Starting phenix.real_space_refine on Sat Sep 12 20:09:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rwl_10041/09_2026/6rwl_10041.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rwl_10041/09_2026/6rwl_10041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rwl_10041/09_2026/6rwl_10041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rwl_10041/09_2026/6rwl_10041.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6rwl_10041/09_2026/6rwl_10041.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rwl_10041/09_2026/6rwl_10041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rwl_10041/09_2026/6rwl_10041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rwl_10041/09_2026/6rwl_10041.map" } resolution = 3.36 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= 0.231 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 84 5.49 5 S 74 5.16 5 C 11312 2.51 5 N 3272 2.21 5 O 3522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18272 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2137 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain: "B" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2014 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain breaks: 2 Chain: "C" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1518 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 2 Chain: "D" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1641 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Chain: "F" 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: "M" 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: "T" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "S" 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 335 SG CYS A 40 79.913 61.881 30.254 1.00 37.53 S ATOM 357 SG CYS A 43 76.936 63.929 31.771 1.00 39.56 S ATOM 2468 SG CYS B 40 71.030 143.477 58.094 1.00 80.15 S ATOM 2490 SG CYS B 43 73.569 141.955 55.534 1.00 83.44 S ATOM 4455 SG CYS C 40 106.176 126.370 21.472 1.00107.25 S ATOM 4477 SG CYS C 43 104.083 128.815 23.704 1.00103.88 S ATOM 8211 SG CYS M 40 37.069 132.725 53.118 1.00 65.37 S ATOM 8233 SG CYS M 43 34.765 130.442 55.342 1.00 72.88 S Restraints were copied for chains: I, J, K, L, N, E, W, Q Time building chain proxies: 4.80, per 1000 atoms: 0.26 Number of scatterers: 18272 At special positions: 0 Unit cell: (131.1, 175.26, 97.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 74 16.00 P 84 15.00 O 3522 8.00 N 3272 7.00 C 11312 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: 1.71 Conformation dependent library (CDL) restraints added in 685.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 12 " 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=" ND1 HIS C 16 " pdb="ZN ZN C 500 " - pdb=" NE2 HIS C 12 " 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 500 " pdb="ZN ZN I 500 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 500 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 500 " - pdb=" SG CYS I 43 " pdb="ZN ZN I 500 " - pdb=" SG CYS I 40 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 16 " pdb="ZN ZN J 500 " - pdb=" NE2 HIS J 12 " 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=" ND1 HIS K 16 " pdb="ZN ZN K 500 " - pdb=" NE2 HIS K 12 " 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 : 14 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: 3864 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 16 sheets defined 49.5% alpha, 19.2% beta 30 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.640A 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: 4.091A 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 148 through 165 removed outlier: 3.735A pdb=" N GLU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.541A 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: 4.018A 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 'B' and resid 2 through 16 Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.544A pdb=" N MET B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.751A 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: 4.156A pdb=" N ALA B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 221 removed outlier: 3.649A pdb=" N ARG B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.619A pdb=" N ALA C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 108 removed outlier: 4.033A pdb=" N THR C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) 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: 3.609A 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: 3.690A 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 'D' and resid 93 through 108 removed outlier: 3.638A pdb=" N THR D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 133 Processing helix chain 'D' and resid 151 through 165 Processing helix chain 'D' and resid 166 through 169 Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 195 through 221 removed outlier: 3.629A pdb=" N ARG D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 221 removed outlier: 4.291A pdb=" N GLN F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 16 Processing helix chain 'M' and resid 18 through 26 Processing helix chain 'M' and resid 29 through 40 removed outlier: 3.772A pdb=" N CYS M 40 " --> pdb=" O ILE M 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 16 Processing helix chain 'I' and resid 18 through 26 removed outlier: 3.640A 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: 4.091A 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 148 through 165 removed outlier: 3.735A pdb=" N GLU I 152 " --> pdb=" O GLN I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 169 removed outlier: 3.542A 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: 4.017A 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 'J' and resid 2 through 16 Processing helix chain 'J' and resid 18 through 26 removed outlier: 3.544A pdb=" N MET J 22 " --> pdb=" O ASN J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 39 Processing helix chain 'J' and resid 93 through 108 removed outlier: 3.751A 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: 4.157A pdb=" N ALA J 175 " --> pdb=" O LYS J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 221 removed outlier: 3.649A pdb=" N ARG J 199 " --> pdb=" O SER J 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 39 removed outlier: 3.620A pdb=" N ALA K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 108 removed outlier: 4.034A pdb=" N THR K 97 " --> pdb=" O THR K 93 " (cutoff:3.500A) 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: 3.610A 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: 3.690A 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 'L' and resid 93 through 108 removed outlier: 3.638A pdb=" N THR L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 133 Processing helix chain 'L' and resid 151 through 165 Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 172 through 186 Processing helix chain 'L' and resid 195 through 221 removed outlier: 3.629A pdb=" N ARG L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER L 218 " --> pdb=" O GLN L 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 221 removed outlier: 4.291A pdb=" N GLN N 221 " --> pdb=" O ILE N 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 16 Processing helix chain 'E' and resid 18 through 26 Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.772A pdb=" N CYS E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 4.248A 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: 7.325A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS A 244 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 250 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 89 removed outlier: 4.225A pdb=" N VAL B 72 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 256 through 261 removed outlier: 7.344A pdb=" N ALA B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS B 244 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 250 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU B 241 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE B 223 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 89 removed outlier: 3.845A pdb=" N VAL C 72 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP C 61 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 89 removed outlier: 4.100A pdb=" N VAL D 72 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP D 116 " --> pdb=" O MET D 63 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N CYS D 65 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 257 through 261 removed outlier: 6.962A pdb=" N ALA D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYS D 244 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL D 250 " --> pdb=" O ILE D 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 257 through 261 removed outlier: 7.366A pdb=" N ALA F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LYS F 244 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL F 250 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN F 234 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU F 229 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE F 227 " --> pdb=" O LYS F 236 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL F 225 " --> pdb=" O PRO F 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 83 through 89 removed outlier: 4.247A pdb=" N VAL I 72 " --> pdb=" O LEU I 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 257 through 261 removed outlier: 7.325A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL I 250 " --> pdb=" O ILE I 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 83 through 89 removed outlier: 4.225A pdb=" N VAL J 72 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP J 61 " --> pdb=" O HIS J 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 256 through 261 removed outlier: 7.344A pdb=" N ALA J 248 " --> pdb=" O LYS J 244 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS J 244 " --> pdb=" O ALA J 248 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL J 250 " --> pdb=" O ILE J 242 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU J 241 " --> pdb=" O PHE J 223 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE J 223 " --> pdb=" O LEU J 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 83 through 89 removed outlier: 3.845A pdb=" N VAL K 72 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP K 61 " --> pdb=" O HIS K 114 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU K 113 " --> pdb=" O THR K 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 83 through 89 removed outlier: 4.101A pdb=" N VAL L 72 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP L 116 " --> pdb=" O MET L 63 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N CYS L 65 " --> pdb=" O ASP L 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 257 through 261 removed outlier: 6.961A pdb=" N ALA L 248 " --> pdb=" O LYS L 244 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LYS L 244 " --> pdb=" O ALA L 248 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL L 250 " --> pdb=" O ILE L 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 257 through 261 removed outlier: 7.366A pdb=" N ALA N 248 " --> pdb=" O LYS N 244 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LYS N 244 " --> pdb=" O ALA N 248 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL N 250 " --> pdb=" O ILE N 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN N 234 " --> pdb=" O GLU N 229 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU N 229 " --> pdb=" O GLN N 234 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE N 227 " --> pdb=" O LYS N 236 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL N 225 " --> pdb=" O PRO N 238 " (cutoff:3.500A) 968 hydrogen bonds defined for protein. 2814 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: 3.61 Time building geometry restraints manager: 2.33 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: 4519 1.33 - 1.45: 3922 1.45 - 1.57: 10095 1.57 - 1.69: 166 1.69 - 1.81: 108 Bond restraints: 18810 Sorted by residual: bond pdb=" C1' DC S 3 " pdb=" N1 DC S 3 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" C1' DC Q 3 " pdb=" N1 DC Q 3 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.43e+01 bond pdb=" C3' DC T 3 " pdb=" C2' DC T 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC W 3 " pdb=" C2' DC W 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT T 17 " pdb=" C2' DT T 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.03e+00 ... (remaining 18805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 22802 0.86 - 1.72: 2291 1.72 - 2.58: 516 2.58 - 3.44: 151 3.44 - 4.30: 16 Bond angle restraints: 25776 Sorted by residual: angle pdb=" N3 DT W 17 " pdb=" C4 DT W 17 " pdb=" O4 DT W 17 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT T 17 " pdb=" C4 DT T 17 " pdb=" O4 DT T 17 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT Q 7 " pdb=" C4 DT Q 7 " pdb=" O4 DT Q 7 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT S 7 " pdb=" C4 DT S 7 " pdb=" O4 DT S 7 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT Q 4 " pdb=" C4 DT Q 4 " pdb=" O4 DT Q 4 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 25771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 9666 16.69 - 33.38: 824 33.38 - 50.07: 412 50.07 - 66.76: 120 66.76 - 83.45: 10 Dihedral angle restraints: 11032 sinusoidal: 5074 harmonic: 5958 Sorted by residual: dihedral pdb=" CA ILE N 220 " pdb=" C ILE N 220 " pdb=" N GLN N 221 " pdb=" CA GLN N 221 " ideal model delta harmonic sigma weight residual -180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ILE F 220 " pdb=" C ILE F 220 " pdb=" N GLN F 221 " pdb=" CA GLN F 221 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA VAL D 77 " pdb=" C VAL D 77 " pdb=" N HIS D 78 " pdb=" CA HIS D 78 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 11029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1616 0.032 - 0.065: 820 0.065 - 0.097: 252 0.097 - 0.129: 133 0.129 - 0.161: 25 Chirality restraints: 2846 Sorted by residual: chirality pdb=" CB VAL I 151 " pdb=" CA VAL I 151 " pdb=" CG1 VAL I 151 " pdb=" CG2 VAL I 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB VAL A 151 " pdb=" CA VAL A 151 " pdb=" CG1 VAL A 151 " pdb=" CG2 VAL A 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA ILE M 28 " pdb=" N ILE M 28 " pdb=" C ILE M 28 " pdb=" CB ILE M 28 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 2843 not shown) Planarity restraints: 3002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 260 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO J 261 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO J 261 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 261 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 260 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO B 261 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 260 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO L 261 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 261 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 261 " -0.023 5.00e-02 4.00e+02 ... (remaining 2999 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5777 2.86 - 3.37: 14633 3.37 - 3.88: 28624 3.88 - 4.39: 31916 4.39 - 4.90: 55735 Nonbonded interactions: 136685 Sorted by model distance: nonbonded pdb=" O TRP B 132 " pdb=" OH TYR I 15 " model vdw 2.348 3.040 nonbonded pdb=" NH1 ARG K 107 " pdb=" OE1 GLN L 177 " model vdw 2.366 3.120 nonbonded pdb=" N ASN I 17 " pdb=" OD1 ASN I 17 " model vdw 2.377 3.120 nonbonded pdb=" N ASN A 17 " pdb=" OD1 ASN A 17 " model vdw 2.378 3.120 nonbonded pdb=" OD1 ASP I 207 " pdb=" NZ LYS L 244 " model vdw 2.391 3.120 ... (remaining 136680 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'M' selection = chain 'E' } ncs_group { reference = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'S' selection = chain 'Q' } 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: 4.110 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.330 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.006 0.169 18842 Z= 0.305 Angle : 0.617 6.483 25790 Z= 0.441 Chirality : 0.046 0.161 2846 Planarity : 0.005 0.044 3002 Dihedral : 16.129 83.447 7168 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.86 % Allowed : 4.12 % Favored : 93.02 % 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: -3.04 (0.15), residues: 2032 helix: -1.93 (0.11), residues: 950 sheet: -0.14 (0.23), residues: 450 loop : -3.35 (0.19), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 199 TYR 0.010 0.001 TYR J 83 PHE 0.013 0.001 PHE L 227 TRP 0.010 0.001 TRP M 19 HIS 0.005 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.28 (18810) covalent geometry : angle 0.60180 / 0.44 (25776) hydrogen bonds : bond 0.12077 / 8.26 ( 1042) hydrogen bonds : angle 6.44152 / 4.56 ( 2962) metal coordination : bond 0.12285 / 7.82 ( 32) metal coordination : angle 5.95554 / 3.46 ( 14) *********************** 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 490 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 440 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8141 (m-40) REVERT: A 18 ASN cc_start: 0.8903 (p0) cc_final: 0.8552 (p0) REVERT: A 35 GLU cc_start: 0.7558 (tp30) cc_final: 0.7289 (tp30) REVERT: A 42 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8515 (mmtp) REVERT: A 63 MET cc_start: 0.8377 (ttm) cc_final: 0.8123 (mtp) REVERT: A 107 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7690 (mpt180) REVERT: B 63 MET cc_start: 0.8165 (mmm) cc_final: 0.7924 (ttm) REVERT: B 256 ASP cc_start: 0.6967 (t0) cc_final: 0.6181 (m-30) REVERT: B 267 ILE cc_start: 0.8956 (mp) cc_final: 0.8657 (mt) REVERT: B 270 ASP cc_start: 0.7441 (t70) cc_final: 0.7064 (t0) REVERT: C 155 ASN cc_start: 0.7781 (m-40) cc_final: 0.7457 (t0) REVERT: C 178 MET cc_start: 0.8460 (mtm) cc_final: 0.8228 (mtp) REVERT: D 154 MET cc_start: 0.7137 (mmt) cc_final: 0.6436 (mmt) REVERT: D 215 ASN cc_start: 0.8449 (t0) cc_final: 0.8201 (t0) REVERT: D 268 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7817 (mm) REVERT: F 246 GLU cc_start: 0.7665 (pp20) cc_final: 0.7350 (pp20) REVERT: F 271 TYR cc_start: 0.7330 (t80) cc_final: 0.7040 (t80) REVERT: M 17 ASN cc_start: 0.8843 (m-40) cc_final: 0.8640 (m-40) REVERT: I 17 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8371 (m-40) REVERT: I 18 ASN cc_start: 0.8766 (p0) cc_final: 0.8415 (p0) REVERT: I 22 MET cc_start: 0.8612 (mtm) cc_final: 0.8329 (mtm) REVERT: I 35 GLU cc_start: 0.7626 (tp30) cc_final: 0.7415 (tp30) REVERT: I 63 MET cc_start: 0.8416 (ttm) cc_final: 0.8162 (mtp) REVERT: I 107 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7478 (mpt180) REVERT: J 63 MET cc_start: 0.8145 (mmm) cc_final: 0.7867 (ttm) REVERT: J 267 ILE cc_start: 0.8842 (mp) cc_final: 0.8500 (mt) REVERT: K 115 THR cc_start: 0.6989 (OUTLIER) cc_final: 0.6624 (p) REVERT: K 155 ASN cc_start: 0.8024 (m-40) cc_final: 0.7674 (t0) REVERT: K 194 TYR cc_start: 0.7596 (m-80) cc_final: 0.7359 (m-10) REVERT: L 88 VAL cc_start: 0.7678 (t) cc_final: 0.7256 (p) REVERT: L 154 MET cc_start: 0.7237 (mmt) cc_final: 0.6129 (mmt) REVERT: L 253 ASP cc_start: 0.7511 (t70) cc_final: 0.7260 (p0) REVERT: N 246 GLU cc_start: 0.7898 (pp20) cc_final: 0.7514 (pp20) REVERT: N 252 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: E 15 TYR cc_start: 0.8004 (m-80) cc_final: 0.7794 (m-80) outliers start: 50 outliers final: 12 residues processed: 479 average time/residue: 0.1619 time to fit residues: 112.9485 Evaluate side-chains 299 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 280 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 148 GLN Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 183 HIS B 44 GLN B 157 GLN B 183 HIS B 216 GLN ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN D 114 HIS D 155 ASN D 216 GLN D 222 ASN M 9 GLN M 17 ASN I 148 GLN J 44 GLN J 157 GLN J 183 HIS K 114 HIS K 168 GLN K 216 GLN L 155 ASN L 216 GLN L 222 ASN E 9 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.150635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111477 restraints weight = 26428.545| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.49 r_work: 0.3286 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18842 Z= 0.176 Angle : 0.550 8.392 25790 Z= 0.314 Chirality : 0.043 0.171 2846 Planarity : 0.004 0.042 3002 Dihedral : 18.661 77.684 3175 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.06 % Allowed : 12.01 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 2032 helix: 0.83 (0.16), residues: 960 sheet: 0.05 (0.24), residues: 460 loop : -3.09 (0.20), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 262 TYR 0.012 0.001 TYR M 15 PHE 0.030 0.001 PHE K 121 TRP 0.018 0.001 TRP K 131 HIS 0.009 0.001 HIS J 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (18810) covalent geometry : angle 0.54883 / 0.31 (25776) hydrogen bonds : bond 0.06085 / 4.13 ( 1042) hydrogen bonds : angle 4.75763 / 3.36 ( 2962) metal coordination : bond 0.00882 / 0.58 ( 32) metal coordination : angle 1.62684 / 1.03 ( 14) *********************** 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 343 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 307 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8588 (tp30) cc_final: 0.8172 (tm-30) REVERT: A 39 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7799 (mm-40) REVERT: A 42 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8742 (mmtp) REVERT: A 63 MET cc_start: 0.8931 (ttm) cc_final: 0.8714 (mtp) REVERT: B 17 ASN cc_start: 0.8662 (m-40) cc_final: 0.8430 (m110) REVERT: B 63 MET cc_start: 0.8874 (mmm) cc_final: 0.8626 (ttm) REVERT: B 256 ASP cc_start: 0.6826 (t0) cc_final: 0.4912 (m-30) REVERT: B 267 ILE cc_start: 0.9013 (mp) cc_final: 0.8692 (mt) REVERT: C 120 ASN cc_start: 0.7728 (m-40) cc_final: 0.7407 (m-40) REVERT: C 135 ILE cc_start: 0.8936 (mt) cc_final: 0.8729 (mt) REVERT: C 136 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7530 (pt0) REVERT: C 155 ASN cc_start: 0.8315 (m-40) cc_final: 0.7532 (t0) REVERT: C 178 MET cc_start: 0.8730 (mtm) cc_final: 0.8199 (mtp) REVERT: D 154 MET cc_start: 0.7232 (mmt) cc_final: 0.6345 (mmt) REVERT: F 246 GLU cc_start: 0.8075 (pp20) cc_final: 0.7636 (pp20) REVERT: F 271 TYR cc_start: 0.7514 (t80) cc_final: 0.7238 (t80) REVERT: M 6 GLU cc_start: 0.8244 (tp30) cc_final: 0.7924 (tp30) REVERT: M 17 ASN cc_start: 0.9105 (m110) cc_final: 0.8886 (m-40) REVERT: I 35 GLU cc_start: 0.8649 (tp30) cc_final: 0.8218 (tm-30) REVERT: I 39 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7795 (mm-40) REVERT: I 63 MET cc_start: 0.8893 (ttm) cc_final: 0.8669 (mtp) REVERT: I 154 MET cc_start: 0.9087 (mmt) cc_final: 0.8796 (mmm) REVERT: I 256 ASP cc_start: 0.7211 (m-30) cc_final: 0.6718 (m-30) REVERT: J 63 MET cc_start: 0.8810 (mmm) cc_final: 0.8539 (ttm) REVERT: J 71 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7139 (mttt) REVERT: J 224 ARG cc_start: 0.8513 (tpp80) cc_final: 0.8093 (tpt-90) REVERT: J 252 GLN cc_start: 0.7296 (tt0) cc_final: 0.6709 (tm-30) REVERT: J 267 ILE cc_start: 0.8853 (mp) cc_final: 0.8542 (mt) REVERT: J 270 ASP cc_start: 0.7989 (t70) cc_final: 0.7515 (t0) REVERT: K 115 THR cc_start: 0.7137 (OUTLIER) cc_final: 0.6858 (p) REVERT: K 155 ASN cc_start: 0.8327 (m-40) cc_final: 0.7708 (t0) REVERT: L 154 MET cc_start: 0.7158 (mmt) cc_final: 0.6595 (mmt) REVERT: L 171 LYS cc_start: 0.6547 (mttt) cc_final: 0.6342 (mmmm) REVERT: L 253 ASP cc_start: 0.7880 (t70) cc_final: 0.7636 (p0) REVERT: N 246 GLU cc_start: 0.8172 (pp20) cc_final: 0.7724 (pp20) outliers start: 36 outliers final: 29 residues processed: 330 average time/residue: 0.1600 time to fit residues: 77.1679 Evaluate side-chains 300 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 242 ILE Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 171 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 192 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 206 optimal weight: 30.0000 chunk 115 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN D 114 HIS D 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.153170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114933 restraints weight = 26315.141| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.51 r_work: 0.3324 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 18842 Z= 0.116 Angle : 0.470 7.210 25790 Z= 0.272 Chirality : 0.041 0.217 2846 Planarity : 0.003 0.041 3002 Dihedral : 18.644 76.040 3154 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.37 % Allowed : 13.16 % Favored : 85.47 % 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: 0.15 (0.19), residues: 2032 helix: 1.75 (0.17), residues: 958 sheet: 0.37 (0.25), residues: 438 loop : -2.82 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.014 0.001 TYR E 15 PHE 0.012 0.001 PHE K 121 TRP 0.019 0.001 TRP K 131 HIS 0.004 0.001 HIS D 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.12 (18810) covalent geometry : angle 0.46546 / 0.27 (25776) hydrogen bonds : bond 0.04632 / 3.17 ( 1042) hydrogen bonds : angle 4.45532 / 3.12 ( 2962) metal coordination : bond 0.01203 / 0.84 ( 32) metal coordination : angle 2.80120 / 1.55 ( 14) *********************** 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 312 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 288 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8257 (tp30) cc_final: 0.7814 (mm-30) REVERT: A 39 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7349 (mm-40) REVERT: A 42 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8581 (mmtp) REVERT: B 63 MET cc_start: 0.8671 (mmm) cc_final: 0.8293 (ttm) REVERT: B 256 ASP cc_start: 0.6383 (t0) cc_final: 0.5532 (m-30) REVERT: B 267 ILE cc_start: 0.8996 (mp) cc_final: 0.8653 (mt) REVERT: B 270 ASP cc_start: 0.7895 (t0) cc_final: 0.7402 (t0) REVERT: B 271 TYR cc_start: 0.8347 (m-80) cc_final: 0.7820 (m-80) REVERT: C 135 ILE cc_start: 0.8913 (mt) cc_final: 0.8704 (mt) REVERT: C 136 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7375 (pt0) REVERT: C 155 ASN cc_start: 0.8291 (m-40) cc_final: 0.7559 (t0) REVERT: C 178 MET cc_start: 0.8707 (mtm) cc_final: 0.8439 (mtp) REVERT: D 154 MET cc_start: 0.7299 (mmt) cc_final: 0.6369 (mmt) REVERT: F 246 GLU cc_start: 0.7852 (pp20) cc_final: 0.7426 (pp20) REVERT: F 271 TYR cc_start: 0.7545 (t80) cc_final: 0.7340 (t80) REVERT: M 6 GLU cc_start: 0.7971 (tp30) cc_final: 0.7680 (tp30) REVERT: M 17 ASN cc_start: 0.9007 (m110) cc_final: 0.8765 (m-40) REVERT: I 35 GLU cc_start: 0.8312 (tp30) cc_final: 0.7840 (mm-30) REVERT: I 39 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7324 (mm-40) REVERT: I 154 MET cc_start: 0.8907 (mmt) cc_final: 0.8595 (mmm) REVERT: J 63 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8237 (ttm) REVERT: J 224 ARG cc_start: 0.8338 (tpp80) cc_final: 0.7875 (tpt-90) REVERT: J 252 GLN cc_start: 0.6974 (tt0) cc_final: 0.6590 (tm-30) REVERT: J 267 ILE cc_start: 0.8857 (mp) cc_final: 0.8521 (mt) REVERT: J 270 ASP cc_start: 0.7750 (t70) cc_final: 0.7253 (t0) REVERT: K 155 ASN cc_start: 0.8309 (m-40) cc_final: 0.7743 (t0) REVERT: L 154 MET cc_start: 0.7199 (mmt) cc_final: 0.6019 (mmt) REVERT: N 246 GLU cc_start: 0.8029 (pp20) cc_final: 0.7580 (pp20) REVERT: E 31 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8261 (p) outliers start: 24 outliers final: 16 residues processed: 303 average time/residue: 0.1607 time to fit residues: 71.4635 Evaluate side-chains 284 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 266 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 63 MET Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 143 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 ASN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS C 120 ASN D 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.151002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111350 restraints weight = 26342.908| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.54 r_work: 0.3291 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18842 Z= 0.147 Angle : 0.496 7.252 25790 Z= 0.285 Chirality : 0.042 0.195 2846 Planarity : 0.003 0.039 3002 Dihedral : 18.737 74.720 3152 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.63 % Allowed : 12.93 % Favored : 84.44 % 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: 0.38 (0.19), residues: 2032 helix: 1.98 (0.17), residues: 960 sheet: 0.29 (0.24), residues: 456 loop : -2.71 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 228 TYR 0.009 0.001 TYR B 83 PHE 0.025 0.001 PHE C 26 TRP 0.023 0.001 TRP J 235 HIS 0.006 0.001 HIS J 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (18810) covalent geometry : angle 0.49073 / 0.28 (25776) hydrogen bonds : bond 0.05129 / 3.49 ( 1042) hydrogen bonds : angle 4.35831 / 3.05 ( 2962) metal coordination : bond 0.00620 / 0.40 ( 32) metal coordination : angle 2.98511 / 1.75 ( 14) *********************** 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 309 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8593 (tp30) cc_final: 0.8085 (mm-30) REVERT: A 39 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7592 (mm-40) REVERT: A 42 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8780 (mmtp) REVERT: B 63 MET cc_start: 0.8910 (mmm) cc_final: 0.8544 (ttm) REVERT: B 154 MET cc_start: 0.6704 (mmt) cc_final: 0.6419 (mmt) REVERT: B 256 ASP cc_start: 0.6148 (t0) cc_final: 0.5303 (m-30) REVERT: B 267 ILE cc_start: 0.8996 (mp) cc_final: 0.8628 (mt) REVERT: B 270 ASP cc_start: 0.8123 (t0) cc_final: 0.7689 (t0) REVERT: B 273 ARG cc_start: 0.7738 (mmt-90) cc_final: 0.7513 (mmt-90) REVERT: C 11 GLU cc_start: 0.7366 (tp30) cc_final: 0.6325 (mt-10) REVERT: C 136 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7373 (pt0) REVERT: C 155 ASN cc_start: 0.8343 (m-40) cc_final: 0.7569 (t0) REVERT: C 178 MET cc_start: 0.8716 (mtm) cc_final: 0.8221 (mtp) REVERT: F 246 GLU cc_start: 0.8010 (pp20) cc_final: 0.7534 (pp20) REVERT: M 6 GLU cc_start: 0.8148 (tp30) cc_final: 0.7733 (tp30) REVERT: M 35 GLU cc_start: 0.9023 (tp30) cc_final: 0.8770 (tp30) REVERT: I 24 GLU cc_start: 0.8324 (tt0) cc_final: 0.7928 (mt-10) REVERT: I 107 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7548 (mpt180) REVERT: I 154 MET cc_start: 0.9090 (mmt) cc_final: 0.8765 (mmm) REVERT: J 63 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8487 (ttm) REVERT: J 224 ARG cc_start: 0.8510 (tpp80) cc_final: 0.8125 (tpt-90) REVERT: J 252 GLN cc_start: 0.7350 (tt0) cc_final: 0.6710 (tm-30) REVERT: J 267 ILE cc_start: 0.8928 (mp) cc_final: 0.8609 (mt) REVERT: J 270 ASP cc_start: 0.7910 (t70) cc_final: 0.7377 (t0) REVERT: K 155 ASN cc_start: 0.8193 (m-40) cc_final: 0.7575 (t0) REVERT: L 154 MET cc_start: 0.7145 (mmt) cc_final: 0.6013 (mmt) REVERT: N 246 GLU cc_start: 0.8168 (pp20) cc_final: 0.7694 (pp20) outliers start: 46 outliers final: 34 residues processed: 289 average time/residue: 0.1545 time to fit residues: 66.2124 Evaluate side-chains 294 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 127 GLN Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 148 optimal weight: 0.0670 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN D 114 HIS D 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.151632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112801 restraints weight = 26175.189| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.52 r_work: 0.3290 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18842 Z= 0.129 Angle : 0.474 6.529 25790 Z= 0.272 Chirality : 0.041 0.180 2846 Planarity : 0.003 0.037 3002 Dihedral : 18.709 73.671 3147 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.06 % Allowed : 13.90 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 2032 helix: 2.15 (0.17), residues: 960 sheet: 0.33 (0.24), residues: 454 loop : -2.53 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 228 TYR 0.008 0.001 TYR I 83 PHE 0.023 0.001 PHE K 26 TRP 0.033 0.001 TRP J 235 HIS 0.004 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (18810) covalent geometry : angle 0.46814 / 0.27 (25776) hydrogen bonds : bond 0.04810 / 3.29 ( 1042) hydrogen bonds : angle 4.30628 / 3.02 ( 2962) metal coordination : bond 0.00840 / 0.57 ( 32) metal coordination : angle 3.29629 / 1.91 ( 14) *********************** 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 301 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8319 (tp30) cc_final: 0.7846 (mm-30) REVERT: A 39 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7380 (mm-40) REVERT: A 42 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8696 (mmtp) REVERT: B 63 MET cc_start: 0.8730 (mmm) cc_final: 0.8295 (ttm) REVERT: B 154 MET cc_start: 0.6335 (mmt) cc_final: 0.6066 (mmt) REVERT: B 256 ASP cc_start: 0.6191 (t0) cc_final: 0.5373 (m-30) REVERT: B 267 ILE cc_start: 0.8992 (mp) cc_final: 0.8612 (mt) REVERT: B 270 ASP cc_start: 0.7910 (t0) cc_final: 0.7475 (t0) REVERT: C 11 GLU cc_start: 0.7260 (tp30) cc_final: 0.6363 (mt-10) REVERT: C 95 LYS cc_start: 0.6685 (mttt) cc_final: 0.6238 (mmmm) REVERT: C 136 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7425 (pt0) REVERT: C 155 ASN cc_start: 0.8305 (m-40) cc_final: 0.7562 (t0) REVERT: C 178 MET cc_start: 0.8730 (mtm) cc_final: 0.8389 (mtp) REVERT: F 246 GLU cc_start: 0.7870 (pp20) cc_final: 0.7417 (pp20) REVERT: M 6 GLU cc_start: 0.7938 (tp30) cc_final: 0.7539 (tp30) REVERT: I 24 GLU cc_start: 0.8034 (tt0) cc_final: 0.7625 (mt-10) REVERT: I 107 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7474 (mpt180) REVERT: I 154 MET cc_start: 0.8919 (mmt) cc_final: 0.8583 (mmm) REVERT: J 63 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8263 (ttm) REVERT: J 224 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7789 (tpt-90) REVERT: J 235 TRP cc_start: 0.6468 (m100) cc_final: 0.6258 (m100) REVERT: J 252 GLN cc_start: 0.7106 (tt0) cc_final: 0.6612 (tm-30) REVERT: J 267 ILE cc_start: 0.8880 (mp) cc_final: 0.8560 (mt) REVERT: J 270 ASP cc_start: 0.7713 (t70) cc_final: 0.7158 (t0) REVERT: K 11 GLU cc_start: 0.7219 (tp30) cc_final: 0.6316 (mt-10) REVERT: K 155 ASN cc_start: 0.8225 (m-40) cc_final: 0.7630 (t0) REVERT: L 154 MET cc_start: 0.7161 (mmt) cc_final: 0.6081 (mmt) REVERT: N 246 GLU cc_start: 0.8032 (pp20) cc_final: 0.7312 (pp20) outliers start: 36 outliers final: 28 residues processed: 282 average time/residue: 0.1513 time to fit residues: 63.5695 Evaluate side-chains 287 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 48 optimal weight: 20.0000 chunk 204 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 128 optimal weight: 0.0010 chunk 140 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 ASN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN D 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.151101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113417 restraints weight = 26066.968| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.40 r_work: 0.3304 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18842 Z= 0.127 Angle : 0.478 7.441 25790 Z= 0.274 Chirality : 0.041 0.150 2846 Planarity : 0.003 0.038 3002 Dihedral : 18.698 72.835 3147 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.95 % Allowed : 14.53 % Favored : 83.52 % 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: 2.24 (0.17), residues: 960 sheet: 0.40 (0.24), residues: 456 loop : -2.48 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.008 0.001 TYR B 83 PHE 0.017 0.001 PHE K 26 TRP 0.019 0.001 TRP K 131 HIS 0.004 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (18810) covalent geometry : angle 0.47038 / 0.27 (25776) hydrogen bonds : bond 0.04717 / 3.22 ( 1042) hydrogen bonds : angle 4.26775 / 2.98 ( 2962) metal coordination : bond 0.00796 / 0.54 ( 32) metal coordination : angle 3.70353 / 2.08 ( 14) *********************** 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 294 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8613 (tp30) cc_final: 0.8228 (mm-30) REVERT: A 39 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7636 (mm-40) REVERT: A 42 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8798 (mmtp) REVERT: B 63 MET cc_start: 0.8916 (mmm) cc_final: 0.8466 (ttm) REVERT: B 256 ASP cc_start: 0.6190 (t0) cc_final: 0.5337 (m-30) REVERT: B 267 ILE cc_start: 0.9036 (mp) cc_final: 0.8690 (mt) REVERT: B 270 ASP cc_start: 0.8110 (t0) cc_final: 0.7647 (t0) REVERT: B 273 ARG cc_start: 0.7535 (mmt-90) cc_final: 0.7326 (mmt90) REVERT: C 11 GLU cc_start: 0.7335 (tp30) cc_final: 0.6368 (mt-10) REVERT: C 136 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7552 (pt0) REVERT: C 155 ASN cc_start: 0.8347 (m-40) cc_final: 0.7584 (t0) REVERT: C 178 MET cc_start: 0.8810 (mtm) cc_final: 0.8514 (mtp) REVERT: M 6 GLU cc_start: 0.8086 (tp30) cc_final: 0.7634 (tp30) REVERT: I 24 GLU cc_start: 0.8363 (tt0) cc_final: 0.7940 (mt-10) REVERT: I 107 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7791 (mpt180) REVERT: I 154 MET cc_start: 0.9043 (mmt) cc_final: 0.8709 (mmm) REVERT: J 63 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8510 (ttm) REVERT: J 224 ARG cc_start: 0.8424 (tpp80) cc_final: 0.7991 (tpt-90) REVERT: J 235 TRP cc_start: 0.6398 (m100) cc_final: 0.6113 (m100) REVERT: J 252 GLN cc_start: 0.7360 (tt0) cc_final: 0.6754 (tm-30) REVERT: J 267 ILE cc_start: 0.8957 (mp) cc_final: 0.8636 (mt) REVERT: J 270 ASP cc_start: 0.7934 (t70) cc_final: 0.7390 (t0) REVERT: K 11 GLU cc_start: 0.7224 (tp30) cc_final: 0.6263 (mt-10) REVERT: K 155 ASN cc_start: 0.8254 (m-40) cc_final: 0.7626 (t0) REVERT: L 154 MET cc_start: 0.7175 (mmt) cc_final: 0.6109 (mmt) REVERT: N 246 GLU cc_start: 0.8158 (pp20) cc_final: 0.7461 (pp20) outliers start: 34 outliers final: 25 residues processed: 279 average time/residue: 0.1421 time to fit residues: 58.7748 Evaluate side-chains 276 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 72 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 206 optimal weight: 30.0000 chunk 183 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 124 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN I 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.152585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114924 restraints weight = 26409.293| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.46 r_work: 0.3294 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18842 Z= 0.110 Angle : 0.470 10.466 25790 Z= 0.268 Chirality : 0.041 0.140 2846 Planarity : 0.003 0.037 3002 Dihedral : 18.616 72.195 3147 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.77 % Allowed : 15.16 % Favored : 83.07 % 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: 0.87 (0.19), residues: 2032 helix: 2.39 (0.17), residues: 960 sheet: 0.34 (0.25), residues: 436 loop : -2.26 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.007 0.001 TYR D 271 PHE 0.011 0.001 PHE K 26 TRP 0.020 0.001 TRP K 131 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (18810) covalent geometry : angle 0.46358 / 0.27 (25776) hydrogen bonds : bond 0.04264 / 2.93 ( 1042) hydrogen bonds : angle 4.20399 / 2.93 ( 2962) metal coordination : bond 0.00868 / 0.60 ( 32) metal coordination : angle 3.34531 / 1.90 ( 14) *********************** 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 295 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8356 (tp30) cc_final: 0.8101 (mm-30) REVERT: A 42 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8658 (mmtp) REVERT: B 63 MET cc_start: 0.8736 (mmm) cc_final: 0.8207 (ttm) REVERT: B 256 ASP cc_start: 0.6176 (t0) cc_final: 0.5309 (m-30) REVERT: B 267 ILE cc_start: 0.9007 (mp) cc_final: 0.8660 (mt) REVERT: B 270 ASP cc_start: 0.7957 (t0) cc_final: 0.7468 (t0) REVERT: C 11 GLU cc_start: 0.7270 (tp30) cc_final: 0.6381 (mt-10) REVERT: C 136 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7439 (pt0) REVERT: C 155 ASN cc_start: 0.8304 (m-40) cc_final: 0.7559 (t0) REVERT: C 178 MET cc_start: 0.8737 (mtm) cc_final: 0.8517 (mtp) REVERT: D 127 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: M 6 GLU cc_start: 0.7944 (tp30) cc_final: 0.7532 (tp30) REVERT: I 24 GLU cc_start: 0.8042 (tt0) cc_final: 0.7661 (mt-10) REVERT: I 154 MET cc_start: 0.8921 (mmt) cc_final: 0.8595 (mmm) REVERT: J 63 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8298 (ttm) REVERT: J 224 ARG cc_start: 0.8214 (tpp80) cc_final: 0.7708 (tpt-90) REVERT: J 235 TRP cc_start: 0.6319 (m100) cc_final: 0.6030 (m100) REVERT: J 267 ILE cc_start: 0.8984 (mp) cc_final: 0.8653 (mt) REVERT: J 270 ASP cc_start: 0.7738 (t70) cc_final: 0.7167 (t0) REVERT: K 11 GLU cc_start: 0.7194 (tp30) cc_final: 0.6310 (mt-10) REVERT: K 136 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7949 (pt0) REVERT: K 155 ASN cc_start: 0.8228 (m-40) cc_final: 0.7626 (t0) REVERT: K 178 MET cc_start: 0.9037 (mtm) cc_final: 0.8591 (mtt) REVERT: L 112 HIS cc_start: 0.8073 (t-90) cc_final: 0.7836 (t-90) REVERT: L 114 HIS cc_start: 0.6484 (t70) cc_final: 0.6275 (m170) REVERT: L 154 MET cc_start: 0.7187 (mmt) cc_final: 0.6016 (mmt) REVERT: N 246 GLU cc_start: 0.7978 (pp20) cc_final: 0.7351 (pp20) outliers start: 31 outliers final: 26 residues processed: 276 average time/residue: 0.1545 time to fit residues: 63.2899 Evaluate side-chains 281 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 122 optimal weight: 0.7980 chunk 142 optimal weight: 0.0770 chunk 182 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN A 252 GLN B 17 ASN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.153059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115511 restraints weight = 26234.868| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.48 r_work: 0.3309 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18842 Z= 0.108 Angle : 0.464 9.281 25790 Z= 0.264 Chirality : 0.040 0.139 2846 Planarity : 0.003 0.049 3002 Dihedral : 18.557 71.728 3143 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.95 % Allowed : 15.16 % Favored : 82.89 % 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: 0.97 (0.19), residues: 2032 helix: 2.48 (0.17), residues: 962 sheet: 0.40 (0.25), residues: 436 loop : -2.24 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 273 TYR 0.007 0.001 TYR D 271 PHE 0.009 0.001 PHE K 26 TRP 0.022 0.001 TRP K 131 HIS 0.004 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (18810) covalent geometry : angle 0.45748 / 0.26 (25776) hydrogen bonds : bond 0.04118 / 2.83 ( 1042) hydrogen bonds : angle 4.15396 / 2.90 ( 2962) metal coordination : bond 0.00865 / 0.60 ( 32) metal coordination : angle 3.25994 / 1.86 ( 14) *********************** 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 298 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8339 (tp30) cc_final: 0.8130 (tp30) REVERT: A 42 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8589 (mmtp) REVERT: A 178 MET cc_start: 0.9156 (mtp) cc_final: 0.8882 (mtt) REVERT: B 253 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6617 (t0) REVERT: B 256 ASP cc_start: 0.6122 (t0) cc_final: 0.5247 (m-30) REVERT: B 267 ILE cc_start: 0.8990 (mp) cc_final: 0.8641 (mt) REVERT: B 270 ASP cc_start: 0.7956 (t0) cc_final: 0.7448 (t0) REVERT: C 11 GLU cc_start: 0.7258 (tp30) cc_final: 0.6340 (mt-10) REVERT: C 136 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7403 (pt0) REVERT: C 155 ASN cc_start: 0.8301 (m-40) cc_final: 0.7532 (t0) REVERT: M 6 GLU cc_start: 0.7925 (tp30) cc_final: 0.7435 (tp30) REVERT: M 27 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8726 (mm-40) REVERT: I 22 MET cc_start: 0.8930 (mtm) cc_final: 0.8501 (mtm) REVERT: I 24 GLU cc_start: 0.8140 (tt0) cc_final: 0.7754 (mt-10) REVERT: I 154 MET cc_start: 0.8903 (mmt) cc_final: 0.8569 (mmm) REVERT: J 63 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8249 (ttm) REVERT: J 224 ARG cc_start: 0.8178 (tpp80) cc_final: 0.7635 (tpt-90) REVERT: J 235 TRP cc_start: 0.6272 (m100) cc_final: 0.5896 (m100) REVERT: J 267 ILE cc_start: 0.8962 (mp) cc_final: 0.8641 (mt) REVERT: K 11 GLU cc_start: 0.7152 (tp30) cc_final: 0.6262 (mt-10) REVERT: K 155 ASN cc_start: 0.8226 (m-40) cc_final: 0.7601 (t0) REVERT: K 178 MET cc_start: 0.9031 (mtm) cc_final: 0.8581 (mtt) REVERT: L 112 HIS cc_start: 0.8042 (t-90) cc_final: 0.7841 (t-90) REVERT: L 114 HIS cc_start: 0.6484 (t70) cc_final: 0.6228 (m170) REVERT: L 154 MET cc_start: 0.7009 (mmt) cc_final: 0.5817 (mmt) REVERT: N 246 GLU cc_start: 0.7930 (pp20) cc_final: 0.7318 (pp20) outliers start: 34 outliers final: 29 residues processed: 278 average time/residue: 0.1595 time to fit residues: 65.1108 Evaluate side-chains 287 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 104 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 0.1980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN I 214 GLN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.150151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111993 restraints weight = 26137.890| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.37 r_work: 0.3249 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18842 Z= 0.153 Angle : 0.514 7.264 25790 Z= 0.289 Chirality : 0.042 0.128 2846 Planarity : 0.003 0.039 3002 Dihedral : 18.703 70.956 3143 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.89 % Allowed : 15.56 % Favored : 82.55 % 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: 0.91 (0.19), residues: 2032 helix: 2.42 (0.17), residues: 962 sheet: 0.36 (0.25), residues: 436 loop : -2.23 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 273 TYR 0.011 0.001 TYR B 83 PHE 0.011 0.001 PHE E 1 TRP 0.023 0.001 TRP K 131 HIS 0.005 0.001 HIS J 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (18810) covalent geometry : angle 0.50769 / 0.29 (25776) hydrogen bonds : bond 0.05080 / 3.47 ( 1042) hydrogen bonds : angle 4.20259 / 2.95 ( 2962) metal coordination : bond 0.00659 / 0.46 ( 32) metal coordination : angle 3.48710 / 2.00 ( 14) *********************** 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 295 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8409 (tp30) cc_final: 0.8191 (tp30) REVERT: A 42 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8607 (mttt) REVERT: A 178 MET cc_start: 0.9225 (mtp) cc_final: 0.8979 (mtt) REVERT: B 63 MET cc_start: 0.8780 (mmm) cc_final: 0.8308 (ttm) REVERT: B 253 ASP cc_start: 0.6846 (OUTLIER) cc_final: 0.6591 (t0) REVERT: B 256 ASP cc_start: 0.6203 (t0) cc_final: 0.5352 (m-30) REVERT: B 267 ILE cc_start: 0.9007 (mp) cc_final: 0.8678 (mt) REVERT: C 11 GLU cc_start: 0.7319 (tp30) cc_final: 0.6377 (mt-10) REVERT: C 136 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7435 (pt0) REVERT: C 155 ASN cc_start: 0.8326 (m-40) cc_final: 0.7564 (t0) REVERT: D 63 MET cc_start: 0.7903 (mtp) cc_final: 0.7676 (mtp) REVERT: M 6 GLU cc_start: 0.8003 (tp30) cc_final: 0.7494 (tp30) REVERT: M 27 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8761 (mm-40) REVERT: I 22 MET cc_start: 0.9034 (mtm) cc_final: 0.8685 (mtm) REVERT: I 24 GLU cc_start: 0.8185 (tt0) cc_final: 0.7713 (mt-10) REVERT: I 154 MET cc_start: 0.8958 (mmt) cc_final: 0.8604 (mmm) REVERT: J 63 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8277 (ttm) REVERT: J 235 TRP cc_start: 0.6360 (m100) cc_final: 0.6066 (m100) REVERT: J 256 ASP cc_start: 0.6994 (t0) cc_final: 0.6270 (m-30) REVERT: J 266 LYS cc_start: 0.7227 (ttpt) cc_final: 0.6729 (pttt) REVERT: J 267 ILE cc_start: 0.8971 (mp) cc_final: 0.8639 (mt) REVERT: J 270 ASP cc_start: 0.7823 (t70) cc_final: 0.7224 (t0) REVERT: K 11 GLU cc_start: 0.7173 (tp30) cc_final: 0.6277 (mt-10) REVERT: K 136 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8014 (pt0) REVERT: K 155 ASN cc_start: 0.8321 (m-40) cc_final: 0.7713 (t0) REVERT: K 178 MET cc_start: 0.9040 (mtm) cc_final: 0.8585 (mtt) REVERT: L 154 MET cc_start: 0.7048 (mmt) cc_final: 0.5990 (mmt) REVERT: N 246 GLU cc_start: 0.7994 (pp20) cc_final: 0.7322 (pp20) outliers start: 33 outliers final: 29 residues processed: 277 average time/residue: 0.1449 time to fit residues: 59.4273 Evaluate side-chains 281 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 152 optimal weight: 0.9980 chunk 204 optimal weight: 0.0870 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 222 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.151947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113779 restraints weight = 26147.589| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.43 r_work: 0.3293 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18842 Z= 0.117 Angle : 0.486 8.182 25790 Z= 0.275 Chirality : 0.041 0.127 2846 Planarity : 0.003 0.079 3002 Dihedral : 18.637 70.643 3143 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.77 % Allowed : 15.96 % Favored : 82.27 % 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: 1.03 (0.19), residues: 2032 helix: 2.51 (0.17), residues: 962 sheet: 0.42 (0.25), residues: 436 loop : -2.16 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 273 TYR 0.007 0.001 TYR B 83 PHE 0.016 0.001 PHE L 121 TRP 0.023 0.001 TRP K 131 HIS 0.004 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (18810) covalent geometry : angle 0.47953 / 0.27 (25776) hydrogen bonds : bond 0.04414 / 3.03 ( 1042) hydrogen bonds : angle 4.16286 / 2.92 ( 2962) metal coordination : bond 0.00805 / 0.56 ( 32) metal coordination : angle 3.46236 / 1.97 ( 14) ********************** 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 287 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8380 (tp30) cc_final: 0.7944 (tp30) REVERT: A 42 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8714 (mmtp) REVERT: B 63 MET cc_start: 0.8722 (mmm) cc_final: 0.8208 (ttm) REVERT: B 224 ARG cc_start: 0.8030 (tpt-90) cc_final: 0.7703 (tpp80) REVERT: B 253 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6549 (t0) REVERT: B 256 ASP cc_start: 0.6188 (t0) cc_final: 0.5339 (m-30) REVERT: B 267 ILE cc_start: 0.9003 (mp) cc_final: 0.8677 (mt) REVERT: B 270 ASP cc_start: 0.7791 (t0) cc_final: 0.7126 (t0) REVERT: C 11 GLU cc_start: 0.7282 (tp30) cc_final: 0.6338 (mt-10) REVERT: C 136 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7433 (pt0) REVERT: C 155 ASN cc_start: 0.8311 (m-40) cc_final: 0.7547 (t0) REVERT: M 6 GLU cc_start: 0.7956 (tp30) cc_final: 0.7455 (tp30) REVERT: M 27 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8760 (mm-40) REVERT: I 22 MET cc_start: 0.8962 (mtm) cc_final: 0.8568 (mtm) REVERT: I 24 GLU cc_start: 0.8136 (tt0) cc_final: 0.7706 (mt-10) REVERT: I 154 MET cc_start: 0.8910 (mmt) cc_final: 0.8584 (mmm) REVERT: J 63 MET cc_start: 0.8565 (mmm) cc_final: 0.8266 (ttm) REVERT: J 235 TRP cc_start: 0.6348 (m100) cc_final: 0.6010 (m100) REVERT: J 252 GLN cc_start: 0.7091 (tt0) cc_final: 0.6557 (tm-30) REVERT: J 256 ASP cc_start: 0.6965 (t0) cc_final: 0.6254 (m-30) REVERT: J 266 LYS cc_start: 0.7240 (ttpt) cc_final: 0.6759 (pttt) REVERT: J 267 ILE cc_start: 0.8968 (mp) cc_final: 0.8627 (mt) REVERT: J 270 ASP cc_start: 0.7786 (t70) cc_final: 0.7164 (t0) REVERT: K 11 GLU cc_start: 0.7159 (tp30) cc_final: 0.6277 (mt-10) REVERT: K 155 ASN cc_start: 0.8246 (m-40) cc_final: 0.7625 (t0) REVERT: K 178 MET cc_start: 0.9019 (mtm) cc_final: 0.8305 (mtt) REVERT: L 112 HIS cc_start: 0.8052 (t-90) cc_final: 0.7843 (t-90) REVERT: L 154 MET cc_start: 0.7033 (mmt) cc_final: 0.5898 (mmt) REVERT: N 246 GLU cc_start: 0.7940 (pp20) cc_final: 0.7311 (pp20) outliers start: 31 outliers final: 28 residues processed: 269 average time/residue: 0.1559 time to fit residues: 61.9863 Evaluate side-chains 280 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 222 ASN J 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.151648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113241 restraints weight = 26239.901| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.57 r_work: 0.3278 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18842 Z= 0.121 Angle : 0.491 7.812 25790 Z= 0.278 Chirality : 0.041 0.130 2846 Planarity : 0.003 0.068 3002 Dihedral : 18.619 70.459 3143 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.77 % Allowed : 16.19 % Favored : 82.04 % 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: 1.07 (0.19), residues: 2032 helix: 2.56 (0.17), residues: 960 sheet: 0.43 (0.25), residues: 436 loop : -2.15 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 273 TYR 0.008 0.001 TYR B 83 PHE 0.014 0.001 PHE L 121 TRP 0.023 0.001 TRP K 131 HIS 0.005 0.001 HIS L 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (18810) covalent geometry : angle 0.48486 / 0.28 (25776) hydrogen bonds : bond 0.04417 / 3.03 ( 1042) hydrogen bonds : angle 4.14854 / 2.91 ( 2962) metal coordination : bond 0.00742 / 0.51 ( 32) metal coordination : angle 3.26150 / 1.87 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4401.22 seconds wall clock time: 76 minutes 13.75 seconds (4573.75 seconds total)