'k' and resid 115 through 130 Processing helix chain 'k' and resid 145 through 156 removed outlier: 3.537A pdb=" N ASP k 149 " --> pdb=" O ASN k 145 " (cutoff:3.500A) Processing helix chain 'k' and resid 163 through 173 Processing helix chain 'k' and resid 188 through 193 Processing helix chain 'k' and resid 197 through 207 removed outlier: 4.081A pdb=" N TYR k 207 " --> pdb=" O ASP k 203 " (cutoff:3.500A) Processing helix chain 'k' and resid 222 through 229 removed outlier: 3.684A pdb=" N MET k 228 " --> pdb=" O GLU k 224 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR k 229 " --> pdb=" O ILE k 225 " (cutoff:3.500A) Processing helix chain 'k' and resid 230 through 232 No H-bonds generated for 'chain 'k' and resid 230 through 232' Processing helix chain 'k' and resid 260 through 262 No H-bonds generated for 'chain 'k' and resid 260 through 262' Processing helix chain 'k' and resid 263 through 271 removed outlier: 3.801A pdb=" N ASP k 270 " --> pdb=" O ASP k 266 " (cutoff:3.500A) Processing helix chain 'k' and resid 271 through 276 Processing helix chain 'k' and resid 286 through 300 Processing helix chain 'k' and resid 312 through 325 Processing helix chain 'k' and resid 357 through 366 removed outlier: 3.581A pdb=" N TYR k 361 " --> pdb=" O ASN k 357 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE k 362 " --> pdb=" O ARG k 358 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS k 363 " --> pdb=" O GLU k 359 " (cutoff:3.500A) Processing helix chain 'k' and resid 385 through 397 Processing helix chain 'l' and resid 53 through 68 Processing helix chain 'l' and resid 69 through 72 Processing helix chain 'l' and resid 106 through 112 removed outlier: 3.744A pdb=" N VAL l 110 " --> pdb=" O SER l 106 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN l 112 " --> pdb=" O ILE l 108 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 142 removed outlier: 3.558A pdb=" N GLN l 127 " --> pdb=" O TYR l 123 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 123 through 135 Processing helix chain 'n' and resid 118 through 127 Processing helix chain 'n' and resid 155 through 167 removed outlier: 3.742A pdb=" N ALA n 159 " --> pdb=" O ARG n 155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 137 through 140 removed outlier: 6.067A pdb=" N HIS A 138 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA A 109 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLY A 162 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 111 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 78 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER A 218 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA A 80 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 307 removed outlier: 6.145A pdb=" N GLN A 279 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 348 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS A 252 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASN A 379 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE A 254 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL A 381 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 256 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N ASP A 401 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN A 253 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.619A pdb=" N GLY B 18 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 95 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 99 through 103 removed outlier: 4.217A pdb=" N ASN C 101 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.552A pdb=" N GLN C 142 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 132 through 139 removed outlier: 5.050A pdb=" N THR D 148 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY D 106 " --> pdb=" O PHE D 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 170 through 171 Processing sheet with id=AA8, first strand: chain 'a' and resid 137 through 140 removed outlier: 6.019A pdb=" N HIS a 138 " --> pdb=" O ALA a 161 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA a 109 " --> pdb=" O VAL a 160 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY a 162 " --> pdb=" O ALA a 109 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE a 111 " --> pdb=" O GLY a 162 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL a 78 " --> pdb=" O LEU a 216 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER a 218 " --> pdb=" O VAL a 78 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA a 80 " --> pdb=" O SER a 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 305 through 307 removed outlier: 6.145A pdb=" N SER a 305 " --> pdb=" O ILE a 332 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLN a 279 " --> pdb=" O SER a 347 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE a 349 " --> pdb=" O GLN a 279 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL a 281 " --> pdb=" O ILE a 349 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ASN a 351 " --> pdb=" O VAL a 281 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE a 283 " --> pdb=" O ASN a 351 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS a 252 " --> pdb=" O ALA a 377 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASN a 379 " --> pdb=" O LYS a 252 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE a 254 " --> pdb=" O ASN a 379 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL a 381 " --> pdb=" O PHE a 254 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL a 256 " --> pdb=" O VAL a 381 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N ASP a 401 " --> pdb=" O ILE a 251 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLN a 253 " --> pdb=" O ASP a 401 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 46 through 51 removed outlier: 3.506A pdb=" N GLY b 18 " --> pdb=" O GLY b 15 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU b 95 " --> pdb=" O ILE b 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 99 through 103 removed outlier: 4.093A pdb=" N ASN c 101 " --> pdb=" O GLU c 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 138 through 139 Processing sheet with id=AB4, first strand: chain 'd' and resid 132 through 139 removed outlier: 6.585A pdb=" N HIS d 152 " --> pdb=" O LYS d 133 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA d 135 " --> pdb=" O ASP d 150 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP d 150 " --> pdb=" O ALA d 135 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL d 137 " --> pdb=" O THR d 148 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N THR d 148 " --> pdb=" O VAL d 137 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR d 139 " --> pdb=" O LEU d 146 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU d 146 " --> pdb=" O TYR d 139 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY d 106 " --> pdb=" O PHE d 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 170 through 171 Processing sheet with id=AB6, first strand: chain 'F' and resid 137 through 140 removed outlier: 6.010A pdb=" N HIS F 138 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA F 109 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLY F 162 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE F 111 " --> pdb=" O GLY F 162 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU F 110 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP F 187 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 112 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL F 78 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N SER F 218 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA F 80 " --> pdb=" O SER F 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 305 through 307 removed outlier: 6.133A pdb=" N SER F 305 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN F 279 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER F 347 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE F 378 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE F 349 " --> pdb=" O ILE F 378 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N PHE F 380 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN F 351 " --> pdb=" O PHE F 380 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS F 252 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASN F 379 " --> pdb=" O LYS F 252 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE F 254 " --> pdb=" O ASN F 379 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL F 381 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL F 256 " --> pdb=" O VAL F 381 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASP F 401 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN F 253 " --> pdb=" O ASP F 401 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 46 through 51 removed outlier: 3.530A pdb=" N GLU G 95 " --> pdb=" O ILE G 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 99 through 103 removed outlier: 4.102A pdb=" N ASN H 101 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 138 through 139 Processing sheet with id=AC2, first strand: chain 'I' and resid 132 through 139 removed outlier: 3.504A pdb=" N LYS I 134 " --> pdb=" O HIS I 152 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR I 148 " --> pdb=" O HIS I 138 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY I 106 " --> pdb=" O PHE I 153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 170 through 171 Processing sheet with id=AC4, first strand: chain 'f' and resid 137 through 140 removed outlier: 6.079A pdb=" N HIS f 138 " --> pdb=" O ALA f 161 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA f 109 " --> pdb=" O VAL f 160 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLY f 162 " --> pdb=" O ALA f 109 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE f 111 " --> pdb=" O GLY f 162 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL f 78 " --> pdb=" O LEU f 216 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N SER f 218 " --> pdb=" O VAL f 78 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA f 80 " --> pdb=" O SER f 218 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'f' and resid 305 through 307 removed outlier: 6.227A pdb=" N SER f 305 " --> pdb=" O ILE f 332 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN f 279 " --> pdb=" O VAL f 346 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS f 252 " --> pdb=" O ALA f 377 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN f 379 " --> pdb=" O LYS f 252 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE f 254 " --> pdb=" O ASN f 379 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL f 381 " --> pdb=" O PHE f 254 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL f 256 " --> pdb=" O VAL f 381 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N ASP f 401 " --> pdb=" O ILE f 251 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN f 253 " --> pdb=" O ASP f 401 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 46 through 51 removed outlier: 3.612A pdb=" N GLY g 18 " --> pdb=" O GLY g 15 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU g 95 " --> pdb=" O ILE g 92 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'h' and resid 99 through 103 removed outlier: 4.216A pdb=" N ASN h 101 " --> pdb=" O GLU h 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 138 through 139 Processing sheet with id=AC9, first strand: chain 'i' and resid 132 through 139 removed outlier: 3.591A pdb=" N LYS i 134 " --> pdb=" O HIS i 152 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N THR i 148 " --> pdb=" O HIS i 138 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY i 106 " --> pdb=" O PHE i 153 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'i' and resid 170 through 171 Processing sheet with id=AD2, first strand: chain 'K' and resid 137 through 140 removed outlier: 6.140A pdb=" N HIS K 138 " --> pdb=" O ALA K 161 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA K 109 " --> pdb=" O VAL K 160 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY K 162 " --> pdb=" O ALA K 109 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE K 111 " --> pdb=" O GLY K 162 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU K 110 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASP K 187 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU K 112 " --> pdb=" O ASP K 187 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL K 78 " --> pdb=" O LEU K 216 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER K 218 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA K 80 " --> pdb=" O SER K 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 305 through 307 removed outlier: 6.220A pdb=" N SER K 305 " --> pdb=" O ILE K 332 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLN K 279 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYS K 252 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASN K 379 " --> pdb=" O LYS K 252 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE K 254 " --> pdb=" O ASN K 379 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL K 381 " --> pdb=" O PHE K 254 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL K 256 " --> pdb=" O VAL K 381 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ASP K 401 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN K 253 " --> pdb=" O ASP K 401 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 46 through 51 removed outlier: 3.522A pdb=" N GLY L 18 " --> pdb=" O GLY L 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 95 " --> pdb=" O ILE L 92 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 99 through 103 removed outlier: 4.100A pdb=" N ASN M 101 " --> pdb=" O GLU M 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 138 through 139 Processing sheet with id=AD7, first strand: chain 'N' and resid 132 through 139 removed outlier: 3.559A pdb=" N LYS N 134 " --> pdb=" O HIS N 152 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR N 148 " --> pdb=" O HIS N 138 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY N 106 " --> pdb=" O PHE N 153 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 170 through 171 Processing sheet with id=AD9, first strand: chain 'k' and resid 137 through 140 removed outlier: 6.013A pdb=" N HIS k 138 " --> pdb=" O ALA k 161 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA k 109 " --> pdb=" O VAL k 160 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY k 162 " --> pdb=" O ALA k 109 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE k 111 " --> pdb=" O GLY k 162 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU k 110 " --> pdb=" O VAL k 185 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASP k 187 " --> pdb=" O LEU k 110 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU k 112 " --> pdb=" O ASP k 187 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL k 78 " --> pdb=" O LEU k 216 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER k 218 " --> pdb=" O VAL k 78 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA k 80 " --> pdb=" O SER k 218 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'k' and resid 305 through 307 removed outlier: 6.030A pdb=" N SER k 305 " --> pdb=" O ILE k 332 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN k 279 " --> pdb=" O VAL k 346 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS k 252 " --> pdb=" O ALA k 377 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN k 379 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE k 254 " --> pdb=" O ASN k 379 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL k 381 " --> pdb=" O PHE k 254 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL k 256 " --> pdb=" O VAL k 381 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASP k 401 " --> pdb=" O ILE k 251 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN k 253 " --> pdb=" O ASP k 401 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'l' and resid 46 through 51 removed outlier: 3.522A pdb=" N GLY l 18 " --> pdb=" O GLY l 15 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'm' and resid 99 through 103 removed outlier: 4.141A pdb=" N ASN m 101 " --> pdb=" O GLU m 120 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'm' and resid 138 through 139 Processing sheet with id=AE5, first strand: chain 'n' and resid 132 through 139 removed outlier: 5.104A pdb=" N THR n 148 " --> pdb=" O HIS n 138 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY n 106 " --> pdb=" O PHE n 153 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'n' and resid 170 through 171 1485 hydrogen bonds defined for protein. 4272 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: 8.49 Time building geometry restraints manager: 4.19 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: 11485 1.34 - 1.46: 8175 1.46 - 1.59: 15811 1.59 - 1.71: 73 1.71 - 1.83: 270 Bond restraints: 35814 Sorted by residual: bond pdb=" O3A ANP a 502 " pdb=" PB ANP a 502 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" O3A ANP F 502 " pdb=" PB ANP F 502 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" O3A ANP f 502 " pdb=" PB ANP f 502 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" O3A ANP k 502 " pdb=" PB ANP k 502 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 ... (remaining 35809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 48267 4.18 - 8.36: 207 8.36 - 12.54: 36 12.54 - 16.72: 9 16.72 - 20.90: 3 Bond angle restraints: 48522 Sorted by residual: angle pdb=" CB LYS D 161 " pdb=" CG LYS D 161 " pdb=" CD LYS D 161 " ideal model delta sigma weight residual 111.30 125.70 -14.40 2.30e+00 1.89e-01 3.92e+01 angle pdb=" C PHE f 58 " pdb=" N GLU f 59 " pdb=" CA GLU f 59 " ideal model delta sigma weight residual 121.54 133.05 -11.51 1.91e+00 2.74e-01 3.63e+01 angle pdb=" CA LEU D 91 " pdb=" CB LEU D 91 " pdb=" CG LEU D 91 " ideal model delta sigma weight residual 116.30 137.20 -20.90 3.50e+00 8.16e-02 3.56e+01 angle pdb=" C PHE A 58 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE F 58 " pdb=" N GLU F 59 " pdb=" CA GLU F 59 " ideal model delta sigma weight residual 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 ... (remaining 48517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 18806 17.70 - 35.39: 1874 35.39 - 53.09: 622 53.09 - 70.78: 124 70.78 - 88.48: 78 Dihedral angle restraints: 21504 sinusoidal: 9240 harmonic: 12264 Sorted by residual: dihedral pdb=" CA TRP i 87 " pdb=" C TRP i 87 " pdb=" N GLN i 88 " pdb=" CA GLN i 88 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA TRP n 87 " pdb=" C TRP n 87 " pdb=" N GLN n 88 " pdb=" CA GLN n 88 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA TRP N 87 " pdb=" C TRP N 87 " pdb=" N GLN N 88 " pdb=" CA GLN N 88 " ideal model delta harmonic sigma weight residual 180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 21501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4125 0.051 - 0.102: 933 0.102 - 0.152: 268 0.152 - 0.203: 8 0.203 - 0.254: 36 Chirality restraints: 5370 Sorted by residual: chirality pdb=" C3' ANP F 502 " pdb=" C2' ANP F 502 " pdb=" C4' ANP F 502 " pdb=" O3' ANP F 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C3' ANP a 502 " pdb=" C2' ANP a 502 " pdb=" C4' ANP a 502 " pdb=" O3' ANP a 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C3' ANP A 502 " pdb=" C2' ANP A 502 " pdb=" C4' ANP A 502 " pdb=" O3' ANP A 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.60 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 5367 not shown) Planarity restraints: 6150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE k 265 " 0.027 2.00e-02 2.50e+03 3.50e-02 2.14e+01 pdb=" CG PHE k 265 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE k 265 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE k 265 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE k 265 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE k 265 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE k 265 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 91 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C LEU I 91 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU I 91 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE I 92 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 58 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C PHE A 58 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE A 58 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 59 " -0.014 2.00e-02 2.50e+03 ... (remaining 6147 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 376 2.65 - 3.22: 28787 3.22 - 3.78: 53569 3.78 - 4.34: 80616 4.34 - 4.90: 126082 Nonbonded interactions: 289430 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O3G ANP A 502 " model vdw 2.092 2.170 nonbonded pdb="MG MG f 501 " pdb=" O3G ANP f 502 " model vdw 2.098 2.170 nonbonded pdb="MG MG k 501 " pdb=" O3G ANP k 502 " model vdw 2.108 2.170 nonbonded pdb="MG MG K 501 " pdb=" O2B ANP K 502 " model vdw 2.133 2.170 nonbonded pdb="MG MG a 501 " pdb=" O2B ANP a 502 " model vdw 2.139 2.170 ... (remaining 289425 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' selection = chain 'a' selection = chain 'f' selection = chain 'k' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' selection = chain 'b' selection = chain 'g' selection = chain 'l' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' selection = chain 'c' selection = chain 'h' selection = chain 'm' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' selection = chain 'd' selection = chain 'i' selection = chain 'n' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' selection = chain 'e' selection = chain 'j' selection = chain 'o' } 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 34.220 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.004 0.146 35814 Z= 0.219 Angle : 0.830 20.896 48522 Z= 0.433 Chirality : 0.050 0.254 5370 Planarity : 0.005 0.084 6150 Dihedral : 16.884 88.479 13620 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.83 % Allowed : 17.42 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.12), residues: 4182 helix: -3.13 (0.07), residues: 1536 sheet: 1.28 (0.16), residues: 912 loop : 0.16 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG a 329 TYR 0.034 0.002 TYR a 155 PHE 0.080 0.002 PHE k 265 TRP 0.038 0.002 TRP k 337 HIS 0.009 0.001 HIS i 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 (35814) covalent geometry : angle 0.83027 / 0.43 (48522) hydrogen bonds : bond 0.26919 / 17.83 ( 1485) hydrogen bonds : angle 8.01503 / 5.59 ( 4272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 625 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7149 (pt0) cc_final: 0.6532 (mt-10) REVERT: A 288 ARG cc_start: 0.6777 (ttp80) cc_final: 0.6372 (tmt170) REVERT: A 297 MET cc_start: 0.6880 (mmm) cc_final: 0.6622 (mtp) REVERT: C 120 GLU cc_start: 0.8688 (tt0) cc_final: 0.8409 (tt0) REVERT: a 202 TYR cc_start: 0.6046 (t80) cc_final: 0.5498 (t80) REVERT: a 329 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7262 (mmm160) REVERT: F 329 ARG cc_start: 0.7312 (mtp85) cc_final: 0.7097 (mmm160) REVERT: H 140 MET cc_start: 0.7449 (mpt) cc_final: 0.6908 (mpt) REVERT: f 224 GLU cc_start: 0.7071 (pt0) cc_final: 0.6624 (mt-10) REVERT: g 127 GLN cc_start: 0.8404 (mt0) cc_final: 0.8168 (mt0) REVERT: h 120 GLU cc_start: 0.8588 (tt0) cc_final: 0.8347 (tt0) REVERT: K 117 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6993 (mt-10) REVERT: K 320 MET cc_start: 0.7070 (tpt) cc_final: 0.6851 (mmm) REVERT: K 354 LEU cc_start: 0.7133 (mp) cc_final: 0.6868 (tt) REVERT: M 120 GLU cc_start: 0.8624 (tt0) cc_final: 0.8406 (tt0) REVERT: k 288 ARG cc_start: 0.6563 (ttp80) cc_final: 0.6281 (tmt170) REVERT: l 57 MET cc_start: 0.8395 (mmm) cc_final: 0.8145 (mmt) REVERT: l 107 LEU cc_start: 0.8550 (tp) cc_final: 0.8330 (mt) REVERT: m 140 MET cc_start: 0.7332 (mpt) cc_final: 0.7039 (mpp) outliers start: 31 outliers final: 7 residues processed: 641 average time/residue: 0.8573 time to fit residues: 641.7963 Evaluate side-chains 545 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 538 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain n residue 158 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 HIS B 42 ASN B 96 HIS C 128 GLN D 123 GLN D 177 ASN ** a 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 351 ASN b 140 HIS c 101 ASN c 128 GLN d 179 GLN G 96 HIS G 140 HIS H 101 ASN H 128 GLN I 179 GLN g 42 ASN g 112 GLN h 128 GLN i 152 HIS i 179 GLN L 42 ASN ** L 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN L 112 GLN L 140 HIS M 128 GLN N 177 ASN N 179 GLN k 213 GLN k 308 HIS k 351 ASN l 42 ASN l 96 HIS l 140 HIS n 179 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.200847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.166378 restraints weight = 29285.509| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.16 r_work: 0.3560 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35814 Z= 0.174 Angle : 0.676 14.824 48522 Z= 0.355 Chirality : 0.048 0.175 5370 Planarity : 0.006 0.051 6150 Dihedral : 7.009 55.361 5123 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.69 % Allowed : 14.30 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 4182 helix: -0.60 (0.11), residues: 1572 sheet: 1.70 (0.16), residues: 912 loop : 0.06 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 329 TYR 0.017 0.002 TYR l 9 PHE 0.029 0.003 PHE f 92 TRP 0.018 0.002 TRP k 292 HIS 0.007 0.001 HIS i 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (35814) covalent geometry : angle 0.67631 / 0.35 (48522) hydrogen bonds : bond 0.05807 / 3.82 ( 1485) hydrogen bonds : angle 4.99609 / 3.49 ( 4272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 560 time to evaluate : 1.360 Fit side-chains REVERT: A 224 GLU cc_start: 0.7332 (pt0) cc_final: 0.6437 (mt-10) REVERT: A 233 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7028 (mtt) REVERT: A 245 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8736 (mt-10) REVERT: A 288 ARG cc_start: 0.6993 (ttp80) cc_final: 0.6339 (tmt170) REVERT: A 289 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7469 (tmtm) REVERT: a 148 GLU cc_start: 0.6783 (tp30) cc_final: 0.6215 (mp0) REVERT: a 288 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6071 (ttt180) REVERT: a 383 ASN cc_start: 0.6351 (m-40) cc_final: 0.6039 (m110) REVERT: c 103 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6812 (m90) REVERT: d 161 LYS cc_start: 0.7701 (mttt) cc_final: 0.7360 (mmpt) REVERT: F 23 MET cc_start: 0.5933 (ptt) cc_final: 0.5065 (ptp) REVERT: F 288 ARG cc_start: 0.7263 (ttp-110) cc_final: 0.7027 (tmt170) REVERT: F 298 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6220 (mtt90) REVERT: H 128 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8193 (tm130) REVERT: I 134 LYS cc_start: 0.7346 (ttpt) cc_final: 0.7092 (ptmm) REVERT: I 161 LYS cc_start: 0.7786 (mttt) cc_final: 0.7415 (mmpt) REVERT: f 23 MET cc_start: 0.5573 (ptt) cc_final: 0.4780 (ptp) REVERT: f 43 MET cc_start: 0.8729 (mtt) cc_final: 0.8205 (mtt) REVERT: f 224 GLU cc_start: 0.7301 (pt0) cc_final: 0.6527 (mt-10) REVERT: f 288 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6322 (ttt180) REVERT: f 289 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7503 (tmtm) REVERT: g 111 ASN cc_start: 0.8208 (m-40) cc_final: 0.7962 (m110) REVERT: h 140 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6883 (mpt) REVERT: i 161 LYS cc_start: 0.7732 (mttt) cc_final: 0.7466 (mmpt) REVERT: K 74 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7203 (mttp) REVERT: K 105 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6991 (ttt180) REVERT: K 148 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: K 170 MET cc_start: 0.7585 (mmt) cc_final: 0.6989 (mmt) REVERT: K 288 ARG cc_start: 0.7069 (ttp-110) cc_final: 0.6780 (tmt170) REVERT: K 329 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7447 (mmm160) REVERT: K 354 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7150 (tt) REVERT: N 161 LYS cc_start: 0.7665 (mmpt) cc_final: 0.7309 (mmtp) REVERT: k 148 GLU cc_start: 0.6794 (tp30) cc_final: 0.6288 (mp0) REVERT: k 191 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: k 287 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7855 (ttmt) REVERT: k 288 ARG cc_start: 0.6880 (ttp80) cc_final: 0.6634 (tmt170) REVERT: k 289 LYS cc_start: 0.7519 (mmmt) cc_final: 0.7255 (tppt) REVERT: k 315 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7224 (tp30) REVERT: k 329 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7522 (mmm160) REVERT: k 337 TRP cc_start: 0.7850 (OUTLIER) cc_final: 0.6833 (m100) REVERT: k 364 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7991 (mtp180) REVERT: l 57 MET cc_start: 0.8784 (mmm) cc_final: 0.8445 (mmt) REVERT: l 107 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7960 (mt) REVERT: m 98 GLU cc_start: 0.6787 (tt0) cc_final: 0.6195 (pm20) REVERT: m 140 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7095 (mpt) REVERT: m 152 ARG cc_start: 0.7442 (mmm-85) cc_final: 0.7170 (tpt-90) REVERT: n 161 LYS cc_start: 0.7746 (mttt) cc_final: 0.7356 (mmpt) outliers start: 137 outliers final: 54 residues processed: 626 average time/residue: 0.8297 time to fit residues: 609.8511 Evaluate side-chains 590 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 516 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 288 ARG Chi-restraints excluded: chain a residue 307 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 228 MET Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 289 LYS Chi-restraints excluded: chain f residue 319 ILE Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain f residue 360 LEU Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 140 MET Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain i residue 180 LEU Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 287 LYS Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 220 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 121 optimal weight: 0.3980 chunk 345 optimal weight: 6.9990 chunk 98 optimal weight: 0.0050 chunk 216 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 413 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN C 128 GLN a 213 GLN b 42 ASN b 111 ASN c 101 ASN d 179 GLN G 42 ASN G 111 ASN H 101 ASN I 179 GLN g 42 ASN h 103 HIS h 128 GLN ** i 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 177 ASN L 111 ASN L 112 GLN l 86 GLN l 111 ASN m 103 HIS n 179 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.201223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.167422 restraints weight = 29182.136| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.12 r_work: 0.3568 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35814 Z= 0.129 Angle : 0.581 14.010 48522 Z= 0.307 Chirality : 0.045 0.151 5370 Planarity : 0.004 0.038 6150 Dihedral : 6.614 55.804 5112 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.31 % Allowed : 13.92 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.12), residues: 4182 helix: 0.45 (0.12), residues: 1554 sheet: 1.48 (0.16), residues: 966 loop : 0.27 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 329 TYR 0.024 0.002 TYR K 155 PHE 0.025 0.002 PHE K 92 TRP 0.015 0.001 TRP k 337 HIS 0.006 0.001 HIS i 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (35814) covalent geometry : angle 0.58109 / 0.31 (48522) hydrogen bonds : bond 0.04681 / 3.08 ( 1485) hydrogen bonds : angle 4.69211 / 3.28 ( 4272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 553 time to evaluate : 1.405 Fit side-chains REVERT: A 148 GLU cc_start: 0.6741 (tp30) cc_final: 0.6218 (mp0) REVERT: A 233 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7304 (mtt) REVERT: A 288 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6473 (tmt170) REVERT: A 289 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7351 (tmtm) REVERT: C 98 GLU cc_start: 0.7176 (tt0) cc_final: 0.6558 (tm-30) REVERT: a 148 GLU cc_start: 0.6822 (tp30) cc_final: 0.6292 (mp0) REVERT: a 224 GLU cc_start: 0.7446 (pt0) cc_final: 0.6595 (mt-10) REVERT: a 329 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7436 (mmm160) REVERT: c 128 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: d 161 LYS cc_start: 0.7633 (mttt) cc_final: 0.7314 (mmpt) REVERT: F 23 MET cc_start: 0.5924 (ptt) cc_final: 0.5079 (ptp) REVERT: F 148 GLU cc_start: 0.7013 (mp0) cc_final: 0.6713 (mp0) REVERT: F 288 ARG cc_start: 0.7198 (ttp-110) cc_final: 0.6970 (tmt170) REVERT: F 315 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7330 (tp30) REVERT: F 337 TRP cc_start: 0.8027 (OUTLIER) cc_final: 0.7543 (m100) REVERT: H 140 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.6813 (mpt) REVERT: I 161 LYS cc_start: 0.7713 (mttt) cc_final: 0.7362 (mmpt) REVERT: f 43 MET cc_start: 0.8730 (mtt) cc_final: 0.8130 (mtt) REVERT: f 74 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7309 (mttp) REVERT: f 224 GLU cc_start: 0.7362 (pt0) cc_final: 0.6576 (mt-10) REVERT: f 296 LYS cc_start: 0.6690 (OUTLIER) cc_final: 0.5722 (mmpt) REVERT: g 54 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8155 (mttt) REVERT: K 74 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7208 (mttp) REVERT: K 117 GLU cc_start: 0.7488 (mp0) cc_final: 0.7238 (mp0) REVERT: K 148 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: K 170 MET cc_start: 0.7583 (mmt) cc_final: 0.6976 (mmt) REVERT: K 288 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6786 (tmt170) REVERT: K 329 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7492 (mmm160) REVERT: M 103 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.6776 (m-70) REVERT: M 140 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7215 (mpt) REVERT: N 181 VAL cc_start: 0.4202 (OUTLIER) cc_final: 0.3901 (p) REVERT: k 148 GLU cc_start: 0.6897 (tp30) cc_final: 0.6370 (mp0) REVERT: k 288 ARG cc_start: 0.6826 (ttp80) cc_final: 0.6497 (tmt170) REVERT: k 307 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7474 (ttp) REVERT: k 315 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: k 335 ASP cc_start: 0.8020 (m-30) cc_final: 0.7760 (m-30) REVERT: k 337 TRP cc_start: 0.7917 (OUTLIER) cc_final: 0.6590 (m100) REVERT: k 353 ASP cc_start: 0.8131 (m-30) cc_final: 0.7897 (m-30) REVERT: l 54 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8076 (mttt) REVERT: l 57 MET cc_start: 0.8722 (mmm) cc_final: 0.8507 (mmt) REVERT: l 107 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7887 (mt) REVERT: m 152 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7317 (tpt-90) REVERT: n 124 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: n 161 LYS cc_start: 0.7818 (mttt) cc_final: 0.7421 (mmpt) outliers start: 123 outliers final: 56 residues processed: 602 average time/residue: 0.8538 time to fit residues: 600.4830 Evaluate side-chains 602 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 525 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 307 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 296 LYS Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain f residue 360 LEU Chi-restraints excluded: chain f residue 386 ILE Chi-restraints excluded: chain g residue 54 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 101 ASN Chi-restraints excluded: chain h residue 103 HIS Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain i residue 180 LEU Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 103 HIS Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 401 ASP Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 103 HIS Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Chi-restraints excluded: chain n residue 124 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 110 optimal weight: 4.9990 chunk 409 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 288 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 264 optimal weight: 2.9990 chunk 417 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN B 140 HIS C 128 GLN D 177 ASN D 179 GLN b 42 ASN b 111 ASN c 101 ASN c 128 GLN d 179 GLN G 42 ASN H 101 ASN H 128 GLN I 179 GLN g 42 ASN g 140 HIS h 128 GLN i 177 ASN i 179 GLN L 112 GLN l 86 GLN n 179 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.196379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.160219 restraints weight = 29067.016| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.12 r_work: 0.3517 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 35814 Z= 0.250 Angle : 0.762 16.452 48522 Z= 0.398 Chirality : 0.052 0.180 5370 Planarity : 0.006 0.066 6150 Dihedral : 7.321 61.931 5112 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.33 % Allowed : 13.33 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.12), residues: 4182 helix: 0.45 (0.12), residues: 1548 sheet: 1.40 (0.16), residues: 906 loop : -0.01 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG k 370 TYR 0.021 0.003 TYR K 371 PHE 0.024 0.003 PHE A 92 TRP 0.013 0.002 TRP k 337 HIS 0.013 0.002 HIS m 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (35814) covalent geometry : angle 0.76152 / 0.40 (48522) hydrogen bonds : bond 0.06020 / 3.95 ( 1485) hydrogen bonds : angle 4.94196 / 3.46 ( 4272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 561 time to evaluate : 1.394 Fit side-chains REVERT: A 148 GLU cc_start: 0.6721 (tp30) cc_final: 0.6034 (mp0) REVERT: A 288 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6548 (tmt170) REVERT: A 329 ARG cc_start: 0.7917 (mtp85) cc_final: 0.7458 (mmm160) REVERT: B 111 ASN cc_start: 0.8238 (m-40) cc_final: 0.7953 (m110) REVERT: C 100 LYS cc_start: 0.6898 (tttt) cc_final: 0.6572 (mmpt) REVERT: C 122 GLU cc_start: 0.8197 (tp30) cc_final: 0.7949 (tp30) REVERT: D 124 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: a 23 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5124 (ptp) REVERT: a 33 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: a 148 GLU cc_start: 0.6763 (tp30) cc_final: 0.6261 (mp0) REVERT: a 191 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7355 (tp30) REVERT: a 195 LYS cc_start: 0.7137 (mmtt) cc_final: 0.6492 (mmpt) REVERT: a 224 GLU cc_start: 0.7483 (pt0) cc_final: 0.6665 (mt-10) REVERT: c 98 GLU cc_start: 0.6917 (tt0) cc_final: 0.6555 (tm-30) REVERT: c 100 LYS cc_start: 0.7016 (tttt) cc_final: 0.6714 (mmpt) REVERT: c 120 GLU cc_start: 0.8716 (tt0) cc_final: 0.8475 (tt0) REVERT: c 128 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8116 (tm130) REVERT: d 161 LYS cc_start: 0.7665 (mttt) cc_final: 0.7379 (mmpt) REVERT: F 74 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6857 (mttm) REVERT: F 148 GLU cc_start: 0.7078 (mp0) cc_final: 0.6843 (mp0) REVERT: F 191 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: F 288 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6788 (tmt170) REVERT: F 315 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7431 (tp30) REVERT: H 98 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6416 (tm-30) REVERT: H 100 LYS cc_start: 0.7007 (tttt) cc_final: 0.6671 (mmpt) REVERT: H 122 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: H 128 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8127 (tm130) REVERT: H 140 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.6878 (mpt) REVERT: I 161 LYS cc_start: 0.7765 (mttt) cc_final: 0.7464 (mmpt) REVERT: f 43 MET cc_start: 0.8698 (mtt) cc_final: 0.8221 (mtt) REVERT: f 74 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7373 (mttp) REVERT: f 224 GLU cc_start: 0.7363 (pt0) cc_final: 0.6568 (mt-10) REVERT: f 288 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6291 (ttt180) REVERT: f 296 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.5683 (mmpt) REVERT: f 317 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7177 (mt-10) REVERT: g 54 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8197 (mttt) REVERT: h 92 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7831 (tptp) REVERT: h 122 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: h 128 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8397 (tm130) REVERT: i 161 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7723 (mmpt) REVERT: i 180 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7018 (tp) REVERT: K 74 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7221 (mttp) REVERT: K 148 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: K 191 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7615 (tp30) REVERT: K 317 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7070 (mt-10) REVERT: K 329 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7521 (mmm160) REVERT: N 161 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7708 (mmpt) REVERT: k 148 GLU cc_start: 0.6954 (tp30) cc_final: 0.6422 (mp0) REVERT: k 191 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: k 306 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8432 (t) REVERT: k 307 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7640 (ttp) REVERT: k 315 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: k 317 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7197 (mt-10) REVERT: k 337 TRP cc_start: 0.8041 (OUTLIER) cc_final: 0.7222 (t60) REVERT: k 364 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8096 (mtp180) REVERT: l 57 MET cc_start: 0.8761 (mmm) cc_final: 0.8549 (mmt) REVERT: l 107 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8008 (mt) REVERT: l 112 GLN cc_start: 0.7280 (mm-40) cc_final: 0.6888 (pt0) REVERT: m 95 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7358 (tm-30) REVERT: m 103 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6459 (t-90) REVERT: m 140 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7347 (mpp) REVERT: n 124 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: n 161 LYS cc_start: 0.7902 (mttt) cc_final: 0.7436 (mmpt) outliers start: 161 outliers final: 61 residues processed: 638 average time/residue: 0.8548 time to fit residues: 637.4160 Evaluate side-chains 630 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 533 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 33 GLU Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 191 GLU Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 297 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 228 MET Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 296 LYS Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain g residue 54 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 101 ASN Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 128 GLN Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain i residue 161 LYS Chi-restraints excluded: chain i residue 180 LEU Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 103 HIS Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 161 LYS Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 306 SER Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 98 GLU Chi-restraints excluded: chain m residue 103 HIS Chi-restraints excluded: chain m residue 128 GLN Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Chi-restraints excluded: chain n residue 124 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 122 optimal weight: 0.0870 chunk 192 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 272 optimal weight: 10.0000 chunk 396 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 406 optimal weight: 10.0000 chunk 359 optimal weight: 1.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN B 112 GLN D 177 ASN d 177 ASN d 179 GLN F 200 GLN G 111 ASN I 179 GLN f 200 GLN g 42 ASN g 111 ASN i 177 ASN i 179 GLN L 111 ASN L 112 GLN k 200 GLN k 213 GLN k 279 GLN l 111 ASN m 103 HIS n 179 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.196244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.162574 restraints weight = 29085.772| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.26 r_work: 0.3480 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35814 Z= 0.125 Angle : 0.573 14.961 48522 Z= 0.303 Chirality : 0.045 0.150 5370 Planarity : 0.004 0.042 6150 Dihedral : 6.684 56.309 5112 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.50 % Allowed : 14.54 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.13), residues: 4182 helix: 0.93 (0.13), residues: 1548 sheet: 1.47 (0.16), residues: 936 loop : 0.21 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG k 329 TYR 0.019 0.002 TYR k 155 PHE 0.021 0.002 PHE K 92 TRP 0.013 0.001 TRP k 337 HIS 0.006 0.001 HIS i 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (35814) covalent geometry : angle 0.57343 / 0.30 (48522) hydrogen bonds : bond 0.04361 / 2.87 ( 1485) hydrogen bonds : angle 4.63507 / 3.24 ( 4272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 550 time to evaluate : 1.453 Fit side-chains REVERT: A 148 GLU cc_start: 0.6717 (tp30) cc_final: 0.6116 (mp0) REVERT: A 224 GLU cc_start: 0.7204 (pt0) cc_final: 0.6431 (mt-10) REVERT: A 288 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6476 (tmt170) REVERT: A 289 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7340 (tmtm) REVERT: A 329 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7404 (mmm160) REVERT: B 111 ASN cc_start: 0.8184 (m-40) cc_final: 0.7901 (m110) REVERT: a 23 MET cc_start: 0.5896 (OUTLIER) cc_final: 0.5194 (ptp) REVERT: a 148 GLU cc_start: 0.6813 (tp30) cc_final: 0.6434 (mp0) REVERT: a 195 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6473 (mmpt) REVERT: a 224 GLU cc_start: 0.7150 (pt0) cc_final: 0.6398 (mt-10) REVERT: a 303 THR cc_start: 0.7299 (p) cc_final: 0.6785 (t) REVERT: a 337 TRP cc_start: 0.7915 (OUTLIER) cc_final: 0.7374 (m100) REVERT: c 98 GLU cc_start: 0.6807 (tt0) cc_final: 0.6526 (tm-30) REVERT: F 74 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6796 (mttm) REVERT: F 148 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: F 315 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7251 (tp30) REVERT: F 329 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7366 (mmm160) REVERT: F 337 TRP cc_start: 0.7910 (OUTLIER) cc_final: 0.7402 (m100) REVERT: H 67 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: H 98 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6172 (tm-30) REVERT: H 140 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6845 (mpt) REVERT: f 43 MET cc_start: 0.8620 (mtt) cc_final: 0.8035 (mtt) REVERT: f 74 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7236 (mttt) REVERT: f 224 GLU cc_start: 0.7215 (pt0) cc_final: 0.6465 (mt-10) REVERT: f 288 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6122 (ttt180) REVERT: f 317 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6956 (mt-10) REVERT: g 54 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8090 (mttt) REVERT: h 92 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7726 (tptp) REVERT: h 98 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: h 122 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: i 180 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6895 (tp) REVERT: K 74 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7167 (mttp) REVERT: K 148 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: K 170 MET cc_start: 0.7596 (mmp) cc_final: 0.7205 (mmt) REVERT: K 173 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6044 (mtt-85) REVERT: K 191 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: K 288 ARG cc_start: 0.6980 (ttp-110) cc_final: 0.6694 (tmt170) REVERT: K 315 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: K 329 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7466 (mmm160) REVERT: N 161 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7431 (mmpt) REVERT: N 181 VAL cc_start: 0.4872 (OUTLIER) cc_final: 0.4467 (p) REVERT: k 148 GLU cc_start: 0.6967 (tp30) cc_final: 0.6507 (mp0) REVERT: k 191 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: k 306 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8231 (t) REVERT: k 315 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: k 317 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6993 (mt-10) REVERT: k 337 TRP cc_start: 0.7923 (OUTLIER) cc_final: 0.6526 (m100) REVERT: k 364 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8162 (mtp180) REVERT: l 57 MET cc_start: 0.8513 (mmm) cc_final: 0.8264 (mmt) REVERT: l 107 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7911 (mt) REVERT: l 112 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6898 (pt0) REVERT: n 161 LYS cc_start: 0.7757 (mttt) cc_final: 0.7384 (mmpt) outliers start: 130 outliers final: 52 residues processed: 610 average time/residue: 0.8526 time to fit residues: 605.7893 Evaluate side-chains 614 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 533 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 297 MET Chi-restraints excluded: chain a residue 307 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 386 ILE Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 289 LYS Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain g residue 54 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 98 GLU Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain i residue 180 LEU Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 315 GLU Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 306 SER Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 98 GLU Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 85 optimal weight: 8.9990 chunk 392 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 308 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 337 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 340 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN B 112 GLN D 177 ASN D 179 GLN a 213 GLN b 42 ASN d 179 GLN G 42 ASN G 111 ASN H 101 ASN I 179 GLN g 42 ASN g 111 ASN i 177 ASN i 179 GLN L 112 GLN l 111 ASN m 103 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.193086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.158779 restraints weight = 29038.264| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.26 r_work: 0.3435 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35814 Z= 0.218 Angle : 0.711 16.875 48522 Z= 0.372 Chirality : 0.050 0.164 5370 Planarity : 0.006 0.055 6150 Dihedral : 7.161 59.656 5112 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.47 % Allowed : 15.08 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.13), residues: 4182 helix: 0.78 (0.13), residues: 1548 sheet: 1.40 (0.17), residues: 906 loop : -0.02 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG l 33 TYR 0.020 0.003 TYR K 155 PHE 0.023 0.003 PHE f 92 TRP 0.015 0.002 TRP k 292 HIS 0.008 0.002 HIS a 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (35814) covalent geometry : angle 0.71077 / 0.37 (48522) hydrogen bonds : bond 0.05598 / 3.68 ( 1485) hydrogen bonds : angle 4.85526 / 3.39 ( 4272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 544 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6826 (tp30) cc_final: 0.6275 (mp0) REVERT: A 288 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6554 (tmt170) REVERT: A 329 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7384 (mmm160) REVERT: C 92 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7897 (tptp) REVERT: a 23 MET cc_start: 0.5764 (OUTLIER) cc_final: 0.4983 (ptp) REVERT: a 148 GLU cc_start: 0.6862 (tp30) cc_final: 0.6464 (mp0) REVERT: a 191 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: a 224 GLU cc_start: 0.7263 (pt0) cc_final: 0.6518 (mt-10) REVERT: c 120 GLU cc_start: 0.8534 (tt0) cc_final: 0.8269 (tt0) REVERT: c 131 MET cc_start: 0.8533 (ttt) cc_final: 0.8266 (ttp) REVERT: F 74 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6869 (mttp) REVERT: F 191 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7298 (tp30) REVERT: F 315 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: F 329 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7455 (mmm160) REVERT: H 67 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: H 98 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6438 (tm-30) REVERT: H 120 GLU cc_start: 0.8534 (tt0) cc_final: 0.8268 (tt0) REVERT: H 131 MET cc_start: 0.8457 (ttp) cc_final: 0.8211 (ttp) REVERT: H 140 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6980 (mpt) REVERT: f 43 MET cc_start: 0.8665 (mtt) cc_final: 0.8166 (mtt) REVERT: f 74 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7358 (mttp) REVERT: f 224 GLU cc_start: 0.7250 (pt0) cc_final: 0.6508 (mt-10) REVERT: f 288 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6083 (ttt180) REVERT: f 317 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7011 (mt-10) REVERT: g 54 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8087 (mttt) REVERT: g 111 ASN cc_start: 0.8175 (m-40) cc_final: 0.7974 (m110) REVERT: h 122 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: K 74 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7200 (mttp) REVERT: K 148 GLU cc_start: 0.6915 (mp0) cc_final: 0.6660 (mp0) REVERT: K 170 MET cc_start: 0.7549 (mmp) cc_final: 0.7312 (mmt) REVERT: K 173 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6284 (mtt-85) REVERT: K 191 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7292 (tp30) REVERT: K 288 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6771 (tmt170) REVERT: K 315 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: M 100 LYS cc_start: 0.7506 (mmpt) cc_final: 0.6956 (mtpt) REVERT: N 161 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7517 (mmpt) REVERT: k 148 GLU cc_start: 0.7057 (tp30) cc_final: 0.6598 (mp0) REVERT: k 191 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7368 (tp30) REVERT: k 306 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8390 (t) REVERT: k 307 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7544 (ttp) REVERT: k 315 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: k 317 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7034 (mt-10) REVERT: k 337 TRP cc_start: 0.7927 (OUTLIER) cc_final: 0.7029 (t60) REVERT: k 364 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8093 (mtp180) REVERT: l 57 MET cc_start: 0.8620 (mmm) cc_final: 0.8387 (mmt) REVERT: l 107 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8009 (mt) REVERT: l 112 GLN cc_start: 0.7320 (mm-40) cc_final: 0.7090 (pt0) REVERT: n 161 LYS cc_start: 0.7794 (mttt) cc_final: 0.7429 (mmpt) outliers start: 129 outliers final: 68 residues processed: 601 average time/residue: 0.8399 time to fit residues: 588.0158 Evaluate side-chains 627 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 535 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 191 GLU Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 288 ARG Chi-restraints excluded: chain a residue 296 LYS Chi-restraints excluded: chain a residue 297 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 296 LYS Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 228 MET Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 289 LYS Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain g residue 54 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 307 MET Chi-restraints excluded: chain K residue 315 GLU Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 306 SER Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 98 GLU Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Chi-restraints excluded: chain m residue 152 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 309 optimal weight: 3.9990 chunk 412 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 224 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 398 optimal weight: 0.9990 chunk 409 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 375 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN B 111 ASN B 112 GLN D 179 GLN b 42 ASN d 177 ASN d 179 GLN F 200 GLN G 42 ASN G 111 ASN H 101 ASN I 179 GLN g 42 ASN g 112 GLN i 177 ASN i 179 GLN L 112 GLN l 111 ASN m 103 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.194233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.159940 restraints weight = 29084.355| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.26 r_work: 0.3451 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35814 Z= 0.162 Angle : 0.627 16.332 48522 Z= 0.330 Chirality : 0.047 0.151 5370 Planarity : 0.005 0.042 6150 Dihedral : 6.849 55.117 5112 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.42 % Allowed : 15.62 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4182 helix: 0.96 (0.13), residues: 1548 sheet: 1.41 (0.16), residues: 936 loop : 0.11 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 329 TYR 0.021 0.002 TYR k 155 PHE 0.022 0.002 PHE f 92 TRP 0.016 0.001 TRP k 292 HIS 0.007 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (35814) covalent geometry : angle 0.62687 / 0.33 (48522) hydrogen bonds : bond 0.04817 / 3.17 ( 1485) hydrogen bonds : angle 4.72449 / 3.30 ( 4272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 551 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6793 (tp30) cc_final: 0.6224 (mp0) REVERT: A 224 GLU cc_start: 0.7238 (pt0) cc_final: 0.6512 (mt-10) REVERT: A 288 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6403 (tmt170) REVERT: A 289 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7406 (tmtm) REVERT: A 329 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7390 (mmm160) REVERT: C 92 LYS cc_start: 0.8143 (ttmm) cc_final: 0.7869 (tptp) REVERT: C 100 LYS cc_start: 0.7642 (mmpt) cc_final: 0.7084 (mtpt) REVERT: a 23 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.4837 (ptp) REVERT: a 33 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: a 148 GLU cc_start: 0.6881 (tp30) cc_final: 0.6455 (mp0) REVERT: a 191 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7215 (tp30) REVERT: a 224 GLU cc_start: 0.7179 (pt0) cc_final: 0.6510 (mt-10) REVERT: a 303 THR cc_start: 0.7331 (p) cc_final: 0.6818 (t) REVERT: a 337 TRP cc_start: 0.7927 (OUTLIER) cc_final: 0.7397 (m100) REVERT: a 360 LEU cc_start: 0.8654 (tp) cc_final: 0.8324 (mt) REVERT: c 120 GLU cc_start: 0.8527 (tt0) cc_final: 0.8236 (tt0) REVERT: c 128 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: F 191 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: F 315 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7328 (tp30) REVERT: F 329 ARG cc_start: 0.7854 (mtp85) cc_final: 0.7438 (mmm160) REVERT: F 337 TRP cc_start: 0.7921 (OUTLIER) cc_final: 0.7400 (m100) REVERT: F 360 LEU cc_start: 0.8632 (tp) cc_final: 0.8318 (mt) REVERT: H 67 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: H 98 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6359 (tm-30) REVERT: H 120 GLU cc_start: 0.8498 (tt0) cc_final: 0.8019 (tt0) REVERT: H 122 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: H 131 MET cc_start: 0.8495 (ttp) cc_final: 0.8194 (ttp) REVERT: H 140 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.6945 (mpt) REVERT: f 43 MET cc_start: 0.8654 (mtt) cc_final: 0.8143 (mtt) REVERT: f 74 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7237 (mttt) REVERT: f 224 GLU cc_start: 0.7241 (pt0) cc_final: 0.6515 (mt-10) REVERT: f 288 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6047 (ttt180) REVERT: f 317 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6989 (mt-10) REVERT: g 54 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8105 (mttt) REVERT: g 111 ASN cc_start: 0.8165 (m-40) cc_final: 0.7931 (m110) REVERT: g 113 SER cc_start: 0.7094 (t) cc_final: 0.6733 (p) REVERT: h 122 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: i 161 LYS cc_start: 0.7774 (mmpt) cc_final: 0.7329 (mmtp) REVERT: K 74 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7187 (mttp) REVERT: K 148 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: K 173 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.6186 (mtt-85) REVERT: K 191 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: K 288 ARG cc_start: 0.7044 (ttp-110) cc_final: 0.6752 (tmt170) REVERT: K 315 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: K 329 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7404 (mmm160) REVERT: M 100 LYS cc_start: 0.7444 (mmpt) cc_final: 0.6970 (mtpt) REVERT: N 161 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7542 (mmpt) REVERT: k 148 GLU cc_start: 0.7002 (tp30) cc_final: 0.6545 (mp0) REVERT: k 191 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: k 307 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7344 (ttp) REVERT: k 315 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7071 (tp30) REVERT: k 317 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6978 (mt-10) REVERT: k 337 TRP cc_start: 0.7927 (OUTLIER) cc_final: 0.6493 (m100) REVERT: k 364 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8192 (mtp180) REVERT: l 107 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7962 (mt) REVERT: l 112 GLN cc_start: 0.7293 (mm-40) cc_final: 0.7060 (pt0) REVERT: n 161 LYS cc_start: 0.7773 (mttt) cc_final: 0.7419 (mmpt) outliers start: 127 outliers final: 67 residues processed: 606 average time/residue: 0.8578 time to fit residues: 605.3837 Evaluate side-chains 634 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 537 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 33 GLU Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 191 GLU Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 297 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 296 LYS Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 228 MET Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain f residue 386 ILE Chi-restraints excluded: chain g residue 54 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain h residue 152 ARG Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 307 MET Chi-restraints excluded: chain K residue 315 GLU Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 128 GLN Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 161 LYS Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 98 GLU Chi-restraints excluded: chain m residue 128 GLN Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Chi-restraints excluded: chain m residue 152 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 50 optimal weight: 4.9990 chunk 210 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 383 optimal weight: 0.6980 chunk 326 optimal weight: 7.9990 chunk 364 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN B 42 ASN B 111 ASN B 112 GLN D 179 GLN b 42 ASN b 96 HIS c 101 ASN d 179 GLN G 42 ASN G 111 ASN H 101 ASN I 179 GLN g 42 ASN g 112 GLN i 179 GLN L 111 ASN L 112 GLN l 111 ASN m 103 HIS n 179 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.195679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.161568 restraints weight = 29145.818| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.15 r_work: 0.3503 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35814 Z= 0.214 Angle : 0.708 17.488 48522 Z= 0.371 Chirality : 0.050 0.161 5370 Planarity : 0.006 0.054 6150 Dihedral : 7.131 58.886 5112 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.39 % Allowed : 15.72 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.13), residues: 4182 helix: 0.85 (0.13), residues: 1542 sheet: 1.35 (0.16), residues: 906 loop : -0.08 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 329 TYR 0.021 0.003 TYR k 155 PHE 0.021 0.003 PHE k 92 TRP 0.018 0.002 TRP k 292 HIS 0.007 0.002 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (35814) covalent geometry : angle 0.70787 / 0.37 (48522) hydrogen bonds : bond 0.05527 / 3.63 ( 1485) hydrogen bonds : angle 4.86071 / 3.40 ( 4272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 541 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6879 (tp30) cc_final: 0.6158 (mp0) REVERT: A 288 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6584 (tmt170) REVERT: A 329 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7418 (mmm160) REVERT: C 92 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7905 (tptp) REVERT: C 98 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: C 100 LYS cc_start: 0.7675 (mmpt) cc_final: 0.7074 (mtpt) REVERT: C 122 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: a 23 MET cc_start: 0.5631 (OUTLIER) cc_final: 0.4884 (ptp) REVERT: a 33 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7775 (pt0) REVERT: a 148 GLU cc_start: 0.6931 (tp30) cc_final: 0.6330 (mp0) REVERT: a 191 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7421 (tp30) REVERT: a 224 GLU cc_start: 0.7337 (pt0) cc_final: 0.6668 (mt-10) REVERT: a 303 THR cc_start: 0.7491 (p) cc_final: 0.6993 (t) REVERT: c 100 LYS cc_start: 0.7706 (mmpt) cc_final: 0.7115 (mtpt) REVERT: c 120 GLU cc_start: 0.8726 (tt0) cc_final: 0.8418 (tt0) REVERT: c 128 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: c 140 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6925 (mpt) REVERT: F 191 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7404 (tp30) REVERT: F 315 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7461 (tp30) REVERT: F 329 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7533 (mmm160) REVERT: H 67 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: H 98 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: H 100 LYS cc_start: 0.7620 (mmpt) cc_final: 0.7356 (mmpt) REVERT: H 122 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: H 128 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: H 140 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.6833 (mpt) REVERT: f 43 MET cc_start: 0.8732 (mtt) cc_final: 0.8237 (mtt) REVERT: f 74 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7288 (mttt) REVERT: f 172 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5714 (mtm110) REVERT: f 224 GLU cc_start: 0.7376 (pt0) cc_final: 0.6578 (mt-10) REVERT: f 288 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6288 (ttt180) REVERT: f 317 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7208 (mt-10) REVERT: f 360 LEU cc_start: 0.8618 (tp) cc_final: 0.8407 (mt) REVERT: g 54 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8185 (mttt) REVERT: h 122 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: h 128 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8410 (tm-30) REVERT: K 74 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7219 (mttp) REVERT: K 148 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: K 173 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6292 (mtt-85) REVERT: K 191 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: K 288 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6775 (tmt170) REVERT: K 315 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: K 329 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7580 (mmm160) REVERT: M 100 LYS cc_start: 0.7413 (mmpt) cc_final: 0.6863 (mtpt) REVERT: N 161 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7590 (mmpt) REVERT: k 148 GLU cc_start: 0.6996 (tp30) cc_final: 0.6474 (mp0) REVERT: k 183 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6489 (ptp) REVERT: k 191 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: k 307 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7564 (ttp) REVERT: k 315 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: k 337 TRP cc_start: 0.8072 (OUTLIER) cc_final: 0.7106 (t60) REVERT: k 364 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8119 (mtp180) REVERT: l 107 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7983 (mt) REVERT: n 161 LYS cc_start: 0.7901 (mttt) cc_final: 0.7447 (mmpt) outliers start: 126 outliers final: 74 residues processed: 593 average time/residue: 0.8317 time to fit residues: 574.7179 Evaluate side-chains 642 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 534 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 33 GLU Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 191 GLU Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 288 ARG Chi-restraints excluded: chain a residue 296 LYS Chi-restraints excluded: chain a residue 297 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 140 MET Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 296 LYS Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 172 ARG Chi-restraints excluded: chain f residue 228 MET Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 289 LYS Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain g residue 54 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 128 GLN Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain h residue 152 ARG Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 315 GLU Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 161 LYS Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 183 MET Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 98 GLU Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Chi-restraints excluded: chain m residue 152 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 74 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 399 optimal weight: 1.9990 chunk 369 optimal weight: 3.9990 chunk 325 optimal weight: 0.8980 chunk 386 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN B 111 ASN B 112 GLN D 177 ASN D 179 GLN b 42 ASN c 101 ASN d 179 GLN G 42 ASN H 101 ASN ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN g 42 ASN g 111 ASN g 112 GLN i 179 GLN L 111 ASN L 112 GLN l 111 ASN m 103 HIS n 179 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.194666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.160528 restraints weight = 29010.161| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.24 r_work: 0.3465 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35814 Z= 0.139 Angle : 0.603 16.737 48522 Z= 0.317 Chirality : 0.046 0.152 5370 Planarity : 0.004 0.042 6150 Dihedral : 6.757 55.894 5112 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.10 % Allowed : 16.05 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.13), residues: 4182 helix: 1.07 (0.13), residues: 1548 sheet: 1.40 (0.16), residues: 936 loop : 0.12 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG k 329 TYR 0.020 0.002 TYR k 155 PHE 0.021 0.002 PHE k 92 TRP 0.022 0.001 TRP k 292 HIS 0.006 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (35814) covalent geometry : angle 0.60315 / 0.32 (48522) hydrogen bonds : bond 0.04532 / 2.99 ( 1485) hydrogen bonds : angle 4.68709 / 3.28 ( 4272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 537 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.5312 (OUTLIER) cc_final: 0.4490 (ptp) REVERT: A 148 GLU cc_start: 0.6787 (tp30) cc_final: 0.6251 (mp0) REVERT: A 224 GLU cc_start: 0.7225 (pt0) cc_final: 0.6459 (mt-10) REVERT: A 288 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6400 (tmt170) REVERT: A 289 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7319 (tmtm) REVERT: A 329 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7381 (mmm160) REVERT: C 92 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7931 (tptp) REVERT: C 98 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: C 100 LYS cc_start: 0.7490 (mmpt) cc_final: 0.7069 (mtpt) REVERT: C 122 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: a 23 MET cc_start: 0.5601 (OUTLIER) cc_final: 0.4916 (ptp) REVERT: a 148 GLU cc_start: 0.6906 (tp30) cc_final: 0.6508 (mp0) REVERT: a 224 GLU cc_start: 0.7148 (pt0) cc_final: 0.6567 (mt-10) REVERT: a 303 THR cc_start: 0.7358 (p) cc_final: 0.6890 (t) REVERT: a 337 TRP cc_start: 0.7921 (OUTLIER) cc_final: 0.7388 (m100) REVERT: a 360 LEU cc_start: 0.8661 (tp) cc_final: 0.8378 (mt) REVERT: c 120 GLU cc_start: 0.8513 (tt0) cc_final: 0.8202 (tt0) REVERT: c 122 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: c 128 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: c 140 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.6861 (mpt) REVERT: F 288 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6027 (ttt180) REVERT: F 315 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: F 337 TRP cc_start: 0.7918 (OUTLIER) cc_final: 0.7389 (m100) REVERT: F 360 LEU cc_start: 0.8647 (tp) cc_final: 0.8341 (mt) REVERT: H 67 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: H 98 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6668 (tt0) REVERT: H 122 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: H 140 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6838 (mpt) REVERT: f 43 MET cc_start: 0.8649 (mtt) cc_final: 0.8138 (mtt) REVERT: f 74 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7218 (mttt) REVERT: f 224 GLU cc_start: 0.7221 (pt0) cc_final: 0.6476 (mt-10) REVERT: f 288 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6024 (ttt180) REVERT: f 317 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6970 (mt-10) REVERT: g 49 GLU cc_start: 0.8286 (pt0) cc_final: 0.7872 (mp0) REVERT: g 54 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8060 (mttt) REVERT: g 113 SER cc_start: 0.7084 (t) cc_final: 0.6746 (p) REVERT: h 122 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: K 74 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7185 (mttp) REVERT: K 148 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: K 173 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6166 (mtt-85) REVERT: K 288 ARG cc_start: 0.7001 (ttp-110) cc_final: 0.6709 (tmt170) REVERT: K 315 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: K 329 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7386 (mmm160) REVERT: M 100 LYS cc_start: 0.7367 (mmpt) cc_final: 0.6954 (mtpt) REVERT: N 161 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7520 (mmpt) REVERT: k 148 GLU cc_start: 0.6983 (tp30) cc_final: 0.6592 (mp0) REVERT: k 307 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7342 (ttp) REVERT: k 315 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: k 317 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6955 (mt-10) REVERT: k 337 TRP cc_start: 0.7920 (OUTLIER) cc_final: 0.6371 (m100) REVERT: k 364 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8123 (mtp180) REVERT: l 107 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7968 (mt) REVERT: n 161 LYS cc_start: 0.7745 (mttt) cc_final: 0.7433 (mmpt) outliers start: 115 outliers final: 66 residues processed: 586 average time/residue: 0.8403 time to fit residues: 573.9077 Evaluate side-chains 628 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 531 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 288 ARG Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 122 GLU Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 140 MET Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 59 GLU Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain f residue 386 ILE Chi-restraints excluded: chain g residue 54 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 98 GLU Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain h residue 152 ARG Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 315 GLU Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 128 GLN Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 161 LYS Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 98 GLU Chi-restraints excluded: chain m residue 128 GLN Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Chi-restraints excluded: chain m residue 152 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 48 optimal weight: 0.0970 chunk 89 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 330 optimal weight: 0.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 ASN B 111 ASN D 179 GLN b 42 ASN b 112 GLN c 101 ASN d 177 ASN d 179 GLN G 42 ASN G 112 GLN I 179 GLN g 42 ASN g 111 ASN g 112 GLN i 179 GLN L 111 ASN L 112 GLN l 111 ASN m 103 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.193386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.159186 restraints weight = 29025.486| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.24 r_work: 0.3451 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35814 Z= 0.188 Angle : 0.675 17.464 48522 Z= 0.353 Chirality : 0.049 0.182 5370 Planarity : 0.005 0.049 6150 Dihedral : 6.946 55.656 5112 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.10 % Allowed : 16.18 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.13), residues: 4182 helix: 0.99 (0.13), residues: 1548 sheet: 1.36 (0.17), residues: 906 loop : -0.02 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 329 TYR 0.027 0.003 TYR F 205 PHE 0.022 0.002 PHE k 92 TRP 0.027 0.002 TRP k 292 HIS 0.007 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (35814) covalent geometry : angle 0.67546 / 0.35 (48522) hydrogen bonds : bond 0.05169 / 3.40 ( 1485) hydrogen bonds : angle 4.78018 / 3.35 ( 4272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 537 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6860 (tp30) cc_final: 0.6331 (mp0) REVERT: A 224 GLU cc_start: 0.7237 (pt0) cc_final: 0.6482 (mt-10) REVERT: A 288 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6466 (tmt170) REVERT: A 289 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7315 (tmtm) REVERT: A 329 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7363 (mmm160) REVERT: C 92 LYS cc_start: 0.8160 (ttmm) cc_final: 0.7948 (tptp) REVERT: C 100 LYS cc_start: 0.7519 (mmpt) cc_final: 0.7108 (mtpt) REVERT: a 23 MET cc_start: 0.5573 (OUTLIER) cc_final: 0.4895 (ptp) REVERT: a 33 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7740 (pt0) REVERT: a 148 GLU cc_start: 0.6887 (tp30) cc_final: 0.6478 (mp0) REVERT: a 224 GLU cc_start: 0.7148 (pt0) cc_final: 0.6579 (mt-10) REVERT: a 303 THR cc_start: 0.7390 (p) cc_final: 0.6940 (t) REVERT: a 360 LEU cc_start: 0.8669 (tp) cc_final: 0.8381 (mt) REVERT: c 101 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7367 (t0) REVERT: c 120 GLU cc_start: 0.8516 (tt0) cc_final: 0.8010 (tt0) REVERT: c 122 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: c 128 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: c 140 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.6824 (mpt) REVERT: F 288 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6008 (ttt180) REVERT: F 315 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: F 360 LEU cc_start: 0.8670 (tp) cc_final: 0.8355 (mt) REVERT: H 67 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: H 98 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: H 122 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: H 140 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.6849 (mpt) REVERT: f 43 MET cc_start: 0.8657 (mtt) cc_final: 0.8149 (mtt) REVERT: f 74 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7266 (mttt) REVERT: f 224 GLU cc_start: 0.7233 (pt0) cc_final: 0.6513 (mt-10) REVERT: f 288 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.5956 (ttt180) REVERT: f 317 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6969 (mt-10) REVERT: g 54 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8009 (mttt) REVERT: h 122 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: K 74 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7207 (mttp) REVERT: K 148 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: K 173 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6233 (mtt-85) REVERT: K 288 ARG cc_start: 0.7033 (ttp-110) cc_final: 0.6732 (tmt170) REVERT: K 329 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7487 (mmm160) REVERT: M 100 LYS cc_start: 0.7383 (mmpt) cc_final: 0.6950 (mtpt) REVERT: N 161 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7516 (mmpt) REVERT: k 148 GLU cc_start: 0.7020 (tp30) cc_final: 0.6615 (mp0) REVERT: k 307 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7566 (ttp) REVERT: k 315 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7182 (tt0) REVERT: k 317 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6930 (mt-10) REVERT: k 364 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8169 (mtp180) REVERT: l 107 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7972 (mt) REVERT: n 161 LYS cc_start: 0.7764 (mttt) cc_final: 0.7454 (mmpt) outliers start: 115 outliers final: 77 residues processed: 580 average time/residue: 0.8768 time to fit residues: 591.5368 Evaluate side-chains 635 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 532 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 33 GLU Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 288 ARG Chi-restraints excluded: chain a residue 296 LYS Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 122 GLU Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 140 MET Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 296 LYS Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 59 GLU Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 228 MET Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 289 LYS Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain f residue 386 ILE Chi-restraints excluded: chain g residue 54 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 98 GLU Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain h residue 152 ARG Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 296 LYS Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 128 GLN Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 161 LYS Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 98 GLU Chi-restraints excluded: chain m residue 128 GLN Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Chi-restraints excluded: chain m residue 152 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 178 optimal weight: 0.6980 chunk 401 optimal weight: 0.9990 chunk 399 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 358 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 351 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 GLN B 42 ASN B 111 ASN D 179 GLN b 42 ASN b 112 GLN c 101 ASN d 179 GLN G 42 ASN G 112 GLN H 128 GLN ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN g 42 ASN g 111 ASN g 112 GLN i 177 ASN i 179 GLN L 111 ASN L 112 GLN l 111 ASN m 103 HIS n 179 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.196082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.161831 restraints weight = 29182.509| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.20 r_work: 0.3493 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35814 Z= 0.112 Angle : 0.555 16.085 48522 Z= 0.292 Chirality : 0.045 0.148 5370 Planarity : 0.004 0.035 6150 Dihedral : 6.459 57.073 5112 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.75 % Allowed : 16.69 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.13), residues: 4182 helix: 1.26 (0.13), residues: 1548 sheet: 1.29 (0.16), residues: 966 loop : 0.30 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG k 329 TYR 0.020 0.002 TYR F 205 PHE 0.020 0.002 PHE f 92 TRP 0.027 0.001 TRP k 292 HIS 0.006 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (35814) covalent geometry : angle 0.55531 / 0.29 (48522) hydrogen bonds : bond 0.03986 / 2.63 ( 1485) hydrogen bonds : angle 4.57069 / 3.20 ( 4272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14979.24 seconds wall clock time: 255 minutes 15.87 seconds (15315.87 seconds total)