Starting phenix.real_space_refine on Sat Sep 12 20:27:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rwo_10044/09_2026/6rwo_10044.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rwo_10044/09_2026/6rwo_10044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rwo_10044/09_2026/6rwo_10044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rwo_10044/09_2026/6rwo_10044.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rwo_10044/09_2026/6rwo_10044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rwo_10044/09_2026/6rwo_10044.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rwo_10044/09_2026/6rwo_10044.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rwo_10044/09_2026/6rwo_10044.cif" } resolution = 3.05 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= 0.465 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 P 84 5.49 5 Mg 4 5.21 5 S 74 5.16 5 Cl 2 4.86 5 C 11364 2.51 5 N 3280 2.21 5 O 3544 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s 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: 18366 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2140 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain: "Q" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "W" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 378 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 566 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1643 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Chain: "K" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1520 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 2 Chain: "J" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2016 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain breaks: 2 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {' CL': 1, ' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 335 SG CYS A 40 79.872 62.097 31.593 1.00 30.55 S ATOM 357 SG CYS A 43 76.869 64.139 33.032 1.00 29.90 S ATOM 3353 SG CYS E 40 92.806 41.139 54.296 1.00 59.10 S ATOM 3375 SG CYS E 43 95.023 43.160 56.977 1.00 64.54 S ATOM 5909 SG CYS K 40 23.885 48.204 22.080 1.00 82.77 S ATOM 5931 SG CYS K 43 25.815 45.648 24.409 1.00 79.38 S ATOM 7456 SG CYS J 40 58.627 30.323 59.508 1.00 70.60 S ATOM 7478 SG CYS J 43 56.683 31.978 56.543 1.00 77.61 S Restraints were copied for chains: I, S, T, M, F, D, C, B Time building chain proxies: 4.42, per 1000 atoms: 0.24 Number of scatterers: 18366 At special positions: 0 Unit cell: (131.1, 175.26, 99.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 Cl 2 17.00 S 74 16.00 P 84 15.00 Mg 4 11.99 F 6 9.00 O 3544 8.00 N 3280 7.00 C 11364 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: 1.63 Conformation dependent library (CDL) restraints added in 709.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 43 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb=" ZN C 500 " pdb="ZN ZN C 500 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 500 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 40 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 43 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 16 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 12 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 43 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 40 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 40 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 43 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" NE2 HIS J 12 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 16 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 43 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 40 " pdb=" ZN K 500 " pdb="ZN ZN K 500 " - pdb=" NE2 HIS K 12 " pdb="ZN ZN K 500 " - pdb=" ND1 HIS K 16 " pdb="ZN ZN K 500 " - pdb=" SG CYS K 40 " pdb="ZN ZN K 500 " - pdb=" SG CYS K 43 " pdb=" ZN M 500 " pdb="ZN ZN M 500 " - pdb=" ND1 HIS M 16 " pdb="ZN ZN M 500 " - pdb=" NE2 HIS M 12 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 43 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 40 " Number of angles added : 10 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3880 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 18 sheets defined 50.2% alpha, 19.4% beta 30 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.593A pdb=" N MET A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.889A pdb=" N THR A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 144 through 147 removed outlier: 3.529A pdb=" N SER A 147 " --> pdb=" O ASN A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 148 through 165 removed outlier: 3.919A pdb=" N GLU A 152 " --> pdb=" O HIS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.577A pdb=" N ALA A 169 " --> pdb=" O ARG A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.797A pdb=" N ALA A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 219 Processing helix chain 'E' and resid 1 through 16 Processing helix chain 'E' and resid 18 through 26 removed outlier: 3.586A pdb=" N MET E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.514A pdb=" N ALA E 33 " --> pdb=" O PRO E 29 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 221 removed outlier: 4.183A pdb=" N GLN N 221 " --> pdb=" O ILE N 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 108 removed outlier: 3.564A pdb=" N THR L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 151 through 165 Processing helix chain 'L' and resid 166 through 169 removed outlier: 3.541A pdb=" N ALA L 169 " --> pdb=" O ARG L 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 166 through 169' Processing helix chain 'L' and resid 171 through 186 removed outlier: 3.940A pdb=" N ALA L 175 " --> pdb=" O LYS L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 221 removed outlier: 3.515A pdb=" N ARG L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER L 218 " --> pdb=" O GLN L 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 16 Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 39 Processing helix chain 'K' and resid 94 through 108 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 150 through 165 Processing helix chain 'K' and resid 166 through 169 removed outlier: 3.569A pdb=" N ALA K 169 " --> pdb=" O ARG K 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 166 through 169' Processing helix chain 'K' and resid 171 through 186 removed outlier: 3.717A pdb=" N ALA K 175 " --> pdb=" O LYS K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 217 Processing helix chain 'J' and resid 2 through 16 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 29 through 39 Processing helix chain 'J' and resid 93 through 108 removed outlier: 3.706A pdb=" N THR J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 151 through 165 Processing helix chain 'J' and resid 166 through 169 Processing helix chain 'J' and resid 171 through 186 removed outlier: 3.620A pdb=" N ALA J 175 " --> pdb=" O LYS J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 221 Processing helix chain 'I' and resid 1 through 16 Processing helix chain 'I' and resid 18 through 26 removed outlier: 3.592A pdb=" N MET I 22 " --> pdb=" O ASN I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 93 through 108 removed outlier: 3.889A pdb=" N THR I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 144 through 147 removed outlier: 3.529A pdb=" N SER I 147 " --> pdb=" O ASN I 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 144 through 147' Processing helix chain 'I' and resid 148 through 165 removed outlier: 3.920A pdb=" N GLU I 152 " --> pdb=" O HIS I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 169 removed outlier: 3.578A pdb=" N ALA I 169 " --> pdb=" O ARG I 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 166 through 169' Processing helix chain 'I' and resid 171 through 186 removed outlier: 3.796A pdb=" N ALA I 175 " --> pdb=" O LYS I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 219 Processing helix chain 'M' and resid 1 through 16 Processing helix chain 'M' and resid 18 through 26 removed outlier: 3.586A pdb=" N MET M 22 " --> pdb=" O ASN M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 40 removed outlier: 3.514A pdb=" N ALA M 33 " --> pdb=" O PRO M 29 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS M 40 " --> pdb=" O ILE M 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 221 removed outlier: 4.183A pdb=" N GLN F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 108 removed outlier: 3.564A pdb=" N THR D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 151 through 165 Processing helix chain 'D' and resid 166 through 169 removed outlier: 3.542A pdb=" N ALA D 169 " --> pdb=" O ARG D 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 169' Processing helix chain 'D' and resid 171 through 186 removed outlier: 3.941A pdb=" N ALA D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 221 removed outlier: 3.515A pdb=" N ARG D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 94 through 108 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 166 through 169 removed outlier: 3.568A pdb=" N ALA C 169 " --> pdb=" O ARG C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 166 through 169' Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.718A pdb=" N ALA C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 217 Processing helix chain 'B' and resid 2 through 16 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.706A pdb=" N THR B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 151 through 165 Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'B' and resid 171 through 186 removed outlier: 3.619A pdb=" N ALA B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 221 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 4.391A pdb=" N VAL A 72 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 261 removed outlier: 7.220A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LYS A 244 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 250 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 227 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 225 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 234 through 235 removed outlier: 3.711A pdb=" N GLN N 234 " --> pdb=" O GLU N 229 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU N 229 " --> pdb=" O GLN N 234 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU N 241 " --> pdb=" O GLN N 252 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN N 252 " --> pdb=" O LEU N 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 234 through 235 removed outlier: 3.711A pdb=" N GLN N 234 " --> pdb=" O GLU N 229 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU N 229 " --> pdb=" O GLN N 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 83 through 89 removed outlier: 4.435A pdb=" N VAL L 72 " --> pdb=" O LEU L 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 257 through 261 removed outlier: 5.803A pdb=" N GLN L 252 " --> pdb=" O LEU L 241 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU L 241 " --> pdb=" O GLN L 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 83 through 89 removed outlier: 3.823A pdb=" N VAL K 72 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU K 113 " --> pdb=" O THR K 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 83 through 89 removed outlier: 4.181A pdb=" N VAL J 72 " --> pdb=" O LEU J 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.096A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU J 241 " --> pdb=" O PHE J 223 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE J 223 " --> pdb=" O LEU J 241 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 83 through 89 removed outlier: 4.391A pdb=" N VAL I 72 " --> pdb=" O LEU I 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 257 through 261 removed outlier: 7.220A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL I 250 " --> pdb=" O ILE I 242 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE I 227 " --> pdb=" O LYS I 236 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL I 225 " --> pdb=" O PRO I 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 234 through 235 removed outlier: 3.710A pdb=" N GLN F 234 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 229 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU F 241 " --> pdb=" O GLN F 252 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN F 252 " --> pdb=" O LEU F 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 234 through 235 removed outlier: 3.710A pdb=" N GLN F 234 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 229 " --> pdb=" O GLN F 234 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 83 through 89 removed outlier: 4.435A pdb=" N VAL D 72 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 257 through 261 removed outlier: 5.802A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 83 through 89 removed outlier: 3.823A pdb=" N VAL C 72 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU C 113 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 89 removed outlier: 4.181A pdb=" N VAL B 72 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 256 through 261 removed outlier: 6.096A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU B 241 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE B 223 " --> pdb=" O LEU B 241 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4173 1.33 - 1.45: 4539 1.45 - 1.58: 9916 1.58 - 1.70: 166 1.70 - 1.83: 108 Bond restraints: 18902 Sorted by residual: bond pdb=" C3' DA W 21 " pdb=" C2' DA W 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DA T 21 " pdb=" C2' DA T 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C1' DC Q 3 " pdb=" N1 DC Q 3 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.92e+00 bond pdb=" C1' DC S 3 " pdb=" N1 DC S 3 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.69e+00 bond pdb=" C3' DA Q 1 " pdb=" O3' DA Q 1 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.64e+00 ... (remaining 18897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 25082 1.89 - 3.78: 776 3.78 - 5.67: 52 5.67 - 7.57: 0 7.57 - 9.46: 6 Bond angle restraints: 25916 Sorted by residual: angle pdb=" N3 DT Q 4 " pdb=" C4 DT Q 4 " pdb=" O4 DT Q 4 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT S 4 " pdb=" C4 DT S 4 " pdb=" O4 DT S 4 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT T 4 " pdb=" C4 DT T 4 " pdb=" O4 DT T 4 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT W 17 " pdb=" C4 DT W 17 " pdb=" O4 DT W 17 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT T 17 " pdb=" C4 DT T 17 " pdb=" O4 DT T 17 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 25911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 9746 17.41 - 34.83: 844 34.83 - 52.24: 461 52.24 - 69.66: 105 69.66 - 87.07: 10 Dihedral angle restraints: 11166 sinusoidal: 5192 harmonic: 5974 Sorted by residual: dihedral pdb=" CA TYR I 194 " pdb=" C TYR I 194 " pdb=" N SER I 195 " pdb=" CA SER I 195 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TYR A 194 " pdb=" C TYR A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LYS L 236 " pdb=" C LYS L 236 " pdb=" N GLY L 237 " pdb=" CA GLY L 237 " ideal model delta harmonic sigma weight residual 180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 11163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1533 0.035 - 0.070: 883 0.070 - 0.105: 302 0.105 - 0.140: 106 0.140 - 0.175: 36 Chirality restraints: 2860 Sorted by residual: chirality pdb=" CA ILE D 268 " pdb=" N ILE D 268 " pdb=" C ILE D 268 " pdb=" CB ILE D 268 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA ILE L 268 " pdb=" N ILE L 268 " pdb=" C ILE L 268 " pdb=" CB ILE L 268 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CB ILE B 74 " pdb=" CA ILE B 74 " pdb=" CG1 ILE B 74 " pdb=" CG2 ILE B 74 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 2857 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 28 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO C 29 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 29 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 29 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 260 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO L 261 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 261 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 261 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 28 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO K 29 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO K 29 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO K 29 " 0.029 5.00e-02 4.00e+02 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 120 2.58 - 3.16: 12829 3.16 - 3.74: 26145 3.74 - 4.32: 38080 4.32 - 4.90: 63520 Nonbonded interactions: 140694 Sorted by model distance: nonbonded pdb=" OAC KLQ A 303 " pdb="MG MG A 305 " model vdw 1.994 2.170 nonbonded pdb=" OAC KLQ I 303 " pdb="MG MG I 305 " model vdw 2.000 2.170 nonbonded pdb="MG MG I 304 " pdb=" O HOH I 401 " model vdw 2.007 2.170 nonbonded pdb="MG MG A 304 " pdb=" O HOH A 401 " model vdw 2.007 2.170 nonbonded pdb="MG MG I 305 " pdb=" O HOH I 403 " model vdw 2.013 2.170 ... (remaining 140689 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'W' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'F' } ncs_group { reference = chain 'L' selection = chain 'D' } ncs_group { reference = chain 'K' selection = chain 'C' } ncs_group { reference = chain 'J' selection = chain 'B' } 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: 3.790 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.210 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.008 0.194 18934 Z= 0.411 Angle : 0.739 9.457 25926 Z= 0.494 Chirality : 0.051 0.175 2860 Planarity : 0.006 0.053 3012 Dihedral : 17.079 87.074 7286 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.10 % Allowed : 6.49 % Favored : 89.41 % 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: -3.00 (0.14), residues: 2032 helix: -1.79 (0.12), residues: 956 sheet: -0.23 (0.22), residues: 432 loop : -3.35 (0.18), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 199 TYR 0.013 0.002 TYR B 83 PHE 0.016 0.002 PHE I 1 TRP 0.015 0.002 TRP M 19 HIS 0.006 0.001 HIS I 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.39 (18902) covalent geometry : angle 0.72907 / 0.49 (25916) hydrogen bonds : bond 0.15617 / 10.42 ( 1046) hydrogen bonds : angle 6.75933 / 4.72 ( 2968) metal coordination : bond 0.12556 / 8.06 ( 32) metal coordination : angle 6.08561 / 3.44 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 323 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.8868 (mtm) cc_final: 0.8331 (mtm) REVERT: A 154 MET cc_start: 0.8976 (mmt) cc_final: 0.8661 (mmt) REVERT: A 264 LYS cc_start: 0.8304 (mttt) cc_final: 0.8036 (mptt) REVERT: E 22 MET cc_start: 0.8469 (mtm) cc_final: 0.8227 (mtm) REVERT: N 229 GLU cc_start: 0.8102 (pt0) cc_final: 0.7747 (pt0) REVERT: N 252 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: L 87 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5975 (mm-30) REVERT: L 207 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7242 (t0) REVERT: L 218 SER cc_start: 0.8434 (m) cc_final: 0.8234 (p) REVERT: L 228 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8602 (mtt180) REVERT: K 27 GLN cc_start: 0.6721 (mt0) cc_final: 0.5751 (tm-30) REVERT: K 104 LEU cc_start: 0.7862 (tp) cc_final: 0.7649 (tp) REVERT: K 151 VAL cc_start: 0.7297 (OUTLIER) cc_final: 0.6999 (m) REVERT: K 155 ASN cc_start: 0.8107 (m-40) cc_final: 0.7907 (m110) REVERT: J 11 GLU cc_start: 0.7327 (tp30) cc_final: 0.7010 (mm-30) REVERT: J 171 LYS cc_start: 0.8117 (mttt) cc_final: 0.7415 (mmmt) REVERT: J 202 ASP cc_start: 0.8161 (t70) cc_final: 0.7876 (t0) REVERT: J 266 LYS cc_start: 0.7617 (mtpp) cc_final: 0.7188 (pttt) REVERT: J 270 ASP cc_start: 0.8372 (t70) cc_final: 0.8161 (t0) REVERT: I 22 MET cc_start: 0.9004 (mtm) cc_final: 0.8584 (mtm) REVERT: I 73 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8208 (mt) REVERT: I 154 MET cc_start: 0.8994 (mmt) cc_final: 0.8722 (mmt) REVERT: M 14 LYS cc_start: 0.7080 (mttt) cc_final: 0.5783 (tptp) REVERT: M 26 PHE cc_start: 0.8127 (m-80) cc_final: 0.7865 (m-80) REVERT: F 229 GLU cc_start: 0.8127 (pt0) cc_final: 0.7755 (pt0) REVERT: F 252 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: D 87 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5889 (mm-30) REVERT: D 207 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7029 (t0) REVERT: D 228 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8571 (mtt180) REVERT: C 27 GLN cc_start: 0.6590 (mt0) cc_final: 0.5601 (tm-30) REVERT: C 69 GLU cc_start: 0.5529 (mt-10) cc_final: 0.5315 (mt-10) REVERT: C 151 VAL cc_start: 0.7348 (OUTLIER) cc_final: 0.7090 (m) REVERT: C 155 ASN cc_start: 0.8305 (m-40) cc_final: 0.8105 (m110) REVERT: B 11 GLU cc_start: 0.7269 (tp30) cc_final: 0.7030 (mm-30) REVERT: B 171 LYS cc_start: 0.8124 (mttt) cc_final: 0.7464 (mmmt) REVERT: B 266 LYS cc_start: 0.7527 (mtpp) cc_final: 0.7089 (pttt) REVERT: B 270 ASP cc_start: 0.8432 (t70) cc_final: 0.8191 (t0) outliers start: 72 outliers final: 33 residues processed: 380 average time/residue: 0.1420 time to fit residues: 80.4054 Evaluate side-chains 278 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 228 ARG Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 165 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0670 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN L 99 HIS L 134 GLN L 216 GLN L 252 GLN K 18 ASN K 168 GLN J 9 GLN J 157 GLN I 222 ASN D 99 HIS D 134 GLN D 216 GLN D 252 GLN C 18 ASN C 168 GLN B 9 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.169846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.155450 restraints weight = 19552.009| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 0.73 r_work: 0.3351 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18934 Z= 0.145 Angle : 0.543 5.582 25926 Z= 0.315 Chirality : 0.044 0.146 2860 Planarity : 0.005 0.056 3012 Dihedral : 18.773 89.362 3330 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.13 % Allowed : 10.02 % Favored : 86.85 % 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: -0.75 (0.17), residues: 2032 helix: 0.95 (0.16), residues: 962 sheet: 0.03 (0.22), residues: 438 loop : -3.25 (0.19), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 166 TYR 0.009 0.001 TYR I 194 PHE 0.010 0.001 PHE I 227 TRP 0.012 0.001 TRP I 19 HIS 0.006 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (18902) covalent geometry : angle 0.53973 / 0.31 (25916) hydrogen bonds : bond 0.06400 / 4.25 ( 1046) hydrogen bonds : angle 5.03126 / 3.47 ( 2968) metal coordination : bond 0.01800 / 1.23 ( 32) metal coordination : angle 3.00893 / 1.68 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8834 (mtm) cc_final: 0.8591 (mtm) REVERT: A 154 MET cc_start: 0.8937 (mmt) cc_final: 0.8681 (mmm) REVERT: N 229 GLU cc_start: 0.7821 (pt0) cc_final: 0.7551 (pt0) REVERT: N 252 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: L 87 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.6011 (mm-30) REVERT: K 27 GLN cc_start: 0.5963 (mt0) cc_final: 0.5678 (tm-30) REVERT: I 22 MET cc_start: 0.8862 (mtm) cc_final: 0.8484 (mtm) REVERT: I 154 MET cc_start: 0.8906 (mmt) cc_final: 0.8658 (mmm) REVERT: M 14 LYS cc_start: 0.7227 (mttt) cc_final: 0.6353 (tptt) REVERT: F 229 GLU cc_start: 0.7850 (pt0) cc_final: 0.7574 (pt0) REVERT: F 252 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: D 87 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5897 (mm-30) REVERT: C 27 GLN cc_start: 0.6003 (mt0) cc_final: 0.5723 (tm-30) outliers start: 55 outliers final: 36 residues processed: 293 average time/residue: 0.1380 time to fit residues: 60.8923 Evaluate side-chains 274 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 151 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 179 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 185 optimal weight: 0.0370 chunk 60 optimal weight: 0.2980 chunk 24 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 189 optimal weight: 0.0770 chunk 118 optimal weight: 0.9990 overall best weight: 0.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 134 GLN J 112 HIS D 134 GLN B 112 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.172612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.163867 restraints weight = 19806.067| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 0.49 r_work: 0.3679 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18934 Z= 0.115 Angle : 0.480 6.505 25926 Z= 0.278 Chirality : 0.042 0.224 2860 Planarity : 0.004 0.059 3012 Dihedral : 18.690 87.738 3295 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.73 % Allowed : 11.16 % Favored : 86.10 % 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: 0.18 (0.18), residues: 2032 helix: 1.88 (0.16), residues: 962 sheet: 0.39 (0.24), residues: 408 loop : -2.88 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 166 TYR 0.007 0.001 TYR J 15 PHE 0.007 0.001 PHE A 227 TRP 0.012 0.001 TRP B 19 HIS 0.003 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.11 (18902) covalent geometry : angle 0.47541 / 0.28 (25916) hydrogen bonds : bond 0.05056 / 3.35 ( 1046) hydrogen bonds : angle 4.70152 / 3.24 ( 2968) metal coordination : bond 0.01364 / 0.95 ( 32) metal coordination : angle 3.26302 / 1.78 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8849 (mmt) cc_final: 0.8602 (mmm) REVERT: A 215 ASN cc_start: 0.8174 (m-40) cc_final: 0.7969 (m-40) REVERT: N 229 GLU cc_start: 0.7845 (pt0) cc_final: 0.7592 (pt0) REVERT: N 252 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: K 37 VAL cc_start: 0.7042 (t) cc_final: 0.6542 (t) REVERT: K 63 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7095 (ttp) REVERT: I 154 MET cc_start: 0.8840 (mmt) cc_final: 0.8567 (mmm) REVERT: F 229 GLU cc_start: 0.7809 (pt0) cc_final: 0.7559 (pt0) REVERT: F 252 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: C 63 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7114 (ttp) outliers start: 48 outliers final: 28 residues processed: 282 average time/residue: 0.1374 time to fit residues: 58.3215 Evaluate side-chains 262 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 63 MET Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 151 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 176 optimal weight: 30.0000 chunk 123 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS J 112 HIS I 99 HIS D 134 GLN B 112 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.168032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.154003 restraints weight = 19731.409| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 0.72 r_work: 0.3316 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18934 Z= 0.184 Angle : 0.556 7.348 25926 Z= 0.314 Chirality : 0.045 0.233 2860 Planarity : 0.005 0.053 3012 Dihedral : 18.702 86.356 3272 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.42 % Allowed : 12.02 % Favored : 84.57 % 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: 0.31 (0.18), residues: 2032 helix: 2.07 (0.16), residues: 958 sheet: 0.21 (0.23), residues: 436 loop : -2.88 (0.20), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 166 TYR 0.012 0.002 TYR J 271 PHE 0.016 0.002 PHE I 1 TRP 0.013 0.002 TRP B 19 HIS 0.004 0.001 HIS J 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (18902) covalent geometry : angle 0.55142 / 0.31 (25916) hydrogen bonds : bond 0.06539 / 4.34 ( 1046) hydrogen bonds : angle 4.70927 / 3.26 ( 2968) metal coordination : bond 0.01523 / 1.08 ( 32) metal coordination : angle 3.83007 / 2.24 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.9089 (mtm) cc_final: 0.8625 (mtm) REVERT: A 154 MET cc_start: 0.9026 (mmt) cc_final: 0.8714 (mmm) REVERT: N 229 GLU cc_start: 0.8320 (pt0) cc_final: 0.8065 (pt0) REVERT: N 252 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: L 222 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7985 (m-40) REVERT: K 37 VAL cc_start: 0.7036 (t) cc_final: 0.6535 (t) REVERT: J 73 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8570 (mm) REVERT: I 22 MET cc_start: 0.9102 (mtm) cc_final: 0.8656 (mtm) REVERT: I 154 MET cc_start: 0.8998 (mmt) cc_final: 0.8700 (mmm) REVERT: F 229 GLU cc_start: 0.8306 (pt0) cc_final: 0.8067 (pt0) REVERT: F 252 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: D 222 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.8003 (m-40) REVERT: B 73 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8606 (mm) REVERT: B 202 ASP cc_start: 0.8708 (t70) cc_final: 0.8503 (t0) outliers start: 60 outliers final: 46 residues processed: 278 average time/residue: 0.1420 time to fit residues: 58.5338 Evaluate side-chains 270 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 193 optimal weight: 0.0270 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 134 GLN J 112 HIS D 134 GLN B 112 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.171149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.162980 restraints weight = 19661.981| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 0.46 r_work: 0.3669 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18934 Z= 0.116 Angle : 0.485 6.018 25926 Z= 0.277 Chirality : 0.042 0.258 2860 Planarity : 0.004 0.049 3012 Dihedral : 18.684 85.307 3270 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.79 % Allowed : 13.61 % Favored : 83.60 % 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: 0.68 (0.19), residues: 2032 helix: 2.38 (0.16), residues: 962 sheet: 0.38 (0.23), residues: 434 loop : -2.74 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 166 TYR 0.011 0.001 TYR B 15 PHE 0.007 0.001 PHE B 185 TRP 0.013 0.001 TRP B 19 HIS 0.004 0.001 HIS I 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.12 (18902) covalent geometry : angle 0.48071 / 0.28 (25916) hydrogen bonds : bond 0.05015 / 3.34 ( 1046) hydrogen bonds : angle 4.51982 / 3.12 ( 2968) metal coordination : bond 0.01142 / 0.81 ( 32) metal coordination : angle 3.33816 / 1.85 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8987 (mtm) cc_final: 0.8483 (mtm) REVERT: A 154 MET cc_start: 0.8876 (mmt) cc_final: 0.8621 (mmm) REVERT: N 229 GLU cc_start: 0.7911 (pt0) cc_final: 0.7694 (pt0) REVERT: N 252 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: L 222 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7645 (m-40) REVERT: K 37 VAL cc_start: 0.7120 (t) cc_final: 0.6620 (t) REVERT: J 73 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8533 (mm) REVERT: I 22 MET cc_start: 0.8976 (mtm) cc_final: 0.8498 (mtm) REVERT: I 154 MET cc_start: 0.8849 (mmt) cc_final: 0.8594 (mmm) REVERT: F 229 GLU cc_start: 0.7877 (pt0) cc_final: 0.7654 (pt0) REVERT: F 252 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: D 222 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7703 (m-40) REVERT: C 37 VAL cc_start: 0.7074 (t) cc_final: 0.6602 (t) REVERT: B 73 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8561 (mm) outliers start: 49 outliers final: 37 residues processed: 267 average time/residue: 0.1372 time to fit residues: 54.8229 Evaluate side-chains 264 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 66 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 134 GLN J 112 HIS D 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.170737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.161862 restraints weight = 19566.077| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 0.48 r_work: 0.3662 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18934 Z= 0.124 Angle : 0.490 6.526 25926 Z= 0.278 Chirality : 0.042 0.255 2860 Planarity : 0.004 0.047 3012 Dihedral : 18.615 84.737 3270 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.13 % Allowed : 13.67 % Favored : 83.20 % 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: 0.77 (0.19), residues: 2032 helix: 2.47 (0.16), residues: 962 sheet: 0.35 (0.23), residues: 436 loop : -2.66 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 231 TYR 0.009 0.001 TYR J 194 PHE 0.009 0.001 PHE I 1 TRP 0.012 0.001 TRP B 19 HIS 0.005 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (18902) covalent geometry : angle 0.48637 / 0.28 (25916) hydrogen bonds : bond 0.05135 / 3.42 ( 1046) hydrogen bonds : angle 4.47981 / 3.09 ( 2968) metal coordination : bond 0.01063 / 0.75 ( 32) metal coordination : angle 3.21328 / 1.81 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 224 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8919 (mmt) cc_final: 0.8675 (mmm) REVERT: N 229 GLU cc_start: 0.7956 (pt0) cc_final: 0.7729 (pt0) REVERT: L 222 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7663 (m-40) REVERT: K 37 VAL cc_start: 0.7120 (t) cc_final: 0.6612 (t) REVERT: J 73 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8571 (mm) REVERT: I 22 MET cc_start: 0.8970 (mtm) cc_final: 0.8521 (mtm) REVERT: I 154 MET cc_start: 0.8868 (mmt) cc_final: 0.8642 (mmm) REVERT: F 229 GLU cc_start: 0.7931 (pt0) cc_final: 0.7711 (pt0) REVERT: D 222 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7732 (m-40) REVERT: B 73 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8588 (mm) outliers start: 55 outliers final: 42 residues processed: 260 average time/residue: 0.1384 time to fit residues: 53.8971 Evaluate side-chains 264 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 185 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 101 optimal weight: 0.0000 chunk 152 optimal weight: 30.0000 chunk 162 optimal weight: 6.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 134 GLN L 216 GLN D 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.169097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.155718 restraints weight = 19750.141| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 0.69 r_work: 0.3348 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18934 Z= 0.152 Angle : 0.521 6.345 25926 Z= 0.293 Chirality : 0.043 0.238 2860 Planarity : 0.004 0.047 3012 Dihedral : 18.637 84.347 3264 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.76 % Allowed : 13.04 % Favored : 83.20 % 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: 0.73 (0.19), residues: 2032 helix: 2.51 (0.16), residues: 952 sheet: 0.26 (0.23), residues: 438 loop : -2.68 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 231 TYR 0.010 0.001 TYR C 83 PHE 0.012 0.001 PHE I 1 TRP 0.013 0.001 TRP B 19 HIS 0.004 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (18902) covalent geometry : angle 0.51659 / 0.29 (25916) hydrogen bonds : bond 0.05751 / 3.84 ( 1046) hydrogen bonds : angle 4.53731 / 3.14 ( 2968) metal coordination : bond 0.01249 / 0.89 ( 32) metal coordination : angle 3.34130 / 1.94 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 221 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.9026 (mtm) cc_final: 0.8199 (mtm) REVERT: A 154 MET cc_start: 0.8994 (mmt) cc_final: 0.8702 (mmm) REVERT: N 229 GLU cc_start: 0.8160 (pt0) cc_final: 0.7907 (pt0) REVERT: L 222 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7918 (m-40) REVERT: K 37 VAL cc_start: 0.6969 (t) cc_final: 0.6469 (t) REVERT: K 87 GLU cc_start: 0.6146 (tp30) cc_final: 0.5945 (tp30) REVERT: J 73 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8640 (mm) REVERT: I 154 MET cc_start: 0.8908 (mmt) cc_final: 0.8627 (mmm) REVERT: F 229 GLU cc_start: 0.8139 (pt0) cc_final: 0.7891 (pt0) REVERT: D 222 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7936 (m-40) REVERT: C 95 LYS cc_start: 0.6551 (pttm) cc_final: 0.6322 (mmmt) REVERT: B 73 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8635 (mm) outliers start: 66 outliers final: 53 residues processed: 270 average time/residue: 0.1360 time to fit residues: 55.7618 Evaluate side-chains 270 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 64 optimal weight: 0.0050 chunk 152 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 overall best weight: 2.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 134 GLN D 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.168304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.159993 restraints weight = 19566.986| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 0.46 r_work: 0.3638 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18934 Z= 0.175 Angle : 0.544 6.701 25926 Z= 0.307 Chirality : 0.045 0.239 2860 Planarity : 0.004 0.047 3012 Dihedral : 18.685 84.637 3264 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.87 % Allowed : 13.04 % Favored : 83.09 % 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 (0.19), residues: 2032 helix: 2.40 (0.16), residues: 960 sheet: 0.14 (0.23), residues: 440 loop : -2.67 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 231 TYR 0.012 0.002 TYR C 83 PHE 0.014 0.002 PHE I 1 TRP 0.014 0.002 TRP B 19 HIS 0.005 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (18902) covalent geometry : angle 0.54021 / 0.31 (25916) hydrogen bonds : bond 0.06269 / 4.18 ( 1046) hydrogen bonds : angle 4.57636 / 3.17 ( 2968) metal coordination : bond 0.01398 / 0.99 ( 32) metal coordination : angle 3.51284 / 2.08 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 220 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.9017 (mtm) cc_final: 0.8197 (mtm) REVERT: A 154 MET cc_start: 0.9047 (mmt) cc_final: 0.8757 (mmm) REVERT: N 229 GLU cc_start: 0.7946 (pt0) cc_final: 0.7746 (pt0) REVERT: L 222 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7746 (m-40) REVERT: J 73 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8532 (mm) REVERT: I 22 MET cc_start: 0.9009 (mtm) cc_final: 0.8252 (mtm) REVERT: I 154 MET cc_start: 0.9013 (mmt) cc_final: 0.8729 (mmm) REVERT: D 222 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7796 (m-40) REVERT: B 73 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8543 (mm) outliers start: 68 outliers final: 58 residues processed: 268 average time/residue: 0.1382 time to fit residues: 55.7086 Evaluate side-chains 269 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 207 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 69 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 134 GLN D 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.170453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161706 restraints weight = 19478.248| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 0.49 r_work: 0.3656 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18934 Z= 0.128 Angle : 0.498 5.848 25926 Z= 0.283 Chirality : 0.043 0.224 2860 Planarity : 0.004 0.045 3012 Dihedral : 18.647 84.088 3264 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.19 % Allowed : 14.24 % Favored : 82.57 % 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: 0.73 (0.19), residues: 2032 helix: 2.47 (0.16), residues: 966 sheet: 0.18 (0.23), residues: 438 loop : -2.66 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 231 TYR 0.009 0.001 TYR B 271 PHE 0.008 0.001 PHE B 185 TRP 0.015 0.001 TRP B 19 HIS 0.004 0.001 HIS I 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (18902) covalent geometry : angle 0.49381 / 0.28 (25916) hydrogen bonds : bond 0.05317 / 3.55 ( 1046) hydrogen bonds : angle 4.49844 / 3.11 ( 2968) metal coordination : bond 0.01138 / 0.81 ( 32) metal coordination : angle 3.33607 / 1.87 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 213 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8993 (mmt) cc_final: 0.8707 (mmm) REVERT: L 222 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7660 (m-40) REVERT: J 73 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8559 (mm) REVERT: I 154 MET cc_start: 0.8953 (mmt) cc_final: 0.8683 (mmm) REVERT: I 219 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.7044 (ttmm) REVERT: D 222 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7737 (m-40) REVERT: B 73 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8566 (mm) outliers start: 56 outliers final: 45 residues processed: 255 average time/residue: 0.1403 time to fit residues: 53.8497 Evaluate side-chains 266 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 164 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 chunk 63 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 91 optimal weight: 0.0970 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 134 GLN D 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.168698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.160392 restraints weight = 19565.756| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 0.46 r_work: 0.3644 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18934 Z= 0.172 Angle : 0.543 6.682 25926 Z= 0.305 Chirality : 0.044 0.207 2860 Planarity : 0.004 0.046 3012 Dihedral : 18.670 84.329 3264 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.25 % Allowed : 14.07 % Favored : 82.69 % 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: 0.60 (0.19), residues: 2032 helix: 2.38 (0.16), residues: 962 sheet: 0.09 (0.23), residues: 440 loop : -2.69 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 231 TYR 0.012 0.002 TYR C 83 PHE 0.014 0.001 PHE I 1 TRP 0.014 0.002 TRP B 19 HIS 0.004 0.001 HIS K 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (18902) covalent geometry : angle 0.53857 / 0.30 (25916) hydrogen bonds : bond 0.06098 / 4.07 ( 1046) hydrogen bonds : angle 4.56024 / 3.15 ( 2968) metal coordination : bond 0.01347 / 0.95 ( 32) metal coordination : angle 3.37031 / 1.96 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.9007 (mtm) cc_final: 0.8194 (mtm) REVERT: A 154 MET cc_start: 0.9034 (mmt) cc_final: 0.8729 (mmm) REVERT: L 222 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7729 (m-40) REVERT: J 73 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8520 (mm) REVERT: I 22 MET cc_start: 0.8998 (mtm) cc_final: 0.8252 (mtm) REVERT: I 154 MET cc_start: 0.9000 (mmt) cc_final: 0.8704 (mmm) REVERT: I 219 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6909 (ttmt) REVERT: D 222 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7793 (m-40) REVERT: B 73 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8553 (mm) outliers start: 57 outliers final: 48 residues processed: 262 average time/residue: 0.1394 time to fit residues: 54.9510 Evaluate side-chains 271 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 129 optimal weight: 0.3980 chunk 167 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.171513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.162746 restraints weight = 19768.222| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 0.49 r_work: 0.3668 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18934 Z= 0.115 Angle : 0.485 5.953 25926 Z= 0.275 Chirality : 0.042 0.216 2860 Planarity : 0.004 0.044 3012 Dihedral : 18.613 83.839 3264 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.85 % Allowed : 14.29 % Favored : 82.86 % 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: 0.81 (0.19), residues: 2032 helix: 2.54 (0.16), residues: 966 sheet: 0.19 (0.23), residues: 438 loop : -2.58 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 231 TYR 0.008 0.001 TYR C 83 PHE 0.007 0.001 PHE I 100 TRP 0.014 0.001 TRP I 19 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 (18902) covalent geometry : angle 0.48101 / 0.27 (25916) hydrogen bonds : bond 0.04879 / 3.25 ( 1046) hydrogen bonds : angle 4.45376 / 3.07 ( 2968) metal coordination : bond 0.01033 / 0.73 ( 32) metal coordination : angle 3.24639 / 1.78 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3926.12 seconds wall clock time: 68 minutes 8.32 seconds (4088.32 seconds total)