Starting phenix.real_space_refine on Thu Mar 5 01:54:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rwo_10044/03_2026/6rwo_10044.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rwo_10044/03_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_10044/03_2026/6rwo_10044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rwo_10044/03_2026/6rwo_10044.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rwo_10044/03_2026/6rwo_10044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rwo_10044/03_2026/6rwo_10044.map" } 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-dev-5986/lib/python3.9/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: 4.20, per 1000 atoms: 0.23 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: 1.54 Conformation dependent library (CDL) restraints added in 763.3 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: 2.28 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: 3.05 Time building geometry restraints manager: 2.03 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=" CAW KLQ A 303 " pdb=" OAD KLQ A 303 " ideal model delta sigma weight residual 1.323 1.370 -0.047 2.00e-02 2.50e+03 5.48e+00 bond pdb=" CAS KLQ A 303 " pdb=" NBE KLQ A 303 " ideal model delta sigma weight residual 1.352 1.394 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" CAW KLQ I 303 " pdb=" OAD KLQ I 303 " ideal model delta sigma weight residual 1.323 1.365 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" CAS KLQ I 303 " pdb=" NBE KLQ I 303 " ideal model delta sigma weight residual 1.352 1.393 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" CAS KLQ I 303 " pdb=" CAZ KLQ I 303 " ideal model delta sigma weight residual 1.491 1.451 0.040 2.00e-02 2.50e+03 3.97e+00 ... (remaining 18897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 25233 1.89 - 3.78: 625 3.78 - 5.67: 52 5.67 - 7.57: 0 7.57 - 9.46: 6 Bond angle restraints: 25916 Sorted by residual: angle pdb=" C LEU I 213 " pdb=" N GLN I 214 " pdb=" CA GLN I 214 " ideal model delta sigma weight residual 121.14 116.10 5.04 1.75e+00 3.27e-01 8.28e+00 angle pdb=" C LEU A 213 " pdb=" N GLN A 214 " pdb=" CA GLN A 214 " ideal model delta sigma weight residual 121.14 116.15 4.99 1.75e+00 3.27e-01 8.12e+00 angle pdb=" CA LEU I 181 " pdb=" CB LEU I 181 " pdb=" CG LEU I 181 " ideal model delta sigma weight residual 116.30 125.76 -9.46 3.50e+00 8.16e-02 7.30e+00 angle pdb=" CA LEU A 181 " pdb=" CB LEU A 181 " pdb=" CG LEU A 181 " ideal model delta sigma weight residual 116.30 125.72 -9.42 3.50e+00 8.16e-02 7.24e+00 angle pdb=" CAX KLQ A 303 " pdb=" CAR KLQ A 303 " pdb=" NAP KLQ A 303 " ideal model delta sigma weight residual 115.86 123.91 -8.05 3.00e+00 1.11e-01 7.19e+00 ... (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: 1606 0.035 - 0.070: 858 0.070 - 0.105: 269 0.105 - 0.140: 95 0.140 - 0.175: 32 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: 0.02 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.020 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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= 0.294 Angle : 0.704 9.457 25926 Z= 0.405 Chirality : 0.049 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 covalent geometry : bond 0.00601 (18902) covalent geometry : angle 0.69353 (25916) hydrogen bonds : bond 0.15617 ( 1046) hydrogen bonds : angle 6.75933 ( 2968) metal coordination : bond 0.12556 ( 32) metal coordination : angle 6.08561 ( 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 : 0.628 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: 0.1469 time to fit residues: 82.4530 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 : 0.474 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 222 ASN L 99 HIS L 134 GLN L 216 GLN L 252 GLN K 18 ASN K 168 GLN J 9 GLN I 99 HIS 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.171672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.156050 restraints weight = 19643.863| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 0.76 r_work: 0.3335 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work: 0.3041 rms_B_bonded: 4.95 restraints_weight: 0.1250 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18934 Z= 0.133 Angle : 0.496 7.244 25926 Z= 0.286 Chirality : 0.042 0.148 2860 Planarity : 0.005 0.053 3012 Dihedral : 18.695 87.397 3330 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.90 % Allowed : 10.08 % Favored : 87.02 % 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: -0.59 (0.17), residues: 2032 helix: 1.11 (0.16), residues: 960 sheet: 0.05 (0.22), residues: 438 loop : -3.18 (0.19), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 263 TYR 0.010 0.001 TYR D 271 PHE 0.010 0.001 PHE B 185 TRP 0.012 0.001 TRP J 19 HIS 0.005 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00278 (18902) covalent geometry : angle 0.48922 (25916) hydrogen bonds : bond 0.05409 ( 1046) hydrogen bonds : angle 4.82861 ( 2968) metal coordination : bond 0.01370 ( 32) metal coordination : angle 4.04007 ( 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 324 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.9018 (mtm) cc_final: 0.8793 (mtm) REVERT: A 154 MET cc_start: 0.8996 (mmt) cc_final: 0.8785 (mmm) REVERT: A 215 ASN cc_start: 0.8551 (m-40) cc_final: 0.8334 (m-40) REVERT: N 229 GLU cc_start: 0.8408 (pt0) cc_final: 0.8142 (pt0) REVERT: N 252 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: L 213 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6945 (tt) REVERT: L 222 ASN cc_start: 0.8418 (m-40) cc_final: 0.8056 (m-40) REVERT: K 27 GLN cc_start: 0.6661 (mt0) cc_final: 0.5732 (tm-30) REVERT: K 37 VAL cc_start: 0.6824 (t) cc_final: 0.6357 (t) REVERT: K 95 LYS cc_start: 0.6793 (pttm) cc_final: 0.6258 (mmmt) REVERT: J 171 LYS cc_start: 0.8114 (mttt) cc_final: 0.7832 (mtmt) REVERT: I 154 MET cc_start: 0.8969 (mmt) cc_final: 0.8748 (mmm) REVERT: I 215 ASN cc_start: 0.8539 (m-40) cc_final: 0.8324 (m-40) REVERT: F 229 GLU cc_start: 0.8409 (pt0) cc_final: 0.8135 (pt0) REVERT: F 252 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: D 222 ASN cc_start: 0.8449 (m-40) cc_final: 0.8081 (m-40) REVERT: C 27 GLN cc_start: 0.6639 (mt0) cc_final: 0.5720 (tm-30) REVERT: C 115 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7554 (t) REVERT: C 191 ILE cc_start: 0.6695 (mt) cc_final: 0.6109 (mt) REVERT: B 171 LYS cc_start: 0.8126 (mttt) cc_final: 0.7875 (mtpt) outliers start: 51 outliers final: 30 residues processed: 308 average time/residue: 0.1437 time to fit residues: 66.1246 Evaluate side-chains 277 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 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 N residue 253 ASP Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 115 THR 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 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 151 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 115 THR 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: 0.9980 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 112 HIS D 134 GLN B 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.172790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.156896 restraints weight = 19835.438| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 0.91 r_work: 0.3292 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18934 Z= 0.115 Angle : 0.456 6.209 25926 Z= 0.262 Chirality : 0.040 0.145 2860 Planarity : 0.004 0.051 3012 Dihedral : 18.315 88.034 3277 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.56 % Allowed : 11.22 % Favored : 86.22 % 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: 0.32 (0.18), residues: 2032 helix: 2.05 (0.16), residues: 964 sheet: 0.34 (0.23), residues: 430 loop : -2.96 (0.19), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 166 TYR 0.007 0.001 TYR I 194 PHE 0.007 0.001 PHE I 1 TRP 0.011 0.001 TRP J 19 HIS 0.004 0.001 HIS I 51 Details of bonding type rmsd covalent geometry : bond 0.00228 (18902) covalent geometry : angle 0.45109 (25916) hydrogen bonds : bond 0.04611 ( 1046) hydrogen bonds : angle 4.53714 ( 2968) metal coordination : bond 0.01142 ( 32) metal coordination : angle 3.30327 ( 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 302 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8941 (mtm) cc_final: 0.8258 (mtm) REVERT: A 116 ASP cc_start: 0.9219 (p0) cc_final: 0.8900 (p0) REVERT: A 154 MET cc_start: 0.8850 (mmt) cc_final: 0.8632 (mmm) REVERT: N 229 GLU cc_start: 0.8341 (pt0) cc_final: 0.8060 (pt0) REVERT: L 87 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6303 (mm-30) REVERT: K 27 GLN cc_start: 0.6694 (mt0) cc_final: 0.5551 (tm-30) REVERT: K 37 VAL cc_start: 0.6448 (t) cc_final: 0.5961 (t) REVERT: K 95 LYS cc_start: 0.6233 (pttm) cc_final: 0.5791 (mmmt) REVERT: J 73 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8638 (mm) REVERT: J 171 LYS cc_start: 0.8149 (mttt) cc_final: 0.7780 (mtpt) REVERT: J 202 ASP cc_start: 0.8766 (t70) cc_final: 0.8527 (t0) REVERT: I 22 MET cc_start: 0.9007 (mtm) cc_final: 0.8369 (mtm) REVERT: I 116 ASP cc_start: 0.9234 (p0) cc_final: 0.8916 (p0) REVERT: I 154 MET cc_start: 0.8819 (mmt) cc_final: 0.8589 (mmm) REVERT: F 229 GLU cc_start: 0.8441 (pt0) cc_final: 0.8201 (pt0) REVERT: D 87 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6336 (mm-30) REVERT: C 27 GLN cc_start: 0.6636 (mt0) cc_final: 0.5518 (tm-30) REVERT: C 37 VAL cc_start: 0.6394 (t) cc_final: 0.5951 (t) REVERT: C 95 LYS cc_start: 0.6794 (pttm) cc_final: 0.5899 (mmmt) REVERT: B 73 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8659 (mm) REVERT: B 171 LYS cc_start: 0.8150 (mttt) cc_final: 0.7785 (mtpt) outliers start: 45 outliers final: 30 residues processed: 285 average time/residue: 0.1512 time to fit residues: 63.4426 Evaluate side-chains 264 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 L residue 87 GLU Chi-restraints excluded: chain L residue 218 SER Chi-restraints excluded: chain L residue 260 VAL 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 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 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 206 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 176 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 112 HIS D 134 GLN B 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.171428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.156770 restraints weight = 19857.937| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 0.74 r_work: 0.3370 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18934 Z= 0.125 Angle : 0.467 6.700 25926 Z= 0.267 Chirality : 0.041 0.148 2860 Planarity : 0.004 0.046 3012 Dihedral : 18.260 88.203 3264 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.96 % Allowed : 12.19 % Favored : 84.85 % 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: 0.72 (0.19), residues: 2032 helix: 2.45 (0.17), residues: 962 sheet: 0.39 (0.23), residues: 434 loop : -2.76 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 231 TYR 0.009 0.001 TYR A 194 PHE 0.009 0.001 PHE I 1 TRP 0.013 0.001 TRP B 19 HIS 0.005 0.001 HIS K 112 Details of bonding type rmsd covalent geometry : bond 0.00262 (18902) covalent geometry : angle 0.46251 (25916) hydrogen bonds : bond 0.04971 ( 1046) hydrogen bonds : angle 4.46213 ( 2968) metal coordination : bond 0.01066 ( 32) metal coordination : angle 3.18395 ( 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 293 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8953 (mtm) cc_final: 0.8323 (mtm) REVERT: A 154 MET cc_start: 0.8880 (mmt) cc_final: 0.8624 (mmm) REVERT: N 229 GLU cc_start: 0.8218 (pt0) cc_final: 0.7959 (pt0) REVERT: L 87 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6393 (mm-30) REVERT: K 27 GLN cc_start: 0.6036 (mt0) cc_final: 0.5730 (tm-30) REVERT: K 37 VAL cc_start: 0.6976 (t) cc_final: 0.6449 (t) REVERT: K 191 ILE cc_start: 0.6779 (mt) cc_final: 0.5964 (mt) REVERT: J 73 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8621 (mm) REVERT: I 22 MET cc_start: 0.8933 (mtm) cc_final: 0.8323 (mtm) REVERT: I 154 MET cc_start: 0.8852 (mmt) cc_final: 0.8595 (mmm) REVERT: F 229 GLU cc_start: 0.8230 (pt0) cc_final: 0.7977 (pt0) REVERT: D 87 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6388 (mm-30) REVERT: C 27 GLN cc_start: 0.5944 (mt0) cc_final: 0.5710 (tm-30) REVERT: C 37 VAL cc_start: 0.6927 (t) cc_final: 0.6442 (t) REVERT: C 95 LYS cc_start: 0.6318 (pttm) cc_final: 0.5974 (mmmt) REVERT: B 73 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8623 (mm) outliers start: 52 outliers final: 38 residues processed: 275 average time/residue: 0.1478 time to fit residues: 60.5021 Evaluate side-chains 258 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 249 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain E residue 6 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 L residue 87 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 156 HIS Chi-restraints excluded: chain L residue 218 SER Chi-restraints excluded: chain L residue 260 VAL 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 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 D residue 87 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 206 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 2.9990 chunk 103 optimal weight: 0.0870 chunk 9 optimal weight: 0.0010 chunk 100 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 193 optimal weight: 0.0770 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 overall best weight: 0.8324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.174205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.165182 restraints weight = 19733.117| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 0.52 r_work: 0.3691 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18934 Z= 0.108 Angle : 0.443 5.600 25926 Z= 0.253 Chirality : 0.040 0.145 2860 Planarity : 0.003 0.043 3012 Dihedral : 18.107 87.615 3264 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.62 % Allowed : 13.21 % Favored : 84.17 % 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: 0.98 (0.19), residues: 2032 helix: 2.70 (0.17), residues: 960 sheet: 0.39 (0.23), residues: 436 loop : -2.58 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 231 TYR 0.008 0.001 TYR A 194 PHE 0.006 0.001 PHE I 1 TRP 0.011 0.001 TRP J 19 HIS 0.004 0.001 HIS K 112 Details of bonding type rmsd covalent geometry : bond 0.00216 (18902) covalent geometry : angle 0.43964 (25916) hydrogen bonds : bond 0.04209 ( 1046) hydrogen bonds : angle 4.35978 ( 2968) metal coordination : bond 0.00888 ( 32) metal coordination : angle 2.84790 ( 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 277 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8866 (mtm) cc_final: 0.8223 (mtm) REVERT: A 154 MET cc_start: 0.8905 (mmt) cc_final: 0.8684 (mmm) REVERT: L 87 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5919 (mm-30) REVERT: K 37 VAL cc_start: 0.7093 (t) cc_final: 0.6584 (t) REVERT: J 73 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8546 (mm) REVERT: I 22 MET cc_start: 0.8839 (mtm) cc_final: 0.8244 (mtm) REVERT: I 154 MET cc_start: 0.8874 (mmt) cc_final: 0.8652 (mmm) REVERT: I 219 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6753 (ttmt) REVERT: C 37 VAL cc_start: 0.7057 (t) cc_final: 0.6574 (t) REVERT: B 73 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8525 (mm) outliers start: 46 outliers final: 28 residues processed: 263 average time/residue: 0.1478 time to fit residues: 57.5504 Evaluate side-chains 247 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 156 HIS Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain J residue 73 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 173 GLU Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain D residue 213 LEU 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 B residue 13 GLU Chi-restraints excluded: chain B residue 73 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: 9.9990 chunk 112 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.161922 restraints weight = 19581.390| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 0.51 r_work: 0.3656 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18934 Z= 0.141 Angle : 0.487 5.756 25926 Z= 0.277 Chirality : 0.041 0.146 2860 Planarity : 0.004 0.044 3012 Dihedral : 18.282 87.440 3262 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.36 % Allowed : 13.72 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 2032 helix: 2.65 (0.16), residues: 964 sheet: 0.36 (0.23), residues: 436 loop : -2.63 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 231 TYR 0.010 0.001 TYR C 83 PHE 0.010 0.001 PHE A 1 TRP 0.013 0.001 TRP J 19 HIS 0.005 0.001 HIS K 112 Details of bonding type rmsd covalent geometry : bond 0.00309 (18902) covalent geometry : angle 0.48313 (25916) hydrogen bonds : bond 0.05254 ( 1046) hydrogen bonds : angle 4.42258 ( 2968) metal coordination : bond 0.00998 ( 32) metal coordination : angle 3.02880 ( 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 274 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8823 (mtm) cc_final: 0.8141 (mtm) REVERT: A 154 MET cc_start: 0.8989 (mmt) cc_final: 0.8650 (mmm) REVERT: L 87 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5825 (mm-30) REVERT: J 73 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8563 (mm) REVERT: I 22 MET cc_start: 0.8807 (mtm) cc_final: 0.8200 (mtm) REVERT: I 154 MET cc_start: 0.8966 (mmt) cc_final: 0.8633 (mmm) REVERT: I 219 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6829 (ttmt) REVERT: B 73 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8546 (mm) outliers start: 59 outliers final: 45 residues processed: 252 average time/residue: 0.1524 time to fit residues: 57.0481 Evaluate side-chains 253 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain A residue 225 VAL 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 45 VAL Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 156 HIS Chi-restraints excluded: chain L residue 207 ASP 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 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 I residue 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 156 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 185 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 138 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 152 optimal weight: 30.0000 chunk 162 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.168467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.154504 restraints weight = 19655.789| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 0.73 r_work: 0.3333 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2407 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= 0.185 Angle : 0.539 6.115 25926 Z= 0.305 Chirality : 0.043 0.149 2860 Planarity : 0.004 0.045 3012 Dihedral : 18.444 85.927 3262 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.64 % Allowed : 13.55 % Favored : 82.80 % 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: 0.72 (0.19), residues: 2032 helix: 2.44 (0.16), residues: 962 sheet: 0.24 (0.23), residues: 440 loop : -2.65 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 231 TYR 0.013 0.002 TYR K 83 PHE 0.013 0.001 PHE I 1 TRP 0.015 0.002 TRP B 19 HIS 0.006 0.001 HIS K 112 Details of bonding type rmsd covalent geometry : bond 0.00427 (18902) covalent geometry : angle 0.53496 (25916) hydrogen bonds : bond 0.06237 ( 1046) hydrogen bonds : angle 4.55017 ( 2968) metal coordination : bond 0.01307 ( 32) metal coordination : angle 3.37405 ( 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 274 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 210 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8910 (mtm) cc_final: 0.8271 (mtm) REVERT: A 154 MET cc_start: 0.9040 (mmt) cc_final: 0.8724 (mmm) REVERT: A 219 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7338 (ttmt) REVERT: L 87 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6368 (mm-30) REVERT: L 207 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7105 (t0) REVERT: J 73 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8593 (mm) REVERT: I 22 MET cc_start: 0.8894 (mtm) cc_final: 0.8290 (mtm) REVERT: I 154 MET cc_start: 0.9015 (mmt) cc_final: 0.8674 (mmm) REVERT: B 73 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8580 (mm) outliers start: 64 outliers final: 52 residues processed: 254 average time/residue: 0.1468 time to fit residues: 54.7941 Evaluate side-chains 264 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 45 VAL Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 156 HIS Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 218 SER 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 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 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 57 optimal weight: 0.0000 chunk 100 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 158 optimal weight: 0.0010 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 152 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.171205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.162481 restraints weight = 19651.431| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 0.51 r_work: 0.3661 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18934 Z= 0.127 Angle : 0.473 5.619 25926 Z= 0.270 Chirality : 0.041 0.146 2860 Planarity : 0.004 0.060 3012 Dihedral : 18.283 85.259 3262 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: 0.90 (0.19), residues: 2032 helix: 2.62 (0.16), residues: 966 sheet: 0.25 (0.23), residues: 440 loop : -2.59 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 231 TYR 0.008 0.001 TYR A 194 PHE 0.008 0.001 PHE I 1 TRP 0.013 0.001 TRP B 19 HIS 0.005 0.001 HIS K 112 Details of bonding type rmsd covalent geometry : bond 0.00269 (18902) covalent geometry : angle 0.46966 (25916) hydrogen bonds : bond 0.04903 ( 1046) hydrogen bonds : angle 4.41329 ( 2968) metal coordination : bond 0.01010 ( 32) metal coordination : angle 2.97909 ( 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 266 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8834 (mtm) cc_final: 0.8179 (mtm) REVERT: A 154 MET cc_start: 0.8906 (mmt) cc_final: 0.8658 (mmm) REVERT: L 87 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5757 (mm-30) REVERT: J 73 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8547 (mm) REVERT: I 18 ASN cc_start: 0.8591 (p0) cc_final: 0.8377 (p0) REVERT: I 22 MET cc_start: 0.8798 (mtm) cc_final: 0.8201 (mtm) REVERT: I 154 MET cc_start: 0.8873 (mmt) cc_final: 0.8635 (mmm) REVERT: I 219 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6707 (ttmt) REVERT: M 15 TYR cc_start: 0.7881 (m-80) cc_final: 0.7673 (m-80) REVERT: B 73 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8512 (mm) outliers start: 56 outliers final: 48 residues processed: 247 average time/residue: 0.1471 time to fit residues: 54.2797 Evaluate side-chains 257 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 87 GLU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU 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 45 VAL Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 156 HIS Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 218 SER 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 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 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 251 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 153 optimal weight: 0.0370 chunk 162 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 87 optimal weight: 0.0050 overall best weight: 0.7474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.174290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.164624 restraints weight = 19637.061| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 0.52 r_work: 0.3684 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18934 Z= 0.106 Angle : 0.445 6.054 25926 Z= 0.253 Chirality : 0.040 0.145 2860 Planarity : 0.003 0.062 3012 Dihedral : 18.036 85.036 3262 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.51 % Allowed : 15.03 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 2032 helix: 2.77 (0.16), residues: 968 sheet: 0.33 (0.23), residues: 440 loop : -2.53 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 231 TYR 0.007 0.001 TYR A 194 PHE 0.006 0.001 PHE I 100 TRP 0.012 0.001 TRP I 19 HIS 0.004 0.001 HIS I 51 Details of bonding type rmsd covalent geometry : bond 0.00211 (18902) covalent geometry : angle 0.44156 (25916) hydrogen bonds : bond 0.04009 ( 1046) hydrogen bonds : angle 4.30044 ( 2968) metal coordination : bond 0.00821 ( 32) metal coordination : angle 2.65114 ( 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 254 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8776 (mtm) cc_final: 0.8108 (mtm) REVERT: A 154 MET cc_start: 0.8904 (mmt) cc_final: 0.8650 (mmm) REVERT: E 15 TYR cc_start: 0.7923 (m-80) cc_final: 0.7721 (m-80) REVERT: L 87 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5843 (mm-30) REVERT: J 73 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8497 (mm) REVERT: I 18 ASN cc_start: 0.8463 (p0) cc_final: 0.8247 (p0) REVERT: I 22 MET cc_start: 0.8815 (mtm) cc_final: 0.8240 (mtm) REVERT: I 154 MET cc_start: 0.8898 (mmt) cc_final: 0.8649 (mmm) REVERT: M 15 TYR cc_start: 0.7815 (m-80) cc_final: 0.7579 (m-80) REVERT: D 134 GLN cc_start: 0.7700 (mt0) cc_final: 0.7418 (mt0) REVERT: B 273 ARG cc_start: 0.8022 (mmt-90) cc_final: 0.7609 (mpt180) outliers start: 44 outliers final: 35 residues processed: 243 average time/residue: 0.1443 time to fit residues: 52.3827 Evaluate side-chains 237 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 251 ILE Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 156 HIS 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 151 VAL 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 173 GLU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 218 SER 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 151 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 164 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 152 optimal weight: 30.0000 chunk 91 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.165818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.156804 restraints weight = 19575.876| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 0.51 r_work: 0.3602 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 18934 Z= 0.284 Angle : 0.644 7.434 25926 Z= 0.358 Chirality : 0.048 0.176 2860 Planarity : 0.005 0.056 3012 Dihedral : 18.471 80.389 3262 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: 0.42 (0.18), residues: 2032 helix: 2.13 (0.16), residues: 960 sheet: 0.14 (0.23), residues: 440 loop : -2.69 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 263 TYR 0.017 0.002 TYR C 83 PHE 0.019 0.002 PHE I 1 TRP 0.015 0.002 TRP J 19 HIS 0.007 0.002 HIS K 112 Details of bonding type rmsd covalent geometry : bond 0.00682 (18902) covalent geometry : angle 0.63936 (25916) hydrogen bonds : bond 0.07747 ( 1046) hydrogen bonds : angle 4.74313 ( 2968) metal coordination : bond 0.01927 ( 32) metal coordination : angle 3.82863 ( 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 268 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8908 (mtm) cc_final: 0.8400 (mtm) REVERT: A 154 MET cc_start: 0.9108 (mmt) cc_final: 0.8895 (mmt) REVERT: J 73 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8652 (mm) REVERT: I 22 MET cc_start: 0.8867 (mtm) cc_final: 0.8402 (mtm) outliers start: 56 outliers final: 47 residues processed: 252 average time/residue: 0.1531 time to fit residues: 57.7848 Evaluate side-chains 260 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 203 ILE 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 45 VAL Chi-restraints excluded: chain N residue 253 ASP 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 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 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 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 115 THR 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 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: 3.9990 chunk 167 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.169436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154766 restraints weight = 19689.596| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 0.75 r_work: 0.3329 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18934 Z= 0.146 Angle : 0.512 6.289 25926 Z= 0.289 Chirality : 0.042 0.154 2860 Planarity : 0.004 0.062 3012 Dihedral : 18.322 80.157 3262 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.45 % Allowed : 14.98 % 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: 0.74 (0.19), residues: 2032 helix: 2.45 (0.16), residues: 962 sheet: 0.20 (0.23), residues: 440 loop : -2.58 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 231 TYR 0.010 0.001 TYR I 194 PHE 0.009 0.001 PHE I 1 TRP 0.015 0.001 TRP B 19 HIS 0.005 0.001 HIS K 112 Details of bonding type rmsd covalent geometry : bond 0.00317 (18902) covalent geometry : angle 0.50813 (25916) hydrogen bonds : bond 0.05405 ( 1046) hydrogen bonds : angle 4.50331 ( 2968) metal coordination : bond 0.01211 ( 32) metal coordination : angle 3.12503 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4133.89 seconds wall clock time: 71 minutes 46.66 seconds (4306.66 seconds total)