Starting phenix.real_space_refine on Sun Aug 24 07:40:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rwl_10041/08_2025/6rwl_10041.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rwl_10041/08_2025/6rwl_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_10041/08_2025/6rwl_10041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rwl_10041/08_2025/6rwl_10041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rwl_10041/08_2025/6rwl_10041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rwl_10041/08_2025/6rwl_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-2.0-5787/lib/python3.9/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: 4.03, per 1000 atoms: 0.22 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: 1.08 Conformation dependent library (CDL) restraints added in 573.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.91 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: 3.03 Time building geometry restraints manager: 1.50 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=" C SER I 57 " pdb=" N PRO I 58 " ideal model delta sigma weight residual 1.335 1.353 -0.018 9.40e-03 1.13e+04 3.64e+00 bond pdb=" C SER A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 1.335 1.353 -0.018 9.40e-03 1.13e+04 3.62e+00 bond pdb=" C TRP A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.01e-02 9.80e+03 1.91e+00 bond pdb=" C TRP I 108 " pdb=" N PRO I 109 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.01e-02 9.80e+03 1.86e+00 bond pdb=" C TRP K 108 " pdb=" N PRO K 109 " ideal model delta sigma weight residual 1.333 1.346 -0.012 1.01e-02 9.80e+03 1.45e+00 ... (remaining 18805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 23205 0.86 - 1.72: 2067 1.72 - 2.58: 355 2.58 - 3.44: 133 3.44 - 4.30: 16 Bond angle restraints: 25776 Sorted by residual: angle pdb=" N LYS D 111 " pdb=" CA LYS D 111 " pdb=" C LYS D 111 " ideal model delta sigma weight residual 114.31 110.80 3.51 1.29e+00 6.01e-01 7.39e+00 angle pdb=" N LYS L 111 " pdb=" CA LYS L 111 " pdb=" C LYS L 111 " ideal model delta sigma weight residual 114.31 110.85 3.46 1.29e+00 6.01e-01 7.19e+00 angle pdb=" N VAL A 45 " pdb=" CA VAL A 45 " pdb=" C VAL A 45 " ideal model delta sigma weight residual 106.42 109.96 -3.54 1.51e+00 4.39e-01 5.50e+00 angle pdb=" N VAL I 45 " pdb=" CA VAL I 45 " pdb=" C VAL I 45 " ideal model delta sigma weight residual 106.42 109.92 -3.50 1.51e+00 4.39e-01 5.36e+00 angle pdb=" C GLY F 254 " pdb=" N GLN F 255 " pdb=" CA GLN F 255 " ideal model delta sigma weight residual 122.07 125.33 -3.26 1.43e+00 4.89e-01 5.19e+00 ... (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: 1731 0.032 - 0.065: 762 0.065 - 0.097: 207 0.097 - 0.129: 121 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: 0.02 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: 3.000 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.320 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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= 0.201 Angle : 0.575 6.483 25790 Z= 0.349 Chirality : 0.044 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 aren 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 covalent geometry : bond 0.00284 (18810) covalent geometry : angle 0.55809 (25776) hydrogen bonds : bond 0.12077 ( 1042) hydrogen bonds : angle 6.44152 ( 2962) metal coordination : bond 0.12285 ( 32) metal coordination : angle 5.95554 ( 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 : 0.751 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: 0.8140 (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: 0.7288 (tp30) REVERT: A 42 LYS cc_start: 0.8726 (mmmt) cc_final: 0.8515 (mmtp) REVERT: A 63 MET cc_start: 0.8377 (ttm) cc_final: 0.8122 (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: 0.6182 (m-30) REVERT: B 267 ILE cc_start: 0.8956 (mp) cc_final: 0.8658 (mt) REVERT: B 270 ASP cc_start: 0.7441 (t70) cc_final: 0.7058 (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: 0.8227 (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: 0.7043 (t80) REVERT: M 17 ASN cc_start: 0.8843 (m-40) cc_final: 0.8640 (m-40) REVERT: M 34 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8302 (mtpt) REVERT: I 17 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8370 (m-40) REVERT: I 18 ASN cc_start: 0.8766 (p0) cc_final: 0.8414 (p0) REVERT: I 22 MET cc_start: 0.8612 (mtm) cc_final: 0.8330 (mtm) REVERT: I 35 GLU cc_start: 0.7626 (tp30) cc_final: 0.7413 (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: 0.7360 (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: 0.7512 (t70) cc_final: 0.7260 (p0) REVERT: N 246 GLU cc_start: 0.7898 (pp20) cc_final: 0.7515 (pp20) REVERT: N 252 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: E 15 TYR cc_start: 0.8004 (m-80) cc_final: 0.7793 (m-80) REVERT: E 34 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8443 (mtpt) outliers start: 50 outliers final: 12 residues processed: 479 average time/residue: 0.1537 time to fit residues: 105.8754 Evaluate side-chains 301 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 282 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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: 5.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 183 HIS B 44 GLN B 157 GLN B 183 HIS B 216 GLN C 114 HIS ** 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 I 183 HIS 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.149106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109378 restraints weight = 26334.678| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.51 r_work: 0.3256 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18842 Z= 0.188 Angle : 0.545 8.689 25790 Z= 0.309 Chirality : 0.043 0.174 2846 Planarity : 0.004 0.043 3002 Dihedral : 18.741 82.138 3175 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.52 % Allowed : 11.10 % Favored : 86.38 % 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 aren not related in a simple way. whole: -0.59 (0.18), residues: 2032 helix: 0.98 (0.16), residues: 958 sheet: 0.16 (0.24), residues: 446 loop : -3.03 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 262 TYR 0.011 0.001 TYR M 15 PHE 0.012 0.001 PHE M 1 TRP 0.015 0.001 TRP K 131 HIS 0.005 0.001 HIS J 12 Details of bonding type rmsd covalent geometry : bond 0.00435 (18810) covalent geometry : angle 0.53848 (25776) hydrogen bonds : bond 0.05913 ( 1042) hydrogen bonds : angle 4.51785 ( 2962) metal coordination : bond 0.01008 ( 32) metal coordination : angle 3.66408 ( 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 351 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 307 time to evaluate : 0.678 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: 0.8650 (tp30) cc_final: 0.8225 (tm-30) REVERT: A 39 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7841 (mm-40) REVERT: A 42 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8771 (mmtp) REVERT: A 63 MET cc_start: 0.8925 (ttm) cc_final: 0.8656 (mtp) REVERT: A 107 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7340 (mpt180) REVERT: B 17 ASN cc_start: 0.8807 (m-40) cc_final: 0.8601 (m110) REVERT: B 63 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8585 (ttm) REVERT: B 154 MET cc_start: 0.6470 (mmt) cc_final: 0.6231 (mmt) REVERT: B 224 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7607 (tpp80) REVERT: B 256 ASP cc_start: 0.6794 (t0) cc_final: 0.5782 (m-30) REVERT: B 267 ILE cc_start: 0.8995 (mp) cc_final: 0.8671 (mt) REVERT: B 270 ASP cc_start: 0.7902 (t70) cc_final: 0.7673 (t70) REVERT: B 271 TYR cc_start: 0.8793 (m-80) cc_final: 0.8309 (m-80) REVERT: C 136 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7618 (pt0) REVERT: C 154 MET cc_start: 0.8312 (mmt) cc_final: 0.8062 (mmm) REVERT: C 155 ASN cc_start: 0.8400 (m-40) cc_final: 0.7644 (t0) REVERT: C 178 MET cc_start: 0.8842 (mtm) cc_final: 0.8638 (mtp) REVERT: D 215 ASN cc_start: 0.8604 (t0) cc_final: 0.8398 (t0) REVERT: F 229 GLU cc_start: 0.7491 (pt0) cc_final: 0.7225 (pt0) REVERT: F 246 GLU cc_start: 0.8085 (pp20) cc_final: 0.7582 (pp20) REVERT: F 271 TYR cc_start: 0.7203 (t80) cc_final: 0.6959 (t80) REVERT: M 6 GLU cc_start: 0.8274 (tp30) cc_final: 0.7994 (tp30) REVERT: I 35 GLU cc_start: 0.8731 (tp30) cc_final: 0.8427 (tm-30) REVERT: I 39 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7731 (tt0) REVERT: I 63 MET cc_start: 0.8927 (ttm) cc_final: 0.8590 (mtp) REVERT: I 107 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7236 (mpt180) REVERT: I 256 ASP cc_start: 0.7202 (m-30) cc_final: 0.6703 (m-30) REVERT: J 63 MET cc_start: 0.8838 (mmm) cc_final: 0.8539 (ttm) REVERT: J 224 ARG cc_start: 0.8441 (tpp80) cc_final: 0.7931 (tpt-90) REVERT: J 256 ASP cc_start: 0.7242 (t0) cc_final: 0.6525 (m-30) REVERT: J 267 ILE cc_start: 0.8869 (mp) cc_final: 0.8562 (mt) REVERT: J 270 ASP cc_start: 0.7971 (t70) cc_final: 0.7477 (t0) REVERT: K 115 THR cc_start: 0.6667 (OUTLIER) cc_final: 0.6264 (p) REVERT: K 155 ASN cc_start: 0.8349 (m-40) cc_final: 0.7725 (t0) REVERT: K 194 TYR cc_start: 0.7885 (m-80) cc_final: 0.7581 (m-80) REVERT: L 154 MET cc_start: 0.7417 (mmt) cc_final: 0.6474 (mmt) REVERT: N 246 GLU cc_start: 0.8200 (pp20) cc_final: 0.7720 (pp20) REVERT: E 31 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8424 (p) REVERT: E 34 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8673 (mtpt) outliers start: 44 outliers final: 32 residues processed: 332 average time/residue: 0.1568 time to fit residues: 75.2041 Evaluate side-chains 300 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 263 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 107 ARG 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 260 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 265 CYS 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 65 CYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 50 MET 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 I residue 260 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 265 CYS 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 115 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 81 SER 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: 4.9990 chunk 37 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 ASN L 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.150219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110828 restraints weight = 26463.429| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.50 r_work: 0.3278 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18842 Z= 0.141 Angle : 0.487 8.245 25790 Z= 0.275 Chirality : 0.041 0.225 2846 Planarity : 0.003 0.035 3002 Dihedral : 18.455 81.935 3154 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.29 % Allowed : 13.39 % Favored : 84.32 % 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 aren not related in a simple way. whole: 0.24 (0.19), residues: 2032 helix: 1.84 (0.17), residues: 960 sheet: 0.32 (0.24), residues: 456 loop : -2.83 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.012 0.001 TYR E 15 PHE 0.008 0.001 PHE E 1 TRP 0.013 0.001 TRP K 131 HIS 0.005 0.001 HIS J 12 Details of bonding type rmsd covalent geometry : bond 0.00313 (18810) covalent geometry : angle 0.47924 (25776) hydrogen bonds : bond 0.04929 ( 1042) hydrogen bonds : angle 4.28428 ( 2962) metal coordination : bond 0.00893 ( 32) metal coordination : angle 3.70524 ( 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 317 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 0.805 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: 0.8624 (tp30) cc_final: 0.8203 (mm-30) REVERT: A 39 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7732 (mm-40) REVERT: A 42 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8724 (mmtp) REVERT: A 63 MET cc_start: 0.8909 (ttm) cc_final: 0.8688 (mtp) REVERT: B 17 ASN cc_start: 0.8866 (m-40) cc_final: 0.8637 (m110) REVERT: B 63 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8523 (ttm) REVERT: B 224 ARG cc_start: 0.8033 (tpp80) cc_final: 0.7796 (tpp80) REVERT: B 256 ASP cc_start: 0.6711 (t0) cc_final: 0.5718 (m-30) REVERT: B 267 ILE cc_start: 0.8917 (mp) cc_final: 0.8583 (mt) REVERT: B 271 TYR cc_start: 0.8917 (m-80) cc_final: 0.8544 (m-80) REVERT: C 136 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7600 (pt0) REVERT: C 154 MET cc_start: 0.8220 (mmt) cc_final: 0.7995 (mmm) REVERT: C 155 ASN cc_start: 0.8342 (m-40) cc_final: 0.7601 (t0) REVERT: F 246 GLU cc_start: 0.7932 (pp20) cc_final: 0.7456 (pp20) REVERT: F 271 TYR cc_start: 0.7211 (t80) cc_final: 0.6950 (t80) REVERT: M 6 GLU cc_start: 0.8173 (tp30) cc_final: 0.7787 (tp30) REVERT: M 22 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8273 (ttm) REVERT: M 34 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8580 (mtpt) REVERT: I 24 GLU cc_start: 0.8402 (tt0) cc_final: 0.7922 (mt-10) REVERT: I 63 MET cc_start: 0.8914 (ttm) cc_final: 0.8661 (mtp) REVERT: I 107 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7705 (mpt180) REVERT: I 154 MET cc_start: 0.9017 (mmt) cc_final: 0.8677 (mmm) REVERT: J 63 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8496 (ttm) REVERT: J 224 ARG cc_start: 0.8466 (tpp80) cc_final: 0.7954 (tpt-90) REVERT: J 252 GLN cc_start: 0.7346 (tt0) cc_final: 0.6694 (tm-30) REVERT: J 256 ASP cc_start: 0.7233 (t0) cc_final: 0.6413 (m-30) REVERT: J 267 ILE cc_start: 0.8944 (mp) cc_final: 0.8625 (mt) REVERT: J 273 ARG cc_start: 0.8023 (mmt-90) cc_final: 0.7803 (mmt-90) REVERT: K 155 ASN cc_start: 0.8248 (m-40) cc_final: 0.7628 (t0) REVERT: K 178 MET cc_start: 0.9110 (mtm) cc_final: 0.8663 (mtt) REVERT: K 194 TYR cc_start: 0.7429 (m-80) cc_final: 0.7093 (m-10) REVERT: L 154 MET cc_start: 0.7425 (mmt) cc_final: 0.6420 (mmt) REVERT: N 246 GLU cc_start: 0.8199 (pp20) cc_final: 0.7471 (pp20) REVERT: E 34 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8696 (mtpt) outliers start: 40 outliers final: 23 residues processed: 301 average time/residue: 0.1555 time to fit residues: 67.4408 Evaluate side-chains 288 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 261 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 260 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 63 MET 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 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain M residue 22 MET 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 I residue 260 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 68 LEU 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 L residue 260 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: 0.9990 chunk 70 optimal weight: 3.9990 chunk 158 optimal weight: 0.2980 chunk 66 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 123 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 ASN L 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.153128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114240 restraints weight = 26249.142| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.55 r_work: 0.3322 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18842 Z= 0.107 Angle : 0.448 6.655 25790 Z= 0.254 Chirality : 0.039 0.169 2846 Planarity : 0.003 0.032 3002 Dihedral : 18.226 81.225 3147 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.95 % Allowed : 14.19 % Favored : 83.87 % 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 aren not related in a simple way. whole: 0.72 (0.19), residues: 2032 helix: 2.28 (0.17), residues: 958 sheet: 0.45 (0.24), residues: 456 loop : -2.57 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 228 TYR 0.010 0.001 TYR K 194 PHE 0.013 0.001 PHE K 26 TRP 0.018 0.001 TRP J 235 HIS 0.004 0.001 HIS M 12 Details of bonding type rmsd covalent geometry : bond 0.00218 (18810) covalent geometry : angle 0.44055 (25776) hydrogen bonds : bond 0.03983 ( 1042) hydrogen bonds : angle 4.12072 ( 2962) metal coordination : bond 0.00940 ( 32) metal coordination : angle 3.47448 ( 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 320 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 0.728 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 42 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8666 (mmtp) REVERT: B 63 MET cc_start: 0.8843 (mmm) cc_final: 0.8429 (ttm) REVERT: B 224 ARG cc_start: 0.8237 (tpp80) cc_final: 0.7904 (tpp80) REVERT: B 266 LYS cc_start: 0.7436 (ttpt) cc_final: 0.7026 (ptmt) REVERT: B 267 ILE cc_start: 0.8993 (mp) cc_final: 0.8659 (mt) REVERT: B 270 ASP cc_start: 0.7963 (t70) cc_final: 0.7740 (t0) REVERT: B 271 TYR cc_start: 0.8879 (m-80) cc_final: 0.8477 (m-80) REVERT: C 136 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7492 (pt0) REVERT: C 155 ASN cc_start: 0.8287 (m-40) cc_final: 0.7554 (t0) REVERT: M 6 GLU cc_start: 0.8107 (tp30) cc_final: 0.7781 (tp30) REVERT: M 22 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8423 (ttm) REVERT: M 34 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8641 (mtpt) REVERT: I 24 GLU cc_start: 0.8351 (tt0) cc_final: 0.7920 (mt-10) REVERT: I 35 GLU cc_start: 0.8392 (tp30) cc_final: 0.8119 (tp30) REVERT: I 154 MET cc_start: 0.9004 (mmt) cc_final: 0.8697 (mmm) REVERT: J 63 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8363 (ttm) REVERT: J 224 ARG cc_start: 0.8397 (tpp80) cc_final: 0.7934 (tpt-90) REVERT: J 252 GLN cc_start: 0.7291 (tt0) cc_final: 0.6663 (tm-30) REVERT: J 266 LYS cc_start: 0.7426 (ttpt) cc_final: 0.6838 (pttt) REVERT: J 267 ILE cc_start: 0.9022 (mp) cc_final: 0.8692 (mt) REVERT: J 270 ASP cc_start: 0.7876 (t70) cc_final: 0.7308 (t0) REVERT: K 11 GLU cc_start: 0.7147 (tp30) cc_final: 0.6213 (mt-10) REVERT: K 136 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8012 (pt0) REVERT: K 155 ASN cc_start: 0.8221 (m-40) cc_final: 0.7593 (t0) REVERT: K 178 MET cc_start: 0.9059 (mtm) cc_final: 0.8605 (mtt) REVERT: L 154 MET cc_start: 0.7109 (mmt) cc_final: 0.5978 (mmt) REVERT: L 217 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8272 (mt) REVERT: N 246 GLU cc_start: 0.8112 (pp20) cc_final: 0.7419 (pp20) REVERT: N 271 TYR cc_start: 0.7441 (t80) cc_final: 0.7043 (t80) REVERT: E 34 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8714 (mtpt) outliers start: 34 outliers final: 19 residues processed: 304 average time/residue: 0.1605 time to fit residues: 70.9374 Evaluate side-chains 275 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 B residue 24 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 65 CYS Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 260 VAL 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: 8.9990 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 252 GLN D 222 ASN I 214 GLN I 252 GLN L 222 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.148640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109771 restraints weight = 26190.557| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.50 r_work: 0.3251 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18842 Z= 0.174 Angle : 0.516 6.640 25790 Z= 0.290 Chirality : 0.042 0.137 2846 Planarity : 0.003 0.036 3002 Dihedral : 18.513 81.273 3143 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.63 % Allowed : 14.42 % Favored : 82.95 % 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 aren not related in a simple way. whole: 0.71 (0.19), residues: 2032 helix: 2.24 (0.17), residues: 962 sheet: 0.44 (0.24), residues: 456 loop : -2.55 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 228 TYR 0.011 0.001 TYR I 83 PHE 0.013 0.001 PHE K 26 TRP 0.017 0.001 TRP J 235 HIS 0.005 0.001 HIS J 12 Details of bonding type rmsd covalent geometry : bond 0.00406 (18810) covalent geometry : angle 0.50917 (25776) hydrogen bonds : bond 0.05441 ( 1042) hydrogen bonds : angle 4.22566 ( 2962) metal coordination : bond 0.00755 ( 32) metal coordination : angle 3.58471 ( 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 319 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.533 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: A 39 GLN cc_start: 0.7724 (tt0) cc_final: 0.7510 (tt0) REVERT: A 42 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8703 (mmtp) REVERT: A 107 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7671 (mpt180) REVERT: B 63 MET cc_start: 0.8737 (mmm) cc_final: 0.8350 (ttm) REVERT: B 224 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7439 (tpt-90) REVERT: B 256 ASP cc_start: 0.6595 (t0) cc_final: 0.5633 (m-30) REVERT: B 267 ILE cc_start: 0.8935 (mp) cc_final: 0.8629 (mt) REVERT: B 271 TYR cc_start: 0.8992 (m-80) cc_final: 0.8614 (m-80) REVERT: C 11 GLU cc_start: 0.7371 (tp30) cc_final: 0.6395 (mt-10) REVERT: C 136 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7479 (pt0) REVERT: C 155 ASN cc_start: 0.8247 (m-40) cc_final: 0.7558 (t0) REVERT: C 194 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: M 6 GLU cc_start: 0.8047 (tp30) cc_final: 0.7642 (tp30) REVERT: M 22 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8231 (ttm) REVERT: M 27 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8782 (mm-40) REVERT: M 34 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8604 (mtpt) REVERT: I 24 GLU cc_start: 0.8134 (tt0) cc_final: 0.7665 (mt-10) REVERT: I 35 GLU cc_start: 0.8226 (tp30) cc_final: 0.7938 (tp30) REVERT: J 63 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8327 (ttm) REVERT: J 235 TRP cc_start: 0.6306 (m100) cc_final: 0.5951 (m100) REVERT: J 256 ASP cc_start: 0.7098 (t0) cc_final: 0.6318 (m-30) REVERT: J 266 LYS cc_start: 0.7216 (ttpt) cc_final: 0.6734 (pttt) REVERT: J 267 ILE cc_start: 0.8928 (mp) cc_final: 0.8599 (mt) REVERT: K 11 GLU cc_start: 0.7218 (tp30) cc_final: 0.6324 (mt-10) REVERT: K 136 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8028 (pt0) REVERT: K 155 ASN cc_start: 0.8239 (m-40) cc_final: 0.7743 (t0) REVERT: K 178 MET cc_start: 0.9012 (mtm) cc_final: 0.8237 (mtt) REVERT: L 154 MET cc_start: 0.7315 (mmt) cc_final: 0.6290 (mmt) REVERT: L 178 MET cc_start: 0.7958 (mtt) cc_final: 0.7732 (mtt) REVERT: L 222 ASN cc_start: 0.9240 (OUTLIER) cc_final: 0.8984 (t0) REVERT: N 246 GLU cc_start: 0.8050 (pp20) cc_final: 0.7342 (pp20) REVERT: E 34 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8647 (mtpt) outliers start: 46 outliers final: 34 residues processed: 299 average time/residue: 0.1501 time to fit residues: 65.6234 Evaluate side-chains 297 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 107 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 24 GLU 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 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 81 SER 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 22 MET Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 203 ILE 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 J residue 63 MET Chi-restraints excluded: chain J residue 234 GLN 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 K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain L residue 65 CYS Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 240 THR 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: 9.9990 chunk 204 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN D 222 ASN J 17 ASN L 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.149452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111274 restraints weight = 26124.505| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.41 r_work: 0.3304 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18842 Z= 0.151 Angle : 0.491 7.147 25790 Z= 0.277 Chirality : 0.041 0.134 2846 Planarity : 0.003 0.041 3002 Dihedral : 18.400 80.899 3143 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.35 % Allowed : 14.82 % Favored : 82.84 % 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 aren not related in a simple way. whole: 0.85 (0.19), residues: 2032 helix: 2.38 (0.17), residues: 960 sheet: 0.46 (0.24), residues: 456 loop : -2.47 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.009 0.001 TYR B 83 PHE 0.011 0.001 PHE C 26 TRP 0.016 0.001 TRP K 131 HIS 0.004 0.001 HIS J 12 Details of bonding type rmsd covalent geometry : bond 0.00342 (18810) covalent geometry : angle 0.48517 (25776) hydrogen bonds : bond 0.04884 ( 1042) hydrogen bonds : angle 4.15078 ( 2962) metal coordination : bond 0.00799 ( 32) metal coordination : angle 3.40920 ( 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 307 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 0.675 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: A 42 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8796 (mmtp) REVERT: B 63 MET cc_start: 0.8878 (mmm) cc_final: 0.8500 (ttm) REVERT: B 224 ARG cc_start: 0.8348 (tpp80) cc_final: 0.7909 (tpp80) REVERT: B 256 ASP cc_start: 0.6635 (t0) cc_final: 0.5627 (m-30) REVERT: B 267 ILE cc_start: 0.9002 (mp) cc_final: 0.8701 (mt) REVERT: B 270 ASP cc_start: 0.7957 (t70) cc_final: 0.7656 (t0) REVERT: B 271 TYR cc_start: 0.9051 (m-80) cc_final: 0.8691 (m-80) REVERT: C 11 GLU cc_start: 0.7432 (tp30) cc_final: 0.6422 (mt-10) REVERT: C 136 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7564 (pt0) REVERT: C 155 ASN cc_start: 0.8288 (m-40) cc_final: 0.7578 (t0) REVERT: C 194 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: M 6 GLU cc_start: 0.8181 (tp30) cc_final: 0.7759 (tp30) REVERT: M 22 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8394 (ttm) REVERT: M 27 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8826 (mm-40) REVERT: M 34 LYS cc_start: 0.9071 (mtmt) cc_final: 0.8732 (mtpt) REVERT: I 24 GLU cc_start: 0.8303 (tt0) cc_final: 0.7828 (mt-10) REVERT: I 35 GLU cc_start: 0.8423 (tp30) cc_final: 0.8074 (tp30) REVERT: I 154 MET cc_start: 0.9035 (mmt) cc_final: 0.8743 (mmm) REVERT: J 63 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8340 (ttm) REVERT: J 235 TRP cc_start: 0.6383 (m100) cc_final: 0.5831 (m100) REVERT: J 256 ASP cc_start: 0.7154 (t0) cc_final: 0.6283 (m-30) REVERT: J 266 LYS cc_start: 0.7359 (ttpt) cc_final: 0.6826 (pttt) REVERT: J 267 ILE cc_start: 0.9031 (mp) cc_final: 0.8690 (mt) REVERT: J 270 ASP cc_start: 0.7937 (t70) cc_final: 0.7369 (t0) REVERT: K 11 GLU cc_start: 0.7230 (tp30) cc_final: 0.6308 (mt-10) REVERT: K 136 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8098 (pt0) REVERT: K 155 ASN cc_start: 0.8250 (m-40) cc_final: 0.7747 (t0) REVERT: K 178 MET cc_start: 0.9043 (mtm) cc_final: 0.8348 (mtt) REVERT: L 69 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6456 (tm-30) REVERT: L 154 MET cc_start: 0.7362 (mmt) cc_final: 0.6340 (mmt) REVERT: L 178 MET cc_start: 0.8075 (mtt) cc_final: 0.7838 (mtt) REVERT: N 246 GLU cc_start: 0.8183 (pp20) cc_final: 0.7942 (pp20) REVERT: N 252 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: E 27 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8832 (mm-40) REVERT: E 34 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8772 (mtpt) outliers start: 41 outliers final: 30 residues processed: 288 average time/residue: 0.1492 time to fit residues: 62.6761 Evaluate side-chains 285 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 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 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain M residue 22 MET 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 J residue 63 MET Chi-restraints excluded: chain J residue 234 GLN 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 K residue 210 THR Chi-restraints excluded: chain L residue 65 CYS Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN 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: 6.9990 chunk 206 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 0.0070 chunk 57 optimal weight: 4.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 ASN D 222 ASN L 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.144406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.107760 restraints weight = 26282.046| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.25 r_work: 0.3211 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18842 Z= 0.152 Angle : 0.495 7.576 25790 Z= 0.280 Chirality : 0.041 0.133 2846 Planarity : 0.003 0.041 3002 Dihedral : 18.405 80.414 3143 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.52 % Allowed : 15.22 % 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 aren not related in a simple way. whole: 0.90 (0.19), residues: 2032 helix: 2.42 (0.17), residues: 960 sheet: 0.47 (0.24), residues: 456 loop : -2.44 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.010 0.001 TYR B 83 PHE 0.010 0.001 PHE M 1 TRP 0.018 0.001 TRP K 131 HIS 0.004 0.001 HIS K 12 Details of bonding type rmsd covalent geometry : bond 0.00345 (18810) covalent geometry : angle 0.48898 (25776) hydrogen bonds : bond 0.04955 ( 1042) hydrogen bonds : angle 4.14075 ( 2962) metal coordination : bond 0.00769 ( 32) metal coordination : angle 3.25675 ( 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 307 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 263 time to evaluate : 0.553 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 42 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8745 (mmtp) REVERT: A 107 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7675 (mpt180) REVERT: B 63 MET cc_start: 0.8807 (mmm) cc_final: 0.8403 (ttm) REVERT: B 256 ASP cc_start: 0.6610 (t0) cc_final: 0.5614 (m-30) REVERT: B 271 TYR cc_start: 0.8954 (m-80) cc_final: 0.8571 (m-80) REVERT: C 11 GLU cc_start: 0.7385 (tp30) cc_final: 0.6361 (mt-10) REVERT: C 136 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7479 (pt0) REVERT: C 155 ASN cc_start: 0.8258 (m-40) cc_final: 0.7552 (t0) REVERT: C 194 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: D 117 ASN cc_start: 0.5873 (m-40) cc_final: 0.5356 (p0) REVERT: M 6 GLU cc_start: 0.8071 (tp30) cc_final: 0.7649 (tp30) REVERT: M 22 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8322 (ttm) REVERT: M 27 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8845 (mm-40) REVERT: M 34 LYS cc_start: 0.9003 (mtmt) cc_final: 0.8651 (mtpt) REVERT: I 24 GLU cc_start: 0.8082 (tt0) cc_final: 0.7609 (mt-10) REVERT: I 35 GLU cc_start: 0.8280 (tp30) cc_final: 0.7989 (tp30) REVERT: J 63 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8221 (ttm) REVERT: J 235 TRP cc_start: 0.6399 (m100) cc_final: 0.5844 (m100) REVERT: J 256 ASP cc_start: 0.6964 (t0) cc_final: 0.5188 (m-30) REVERT: J 266 LYS cc_start: 0.7286 (ttpt) cc_final: 0.6738 (pttt) REVERT: J 267 ILE cc_start: 0.8941 (mp) cc_final: 0.8641 (mt) REVERT: J 270 ASP cc_start: 0.7758 (t70) cc_final: 0.7191 (t0) REVERT: K 11 GLU cc_start: 0.7191 (tp30) cc_final: 0.6284 (mt-10) REVERT: K 136 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8037 (pt0) REVERT: K 155 ASN cc_start: 0.8245 (m-40) cc_final: 0.7746 (t0) REVERT: K 178 MET cc_start: 0.8990 (mtm) cc_final: 0.8232 (mtt) REVERT: K 210 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7285 (t) REVERT: L 154 MET cc_start: 0.7299 (mmt) cc_final: 0.6285 (mmt) REVERT: L 178 MET cc_start: 0.7908 (mtt) cc_final: 0.7702 (mtt) REVERT: L 222 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8986 (t0) REVERT: N 246 GLU cc_start: 0.8066 (pp20) cc_final: 0.7845 (pp20) REVERT: N 252 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: E 27 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8866 (mm-40) REVERT: E 34 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8666 (mtpt) outliers start: 44 outliers final: 32 residues processed: 290 average time/residue: 0.1377 time to fit residues: 58.7635 Evaluate side-chains 295 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 107 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 203 ILE 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 C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 ILE 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 203 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 203 ILE 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 234 GLN 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 K residue 210 THR Chi-restraints excluded: chain L residue 65 CYS Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 47 optimal weight: 0.0370 chunk 156 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN D 222 ASN J 222 ASN L 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.149634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111829 restraints weight = 26255.165| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.43 r_work: 0.3278 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18842 Z= 0.137 Angle : 0.484 7.873 25790 Z= 0.274 Chirality : 0.040 0.132 2846 Planarity : 0.003 0.038 3002 Dihedral : 18.342 79.989 3142 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.40 % Allowed : 15.50 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 2032 helix: 2.49 (0.17), residues: 960 sheet: 0.50 (0.24), residues: 456 loop : -2.42 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.009 0.001 TYR B 83 PHE 0.009 0.001 PHE C 26 TRP 0.019 0.001 TRP K 131 HIS 0.004 0.001 HIS J 12 Details of bonding type rmsd covalent geometry : bond 0.00305 (18810) covalent geometry : angle 0.47858 (25776) hydrogen bonds : bond 0.04621 ( 1042) hydrogen bonds : angle 4.09352 ( 2962) metal coordination : bond 0.00739 ( 32) metal coordination : angle 3.23057 ( 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 311 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 0.694 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 42 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8710 (mmtp) REVERT: B 63 MET cc_start: 0.8731 (mmm) cc_final: 0.8297 (ttm) REVERT: B 256 ASP cc_start: 0.6606 (t0) cc_final: 0.5654 (m-30) REVERT: B 271 TYR cc_start: 0.8986 (m-80) cc_final: 0.8583 (m-80) REVERT: C 11 GLU cc_start: 0.7356 (tp30) cc_final: 0.6387 (mt-10) REVERT: C 136 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7466 (pt0) REVERT: C 155 ASN cc_start: 0.8239 (m-40) cc_final: 0.7534 (t0) REVERT: C 194 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.6820 (m-80) REVERT: D 117 ASN cc_start: 0.5900 (m-40) cc_final: 0.5392 (p0) REVERT: M 6 GLU cc_start: 0.8011 (tp30) cc_final: 0.7604 (tp30) REVERT: M 22 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8309 (ttm) REVERT: M 34 LYS cc_start: 0.8988 (mtmt) cc_final: 0.8654 (mtpt) REVERT: I 24 GLU cc_start: 0.7968 (tt0) cc_final: 0.7519 (mt-10) REVERT: I 35 GLU cc_start: 0.8160 (tp30) cc_final: 0.7925 (tp30) REVERT: I 154 MET cc_start: 0.8894 (mmt) cc_final: 0.8620 (mmm) REVERT: J 63 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8115 (ttm) REVERT: J 235 TRP cc_start: 0.6475 (m100) cc_final: 0.6012 (m100) REVERT: J 256 ASP cc_start: 0.6491 (t0) cc_final: 0.5776 (m-30) REVERT: J 266 LYS cc_start: 0.7269 (ttpt) cc_final: 0.6762 (pttt) REVERT: J 267 ILE cc_start: 0.8935 (mp) cc_final: 0.8630 (mt) REVERT: J 270 ASP cc_start: 0.7693 (t70) cc_final: 0.7129 (t0) REVERT: K 11 GLU cc_start: 0.7174 (tp30) cc_final: 0.6300 (mt-10) REVERT: K 136 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8007 (pt0) REVERT: K 155 ASN cc_start: 0.8231 (m-40) cc_final: 0.7744 (t0) REVERT: K 178 MET cc_start: 0.8967 (mtm) cc_final: 0.8196 (mtt) REVERT: K 210 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7328 (t) REVERT: L 154 MET cc_start: 0.7316 (mmt) cc_final: 0.6257 (mmt) REVERT: N 252 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: E 27 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8843 (mm-40) REVERT: E 34 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8565 (mtpt) outliers start: 42 outliers final: 33 residues processed: 293 average time/residue: 0.1371 time to fit residues: 58.8451 Evaluate side-chains 296 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 203 ILE 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 C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 203 ILE 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 234 GLN 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 K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 104 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 ASN M 39 GLN J 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.149228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.111482 restraints weight = 26161.706| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.32 r_work: 0.3273 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18842 Z= 0.151 Angle : 0.506 9.382 25790 Z= 0.287 Chirality : 0.041 0.128 2846 Planarity : 0.003 0.037 3002 Dihedral : 18.376 79.616 3142 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.46 % Allowed : 15.68 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.19), residues: 2032 helix: 2.46 (0.17), residues: 960 sheet: 0.47 (0.24), residues: 456 loop : -2.46 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 263 TYR 0.010 0.001 TYR B 83 PHE 0.010 0.001 PHE M 1 TRP 0.020 0.001 TRP K 131 HIS 0.004 0.001 HIS J 12 Details of bonding type rmsd covalent geometry : bond 0.00340 (18810) covalent geometry : angle 0.50085 (25776) hydrogen bonds : bond 0.04865 ( 1042) hydrogen bonds : angle 4.11390 ( 2962) metal coordination : bond 0.00710 ( 32) metal coordination : angle 3.18869 ( 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 302 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 259 time to evaluate : 0.507 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: B 63 MET cc_start: 0.8710 (mmm) cc_final: 0.8310 (ttm) REVERT: B 256 ASP cc_start: 0.6400 (t0) cc_final: 0.5205 (m-30) REVERT: B 271 TYR cc_start: 0.9012 (m-80) cc_final: 0.8609 (m-80) REVERT: C 11 GLU cc_start: 0.7410 (tp30) cc_final: 0.6409 (mt-10) REVERT: C 155 ASN cc_start: 0.8240 (m-40) cc_final: 0.7562 (t0) REVERT: C 194 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: D 117 ASN cc_start: 0.6127 (m-40) cc_final: 0.5641 (p0) REVERT: D 221 GLN cc_start: 0.8800 (mt0) cc_final: 0.8597 (tt0) REVERT: M 6 GLU cc_start: 0.8063 (tp30) cc_final: 0.7652 (tp30) REVERT: M 22 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8396 (ttm) REVERT: M 34 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8692 (mtpt) REVERT: I 24 GLU cc_start: 0.7862 (tt0) cc_final: 0.7403 (mt-10) REVERT: I 35 GLU cc_start: 0.8199 (tp30) cc_final: 0.7987 (tp30) REVERT: I 154 MET cc_start: 0.8892 (mmt) cc_final: 0.8636 (mmm) REVERT: J 63 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8113 (ttm) REVERT: J 235 TRP cc_start: 0.6524 (m100) cc_final: 0.6049 (m100) REVERT: J 256 ASP cc_start: 0.6289 (t0) cc_final: 0.5573 (m-30) REVERT: J 266 LYS cc_start: 0.7341 (ttpt) cc_final: 0.6849 (pttt) REVERT: J 267 ILE cc_start: 0.8975 (mp) cc_final: 0.8661 (mt) REVERT: J 270 ASP cc_start: 0.7747 (t70) cc_final: 0.7199 (t0) REVERT: K 11 GLU cc_start: 0.7255 (tp30) cc_final: 0.6346 (mt-10) REVERT: K 136 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8059 (pt0) REVERT: K 155 ASN cc_start: 0.8233 (m-40) cc_final: 0.7773 (t0) REVERT: K 178 MET cc_start: 0.8983 (mtm) cc_final: 0.8239 (mtt) REVERT: K 210 THR cc_start: 0.7761 (OUTLIER) cc_final: 0.7460 (t) REVERT: L 154 MET cc_start: 0.7359 (mmt) cc_final: 0.6301 (mmt) REVERT: N 252 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: E 34 LYS cc_start: 0.9084 (mtmt) cc_final: 0.8741 (mtpt) outliers start: 43 outliers final: 34 residues processed: 286 average time/residue: 0.1369 time to fit residues: 57.5917 Evaluate side-chains 295 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 203 ILE 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 C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 203 ILE 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 234 GLN 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 81 SER Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 152 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 ASN L 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.149573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111210 restraints weight = 26135.469| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.53 r_work: 0.3295 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18842 Z= 0.144 Angle : 0.501 7.550 25790 Z= 0.284 Chirality : 0.041 0.134 2846 Planarity : 0.003 0.038 3002 Dihedral : 18.353 79.524 3142 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.12 % Allowed : 16.25 % Favored : 81.64 % 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 aren not related in a simple way. whole: 0.95 (0.19), residues: 2032 helix: 2.50 (0.17), residues: 960 sheet: 0.49 (0.24), residues: 456 loop : -2.46 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 273 TYR 0.009 0.001 TYR B 83 PHE 0.010 0.001 PHE F 227 TRP 0.021 0.001 TRP K 131 HIS 0.004 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00323 (18810) covalent geometry : angle 0.49549 (25776) hydrogen bonds : bond 0.04696 ( 1042) hydrogen bonds : angle 4.08134 ( 2962) metal coordination : bond 0.00767 ( 32) metal coordination : angle 3.18404 ( 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 298 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 0.712 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: B 63 MET cc_start: 0.8697 (mmm) cc_final: 0.8277 (ttm) REVERT: B 256 ASP cc_start: 0.6474 (t0) cc_final: 0.4543 (m-30) REVERT: B 271 TYR cc_start: 0.9006 (m-80) cc_final: 0.8591 (m-80) REVERT: C 11 GLU cc_start: 0.7384 (tp30) cc_final: 0.6423 (mt-10) REVERT: C 19 TRP cc_start: 0.7598 (p-90) cc_final: 0.7305 (p-90) REVERT: C 155 ASN cc_start: 0.8233 (m-40) cc_final: 0.7554 (t0) REVERT: C 194 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: D 117 ASN cc_start: 0.6148 (m-40) cc_final: 0.5608 (p0) REVERT: M 6 GLU cc_start: 0.8040 (tp30) cc_final: 0.7672 (tp30) REVERT: M 22 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8300 (ttm) REVERT: M 34 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8680 (mtpt) REVERT: I 24 GLU cc_start: 0.7848 (tt0) cc_final: 0.7367 (mt-10) REVERT: I 35 GLU cc_start: 0.8213 (tp30) cc_final: 0.8006 (tp30) REVERT: I 154 MET cc_start: 0.8900 (mmt) cc_final: 0.8628 (mmm) REVERT: I 178 MET cc_start: 0.9176 (mtt) cc_final: 0.8951 (mtm) REVERT: J 63 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8078 (ttm) REVERT: J 235 TRP cc_start: 0.6508 (m100) cc_final: 0.5995 (m100) REVERT: J 256 ASP cc_start: 0.6368 (t0) cc_final: 0.5592 (m-30) REVERT: J 266 LYS cc_start: 0.7336 (ttpt) cc_final: 0.6865 (pttt) REVERT: J 267 ILE cc_start: 0.8964 (mp) cc_final: 0.8658 (mt) REVERT: K 11 GLU cc_start: 0.7240 (tp30) cc_final: 0.6320 (mt-10) REVERT: K 24 GLU cc_start: 0.7782 (tt0) cc_final: 0.7318 (pp20) REVERT: K 136 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8028 (pt0) REVERT: K 155 ASN cc_start: 0.8226 (m-40) cc_final: 0.7768 (t0) REVERT: K 178 MET cc_start: 0.8969 (mtm) cc_final: 0.8220 (mtt) REVERT: K 210 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7460 (t) REVERT: L 154 MET cc_start: 0.7369 (mmt) cc_final: 0.6314 (mmt) REVERT: L 246 GLU cc_start: 0.8352 (tp30) cc_final: 0.8128 (tp30) REVERT: N 252 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: E 34 LYS cc_start: 0.9073 (mtmt) cc_final: 0.8730 (mtpt) outliers start: 37 outliers final: 31 residues processed: 283 average time/residue: 0.1371 time to fit residues: 57.6622 Evaluate side-chains 291 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 203 ILE 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 234 GLN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 203 ILE 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 234 GLN 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 81 SER Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.150011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112138 restraints weight = 26340.733| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.51 r_work: 0.3256 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18842 Z= 0.132 Angle : 0.490 7.586 25790 Z= 0.279 Chirality : 0.040 0.131 2846 Planarity : 0.003 0.038 3002 Dihedral : 18.277 79.532 3142 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.12 % Allowed : 16.42 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.19), residues: 2032 helix: 2.57 (0.17), residues: 960 sheet: 0.39 (0.25), residues: 436 loop : -2.28 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 263 TYR 0.008 0.001 TYR B 83 PHE 0.012 0.001 PHE D 223 TRP 0.021 0.001 TRP K 131 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00289 (18810) covalent geometry : angle 0.48556 (25776) hydrogen bonds : bond 0.04407 ( 1042) hydrogen bonds : angle 4.03979 ( 2962) metal coordination : bond 0.00716 ( 32) metal coordination : angle 2.95576 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4129.42 seconds wall clock time: 71 minutes 26.17 seconds (4286.17 seconds total)