Starting phenix.real_space_refine on Thu Mar 5 02:04:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rwm_10042/03_2026/6rwm_10042.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rwm_10042/03_2026/6rwm_10042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rwm_10042/03_2026/6rwm_10042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rwm_10042/03_2026/6rwm_10042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rwm_10042/03_2026/6rwm_10042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rwm_10042/03_2026/6rwm_10042.map" } resolution = 2.81 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= 0.001 sd= 0.172 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 P 84 5.49 5 Mg 4 5.21 5 S 74 5.16 5 Cl 2 4.86 5 C 11354 2.51 5 N 3278 2.21 5 O 3640 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18450 Number of models: 1 Model: "" Number of chains: 24 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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {' CL': 1, ' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "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} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "S" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Q" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 335 SG CYS A 40 79.792 61.576 30.481 1.00 17.41 S ATOM 357 SG CYS A 43 76.742 63.586 31.856 1.00 17.29 S ATOM 2468 SG CYS B 40 71.227 142.884 58.209 1.00 47.60 S ATOM 2490 SG CYS B 43 73.085 141.223 55.153 1.00 49.95 S ATOM 4455 SG CYS C 40 106.007 124.964 21.006 1.00 59.27 S ATOM 4477 SG CYS C 43 103.780 127.438 23.073 1.00 53.33 S ATOM 8211 SG CYS M 40 37.412 132.358 52.505 1.00 39.13 S ATOM 8233 SG CYS M 43 35.342 130.439 55.372 1.00 44.52 S Restraints were copied for chains: I, J, K, L, N, E, W, Q Time building chain proxies: 4.33, per 1000 atoms: 0.23 Number of scatterers: 18450 At special positions: 0 Unit cell: (130.68, 173.88, 98.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 Cl 2 17.00 S 74 16.00 P 84 15.00 Mg 4 11.99 F 6 9.00 O 3640 8.00 N 3278 7.00 C 11354 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: 1.65 Conformation dependent library (CDL) restraints added in 743.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 43 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb=" ZN C 500 " pdb="ZN ZN C 500 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 500 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 40 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 16 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 12 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 43 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 40 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 40 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 43 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" NE2 HIS J 12 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 16 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 43 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 40 " pdb=" ZN K 500 " pdb="ZN ZN K 500 " - pdb=" NE2 HIS K 12 " pdb="ZN ZN K 500 " - pdb=" ND1 HIS K 16 " pdb="ZN ZN K 500 " - pdb=" SG CYS K 40 " pdb="ZN ZN K 500 " - pdb=" SG CYS K 43 " pdb=" ZN M 500 " pdb="ZN ZN M 500 " - pdb=" ND1 HIS M 16 " pdb="ZN ZN M 500 " - pdb=" NE2 HIS M 12 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 43 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 40 " Number of angles added : 10 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 18 sheets defined 49.8% alpha, 19.1% beta 34 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.807A 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: 3.738A pdb=" N GLU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.589A pdb=" N ALA A 169 " --> pdb=" O ARG A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.718A 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 Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.710A pdb=" N THR B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 151 through 165 Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'B' and resid 171 through 186 removed outlier: 3.760A pdb=" N ALA B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 221 Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.604A pdb=" N ALA C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 108 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 166 through 169 removed outlier: 3.690A 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: 3.587A 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 Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 151 through 165 Processing helix chain 'D' and resid 166 through 169 removed outlier: 3.844A pdb=" N ALA D 169 " --> pdb=" O ARG D 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 169' Processing helix chain 'D' and resid 171 through 186 removed outlier: 3.597A pdb=" N ALA D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 221 removed outlier: 3.526A pdb=" N ARG D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 221 removed outlier: 4.226A 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 27 Processing helix chain 'M' and resid 29 through 40 removed outlier: 3.544A pdb=" N ALA M 33 " --> pdb=" O PRO M 29 " (cutoff:3.500A) removed outlier: 3.796A 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 Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 93 through 108 removed outlier: 3.807A 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: 3.738A pdb=" N GLU I 152 " --> pdb=" O GLN I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 169 removed outlier: 3.588A pdb=" N ALA I 169 " --> pdb=" O ARG I 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 166 through 169' Processing helix chain 'I' and resid 171 through 186 removed outlier: 3.717A 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 Processing helix chain 'J' and resid 29 through 39 Processing helix chain 'J' and resid 93 through 108 removed outlier: 3.710A pdb=" N THR J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 151 through 165 Processing helix chain 'J' and resid 166 through 169 Processing helix chain 'J' and resid 171 through 186 removed outlier: 3.760A pdb=" N ALA J 175 " --> pdb=" O LYS J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 221 Processing helix chain 'K' and resid 5 through 16 Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 39 removed outlier: 3.603A pdb=" N ALA K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 108 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 150 through 165 Processing helix chain 'K' and resid 166 through 169 removed outlier: 3.690A 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: 3.586A 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 Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 151 through 165 Processing helix chain 'L' and resid 166 through 169 removed outlier: 3.843A pdb=" N ALA L 169 " --> pdb=" O ARG L 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 166 through 169' Processing helix chain 'L' and resid 171 through 186 removed outlier: 3.598A pdb=" N ALA L 175 " --> pdb=" O LYS L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 221 removed outlier: 3.525A pdb=" N ARG L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER L 218 " --> pdb=" O GLN L 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 221 removed outlier: 4.228A 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 27 Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.545A pdb=" N ALA E 33 " --> pdb=" O PRO E 29 " (cutoff:3.500A) removed outlier: 3.796A 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: 4.373A pdb=" N VAL A 72 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 261 removed outlier: 6.343A pdb=" N GLN A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU A 241 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 239 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 89 removed outlier: 4.385A 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: 6.141A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE B 227 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL B 225 " --> pdb=" O PRO B 238 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N THR B 240 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N PHE B 223 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 89 removed outlier: 4.338A pdb=" N VAL C 72 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 89 removed outlier: 4.226A pdb=" N VAL D 72 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 257 through 261 removed outlier: 5.986A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 234 through 236 removed outlier: 3.703A pdb=" N GLN F 234 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU F 229 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE F 227 " --> pdb=" O LYS F 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 240 through 244 removed outlier: 5.687A pdb=" N LEU F 241 " --> pdb=" O GLN F 252 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLN F 252 " --> pdb=" O LEU F 241 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 83 through 89 removed outlier: 4.373A pdb=" N VAL I 72 " --> pdb=" O LEU I 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 256 through 261 removed outlier: 6.342A pdb=" N GLN I 252 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU I 241 " --> pdb=" O GLN I 252 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA I 239 " --> pdb=" O VAL I 225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 83 through 89 removed outlier: 4.384A pdb=" N VAL J 72 " --> pdb=" O LEU J 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.141A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE J 227 " --> pdb=" O LYS J 236 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL J 225 " --> pdb=" O PRO J 238 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N THR J 240 " --> pdb=" O PHE J 223 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE J 223 " --> pdb=" O THR J 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 83 through 89 removed outlier: 4.338A pdb=" N VAL K 72 " --> pdb=" O LEU K 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 83 through 89 removed outlier: 4.226A pdb=" N VAL L 72 " --> pdb=" O LEU L 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 257 through 261 removed outlier: 5.986A pdb=" N GLN L 252 " --> pdb=" O LEU L 241 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU L 241 " --> pdb=" O GLN L 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 234 through 236 removed outlier: 3.704A pdb=" N GLN N 234 " --> pdb=" O GLU N 229 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU N 229 " --> pdb=" O GLN N 234 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE N 227 " --> pdb=" O LYS N 236 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 240 through 244 removed outlier: 5.688A pdb=" N LEU N 241 " --> pdb=" O GLN N 252 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLN N 252 " --> pdb=" O LEU N 241 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4466 1.33 - 1.46: 4963 1.46 - 1.58: 9183 1.58 - 1.71: 162 1.71 - 1.84: 108 Bond restraints: 18882 Sorted by residual: bond pdb=" CAJ KLQ I 304 " pdb=" NBF KLQ I 304 " ideal model delta sigma weight residual 1.327 1.371 -0.044 2.00e-02 2.50e+03 4.83e+00 bond pdb=" CAW KLQ A 304 " pdb=" OAD KLQ A 304 " ideal model delta sigma weight residual 1.323 1.367 -0.044 2.00e-02 2.50e+03 4.79e+00 bond pdb=" CAJ KLQ A 304 " pdb=" NBF KLQ A 304 " ideal model delta sigma weight residual 1.327 1.370 -0.043 2.00e-02 2.50e+03 4.71e+00 bond pdb=" CAW KLQ I 304 " pdb=" OAD KLQ I 304 " ideal model delta sigma weight residual 1.323 1.363 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" CAR KLQ I 304 " pdb=" NAP KLQ I 304 " ideal model delta sigma weight residual 1.338 1.378 -0.040 2.00e-02 2.50e+03 4.01e+00 ... (remaining 18877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 25039 1.85 - 3.70: 781 3.70 - 5.55: 59 5.55 - 7.41: 1 7.41 - 9.26: 6 Bond angle restraints: 25886 Sorted by residual: angle pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta sigma weight residual 121.03 126.51 -5.48 1.60e+00 3.91e-01 1.17e+01 angle pdb=" C ALA I 56 " pdb=" N SER I 57 " pdb=" CA SER I 57 " ideal model delta sigma weight residual 121.03 126.50 -5.47 1.60e+00 3.91e-01 1.17e+01 angle pdb=" C LEU I 213 " pdb=" N GLN I 214 " pdb=" CA GLN I 214 " ideal model delta sigma weight residual 121.58 116.25 5.33 1.95e+00 2.63e-01 7.48e+00 angle pdb=" C LEU A 213 " pdb=" N GLN A 214 " pdb=" CA GLN A 214 " ideal model delta sigma weight residual 121.58 116.31 5.27 1.95e+00 2.63e-01 7.32e+00 angle pdb=" CAX KLQ A 304 " pdb=" CAR KLQ A 304 " pdb=" NAP KLQ A 304 " ideal model delta sigma weight residual 115.86 123.90 -8.04 3.00e+00 1.11e-01 7.19e+00 ... (remaining 25881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 9693 17.36 - 34.71: 910 34.71 - 52.07: 439 52.07 - 69.43: 92 69.43 - 86.79: 10 Dihedral angle restraints: 11144 sinusoidal: 5186 harmonic: 5958 Sorted by residual: dihedral pdb=" CA TYR A 194 " pdb=" C TYR A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TYR I 194 " pdb=" C TYR I 194 " pdb=" N SER I 195 " pdb=" CA SER I 195 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LYS M 14 " pdb=" C LYS M 14 " pdb=" N TYR M 15 " pdb=" CA TYR M 15 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 11141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1630 0.038 - 0.075: 856 0.075 - 0.113: 259 0.113 - 0.150: 81 0.150 - 0.188: 26 Chirality restraints: 2852 Sorted by residual: chirality pdb=" CB ILE B 74 " pdb=" CA ILE B 74 " pdb=" CG1 ILE B 74 " pdb=" CG2 ILE B 74 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CB ILE J 74 " pdb=" CA ILE J 74 " pdb=" CG1 ILE J 74 " pdb=" CG2 ILE J 74 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA ILE L 268 " pdb=" N ILE L 268 " pdb=" C ILE L 268 " pdb=" CB ILE L 268 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 ... (remaining 2849 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I 45 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C VAL I 45 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL I 45 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS I 46 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 45 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C VAL A 45 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL A 45 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 46 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 28 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO E 29 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 29 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 29 " 0.031 5.00e-02 4.00e+02 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 131 2.58 - 3.16: 12952 3.16 - 3.74: 26485 3.74 - 4.32: 39412 4.32 - 4.90: 63934 Nonbonded interactions: 142914 Sorted by model distance: nonbonded pdb="MG MG A 303 " pdb=" OAC KLQ A 304 " model vdw 2.005 2.170 nonbonded pdb="MG MG I 303 " pdb=" OAC KLQ I 304 " model vdw 2.010 2.170 nonbonded pdb="MG MG I 302 " pdb=" O HOH I 404 " model vdw 2.011 2.170 nonbonded pdb="MG MG A 302 " pdb=" O HOH A 403 " model vdw 2.011 2.170 nonbonded pdb="MG MG A 303 " pdb=" O HOH T 103 " model vdw 2.021 2.170 ... (remaining 142909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain '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: 6.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.990 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.181 18914 Z= 0.297 Angle : 0.744 9.257 25896 Z= 0.438 Chirality : 0.051 0.188 2852 Planarity : 0.006 0.055 3012 Dihedral : 16.838 86.786 7280 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.20 % Allowed : 5.26 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.15), residues: 2032 helix: -1.77 (0.12), residues: 954 sheet: 0.11 (0.23), residues: 446 loop : -3.28 (0.19), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 228 TYR 0.011 0.002 TYR K 83 PHE 0.016 0.002 PHE A 1 TRP 0.014 0.002 TRP E 19 HIS 0.005 0.001 HIS I 51 Details of bonding type rmsd covalent geometry : bond 0.00603 (18882) covalent geometry : angle 0.73466 (25886) hydrogen bonds : bond 0.16273 ( 1062) hydrogen bonds : angle 6.57742 ( 3014) metal coordination : bond 0.12654 ( 32) metal coordination : angle 5.98522 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 317 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8813 (mtm) cc_final: 0.8449 (mtp) REVERT: B 154 MET cc_start: 0.7468 (mmt) cc_final: 0.7051 (mmt) REVERT: C 62 GLN cc_start: 0.7430 (mt0) cc_final: 0.7126 (mt0) REVERT: C 194 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.5792 (t80) REVERT: D 234 GLN cc_start: 0.7653 (mt0) cc_final: 0.7410 (mp10) REVERT: M 7 LYS cc_start: 0.8180 (mttt) cc_final: 0.7801 (mtmt) REVERT: M 35 GLU cc_start: 0.7884 (tp30) cc_final: 0.7575 (tp30) REVERT: I 10 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7259 (mt-10) REVERT: I 22 MET cc_start: 0.8936 (mtm) cc_final: 0.8666 (mtp) REVERT: I 50 MET cc_start: 0.8776 (ppp) cc_final: 0.8549 (ppp) REVERT: I 154 MET cc_start: 0.8689 (mmt) cc_final: 0.8283 (mmt) REVERT: J 39 GLN cc_start: 0.7365 (mt0) cc_final: 0.7130 (mm110) REVERT: J 154 MET cc_start: 0.7558 (mmt) cc_final: 0.7302 (mmt) REVERT: J 224 ARG cc_start: 0.7610 (tpp80) cc_final: 0.7076 (mmt-90) REVERT: K 62 GLN cc_start: 0.7511 (mt0) cc_final: 0.7179 (mt0) REVERT: K 194 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.5549 (t80) REVERT: L 194 TYR cc_start: 0.5764 (m-80) cc_final: 0.5334 (m-80) REVERT: L 234 GLN cc_start: 0.7643 (mt0) cc_final: 0.7407 (mp10) REVERT: E 7 LYS cc_start: 0.8135 (mttt) cc_final: 0.7758 (mtmt) REVERT: E 32 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8041 (t) REVERT: E 35 GLU cc_start: 0.7882 (tp30) cc_final: 0.7578 (tp30) outliers start: 56 outliers final: 13 residues processed: 363 average time/residue: 0.7392 time to fit residues: 294.7582 Evaluate side-chains 210 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain F residue 229 GLU Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain E residue 32 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: 7.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 216 GLN B 9 GLN B 157 GLN C 17 ASN C 112 HIS C 114 HIS C 168 GLN C 214 GLN C 216 GLN D 67 HIS M 17 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 GLN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN J 9 GLN J 157 GLN K 112 HIS K 114 HIS K 168 GLN K 214 GLN K 216 GLN L 67 HIS L 157 GLN E 17 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.197799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.159037 restraints weight = 17861.527| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.23 r_work: 0.3351 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18914 Z= 0.137 Angle : 0.495 5.204 25896 Z= 0.288 Chirality : 0.041 0.152 2852 Planarity : 0.004 0.045 3012 Dihedral : 18.305 87.834 3271 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.69 % Allowed : 12.81 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2032 helix: 1.06 (0.16), residues: 964 sheet: 0.61 (0.23), residues: 438 loop : -3.06 (0.19), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 263 TYR 0.011 0.001 TYR J 83 PHE 0.013 0.001 PHE E 1 TRP 0.011 0.001 TRP B 19 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00284 (18882) covalent geometry : angle 0.49199 (25886) hydrogen bonds : bond 0.05537 ( 1062) hydrogen bonds : angle 4.71801 ( 3014) metal coordination : bond 0.01379 ( 32) metal coordination : angle 2.93697 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: B 154 MET cc_start: 0.8026 (mmt) cc_final: 0.7554 (mmt) REVERT: C 62 GLN cc_start: 0.7647 (mt0) cc_final: 0.7231 (mt0) REVERT: C 194 TYR cc_start: 0.6676 (OUTLIER) cc_final: 0.5337 (t80) REVERT: D 68 LEU cc_start: 0.7212 (tp) cc_final: 0.6872 (tt) REVERT: D 73 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7423 (mm) REVERT: D 194 TYR cc_start: 0.5996 (m-80) cc_final: 0.5222 (m-80) REVERT: D 234 GLN cc_start: 0.8489 (mt0) cc_final: 0.8158 (mp10) REVERT: M 7 LYS cc_start: 0.7953 (mttt) cc_final: 0.7397 (mtmt) REVERT: I 10 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7857 (mt-10) REVERT: J 87 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: J 154 MET cc_start: 0.8041 (mmt) cc_final: 0.7509 (mmt) REVERT: K 62 GLN cc_start: 0.7705 (mt0) cc_final: 0.7294 (mt0) REVERT: L 68 LEU cc_start: 0.7177 (tp) cc_final: 0.6817 (tt) REVERT: L 234 GLN cc_start: 0.8489 (mt0) cc_final: 0.8155 (mp10) REVERT: N 224 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7470 (mtp-110) REVERT: N 252 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: E 7 LYS cc_start: 0.7891 (mttt) cc_final: 0.7324 (mtmt) outliers start: 47 outliers final: 20 residues processed: 249 average time/residue: 0.6310 time to fit residues: 174.8532 Evaluate side-chains 221 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain N residue 224 ARG Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 18 ASN 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 145 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 127 GLN A 216 GLN B 112 HIS C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS I 127 GLN I 216 GLN J 112 HIS K 214 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.197847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156576 restraints weight = 17730.348| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.59 r_work: 0.3304 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18914 Z= 0.153 Angle : 0.505 4.833 25896 Z= 0.292 Chirality : 0.042 0.148 2852 Planarity : 0.004 0.048 3012 Dihedral : 18.349 87.188 3262 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.26 % Allowed : 14.19 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2032 helix: 2.00 (0.16), residues: 964 sheet: 0.84 (0.23), residues: 434 loop : -2.89 (0.20), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 166 TYR 0.010 0.001 TYR K 83 PHE 0.016 0.001 PHE E 1 TRP 0.012 0.001 TRP E 19 HIS 0.006 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00335 (18882) covalent geometry : angle 0.50211 (25886) hydrogen bonds : bond 0.06033 ( 1062) hydrogen bonds : angle 4.54902 ( 3014) metal coordination : bond 0.01519 ( 32) metal coordination : angle 2.98964 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 194 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 HIS cc_start: 0.8680 (t70) cc_final: 0.8096 (m90) REVERT: B 154 MET cc_start: 0.8053 (mmt) cc_final: 0.7631 (mmt) REVERT: B 273 ARG cc_start: 0.7723 (mpt180) cc_final: 0.7062 (mmt180) REVERT: C 17 ASN cc_start: 0.7850 (m-40) cc_final: 0.7526 (m110) REVERT: C 62 GLN cc_start: 0.7674 (mt0) cc_final: 0.7168 (mt0) REVERT: D 68 LEU cc_start: 0.7096 (tp) cc_final: 0.6807 (tt) REVERT: D 73 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7402 (mm) REVERT: D 234 GLN cc_start: 0.8537 (mt0) cc_final: 0.8164 (mp10) REVERT: F 252 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8704 (tt0) REVERT: M 7 LYS cc_start: 0.7852 (mttt) cc_final: 0.7252 (mtmt) REVERT: M 17 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.7688 (m-40) REVERT: J 112 HIS cc_start: 0.8711 (t70) cc_final: 0.8105 (m90) REVERT: J 273 ARG cc_start: 0.7702 (mpt180) cc_final: 0.7177 (mmt180) REVERT: K 62 GLN cc_start: 0.7682 (mt0) cc_final: 0.7231 (mt0) REVERT: L 68 LEU cc_start: 0.7056 (tp) cc_final: 0.6754 (tt) REVERT: L 234 GLN cc_start: 0.8537 (mt0) cc_final: 0.8161 (mp10) REVERT: N 252 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: E 7 LYS cc_start: 0.7900 (mttt) cc_final: 0.7316 (mtmt) REVERT: E 17 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.7758 (m110) outliers start: 57 outliers final: 25 residues processed: 231 average time/residue: 0.6587 time to fit residues: 168.4840 Evaluate side-chains 218 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN 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 194 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.198165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.157198 restraints weight = 17786.697| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.58 r_work: 0.3325 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18914 Z= 0.152 Angle : 0.498 4.679 25896 Z= 0.287 Chirality : 0.042 0.146 2852 Planarity : 0.004 0.044 3012 Dihedral : 18.350 86.665 3262 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.60 % Allowed : 14.36 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 2032 helix: 2.29 (0.16), residues: 964 sheet: 0.93 (0.23), residues: 434 loop : -2.76 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 166 TYR 0.010 0.001 TYR J 83 PHE 0.015 0.001 PHE E 1 TRP 0.012 0.001 TRP M 19 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00334 (18882) covalent geometry : angle 0.49476 (25886) hydrogen bonds : bond 0.05785 ( 1062) hydrogen bonds : angle 4.48564 ( 3014) metal coordination : bond 0.01388 ( 32) metal coordination : angle 2.75056 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 GLU cc_start: 0.7992 (tt0) cc_final: 0.7759 (tt0) REVERT: B 112 HIS cc_start: 0.8673 (t70) cc_final: 0.8163 (m90) REVERT: B 136 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: B 154 MET cc_start: 0.8048 (mmt) cc_final: 0.7718 (mmt) REVERT: B 273 ARG cc_start: 0.7665 (mpt180) cc_final: 0.7319 (mmt90) REVERT: C 62 GLN cc_start: 0.7664 (mt0) cc_final: 0.7220 (mt0) REVERT: D 68 LEU cc_start: 0.7108 (tp) cc_final: 0.6855 (tt) REVERT: D 73 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7401 (mm) REVERT: D 150 VAL cc_start: 0.6088 (t) cc_final: 0.5811 (t) REVERT: D 234 GLN cc_start: 0.8590 (mt0) cc_final: 0.8211 (mp10) REVERT: F 252 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: M 7 LYS cc_start: 0.7894 (mttt) cc_final: 0.7300 (mtmt) REVERT: M 17 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.7789 (m-40) REVERT: I 264 LYS cc_start: 0.7156 (mttt) cc_final: 0.6740 (mtpp) REVERT: J 87 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: J 112 HIS cc_start: 0.8718 (t70) cc_final: 0.8193 (m90) REVERT: J 273 ARG cc_start: 0.7700 (mpt180) cc_final: 0.7369 (mmt90) REVERT: K 62 GLN cc_start: 0.7669 (mt0) cc_final: 0.7227 (mt0) REVERT: K 103 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7163 (mtmm) REVERT: L 68 LEU cc_start: 0.7061 (tp) cc_final: 0.6710 (tt) REVERT: L 234 GLN cc_start: 0.8574 (mt0) cc_final: 0.8182 (mp10) REVERT: N 252 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: E 7 LYS cc_start: 0.7909 (mttt) cc_final: 0.7327 (mtmt) REVERT: E 17 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.7798 (m110) outliers start: 63 outliers final: 41 residues processed: 234 average time/residue: 0.6580 time to fit residues: 170.2574 Evaluate side-chains 239 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 42 LYS 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 5 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 122 optimal weight: 0.1980 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.198818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.157694 restraints weight = 17730.597| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.57 r_work: 0.3324 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18914 Z= 0.140 Angle : 0.482 4.810 25896 Z= 0.278 Chirality : 0.042 0.144 2852 Planarity : 0.004 0.042 3012 Dihedral : 18.292 86.487 3258 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.89 % Allowed : 14.47 % 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 are not related in a simple way. whole: 1.00 (0.19), residues: 2032 helix: 2.48 (0.16), residues: 964 sheet: 1.06 (0.23), residues: 434 loop : -2.73 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 166 TYR 0.011 0.001 TYR B 83 PHE 0.013 0.001 PHE E 1 TRP 0.012 0.001 TRP M 19 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00302 (18882) covalent geometry : angle 0.47911 (25886) hydrogen bonds : bond 0.05421 ( 1062) hydrogen bonds : angle 4.42669 ( 3014) metal coordination : bond 0.01314 ( 32) metal coordination : angle 2.70980 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 208 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: B 112 HIS cc_start: 0.8675 (t70) cc_final: 0.8177 (m90) REVERT: B 136 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8095 (mm-30) REVERT: B 273 ARG cc_start: 0.7703 (mpt180) cc_final: 0.7378 (mmt90) REVERT: C 62 GLN cc_start: 0.7724 (mt0) cc_final: 0.7255 (mt0) REVERT: D 68 LEU cc_start: 0.7039 (tp) cc_final: 0.6817 (tt) REVERT: D 73 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7339 (mm) REVERT: D 150 VAL cc_start: 0.6168 (t) cc_final: 0.5887 (t) REVERT: D 234 GLN cc_start: 0.8571 (mt0) cc_final: 0.8191 (mp10) REVERT: F 252 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: M 7 LYS cc_start: 0.7857 (mttt) cc_final: 0.7264 (mtmt) REVERT: M 17 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.7796 (m-40) REVERT: I 11 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: I 264 LYS cc_start: 0.7131 (mttt) cc_final: 0.6697 (mtpp) REVERT: J 87 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: J 112 HIS cc_start: 0.8720 (t70) cc_final: 0.8195 (m90) REVERT: J 136 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: J 273 ARG cc_start: 0.7767 (mpt180) cc_final: 0.7439 (mmt90) REVERT: K 62 GLN cc_start: 0.7679 (mt0) cc_final: 0.7207 (mt0) REVERT: K 103 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7143 (mtmm) REVERT: K 154 MET cc_start: 0.8137 (mmt) cc_final: 0.7348 (mmt) REVERT: K 159 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7444 (mtpt) REVERT: L 68 LEU cc_start: 0.7039 (tp) cc_final: 0.6694 (tt) REVERT: L 234 GLN cc_start: 0.8546 (mt0) cc_final: 0.8157 (mp10) REVERT: N 252 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: E 7 LYS cc_start: 0.7854 (mttt) cc_final: 0.7256 (mtmt) REVERT: E 17 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.7848 (m110) outliers start: 68 outliers final: 40 residues processed: 251 average time/residue: 0.7274 time to fit residues: 200.5922 Evaluate side-chains 253 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 42 LYS 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 124 optimal weight: 0.1980 chunk 181 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 0.0770 chunk 139 optimal weight: 0.0670 overall best weight: 0.8478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.202853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.162160 restraints weight = 17649.118| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.55 r_work: 0.3414 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.002 0.034 18914 Z= 0.107 Angle : 0.435 5.286 25896 Z= 0.252 Chirality : 0.040 0.141 2852 Planarity : 0.003 0.036 3012 Dihedral : 18.139 86.900 3258 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.55 % Allowed : 14.99 % 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 are not related in a simple way. whole: 1.29 (0.19), residues: 2032 helix: 2.67 (0.16), residues: 976 sheet: 1.13 (0.23), residues: 438 loop : -2.59 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 166 TYR 0.010 0.001 TYR B 83 PHE 0.009 0.001 PHE E 1 TRP 0.012 0.001 TRP I 19 HIS 0.003 0.000 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00216 (18882) covalent geometry : angle 0.43284 (25886) hydrogen bonds : bond 0.04189 ( 1062) hydrogen bonds : angle 4.31418 ( 3014) metal coordination : bond 0.00849 ( 32) metal coordination : angle 2.42202 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: B 112 HIS cc_start: 0.8621 (t70) cc_final: 0.8147 (m90) REVERT: B 273 ARG cc_start: 0.7892 (mpt180) cc_final: 0.7577 (mmt90) REVERT: C 62 GLN cc_start: 0.7677 (mt0) cc_final: 0.7201 (mt0) REVERT: D 68 LEU cc_start: 0.7297 (tp) cc_final: 0.7049 (tt) REVERT: D 73 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7428 (mm) REVERT: D 134 GLN cc_start: 0.8227 (mt0) cc_final: 0.7903 (mp10) REVERT: D 234 GLN cc_start: 0.8553 (mt0) cc_final: 0.8016 (mp10) REVERT: F 252 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: M 7 LYS cc_start: 0.7770 (mttt) cc_final: 0.7149 (mtmt) REVERT: M 17 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.7722 (m-40) REVERT: I 11 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7826 (mm-30) REVERT: I 264 LYS cc_start: 0.7126 (mttt) cc_final: 0.6702 (mtpp) REVERT: J 87 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: J 112 HIS cc_start: 0.8661 (t70) cc_final: 0.8159 (m90) REVERT: J 273 ARG cc_start: 0.7761 (mpt180) cc_final: 0.7489 (mmt90) REVERT: K 62 GLN cc_start: 0.7716 (mt0) cc_final: 0.7215 (mt0) REVERT: K 178 MET cc_start: 0.8798 (mtp) cc_final: 0.8534 (mtm) REVERT: L 68 LEU cc_start: 0.7046 (tp) cc_final: 0.6745 (tt) REVERT: L 234 GLN cc_start: 0.8558 (mt0) cc_final: 0.8160 (mp10) REVERT: E 7 LYS cc_start: 0.7726 (mttt) cc_final: 0.7116 (mtmt) REVERT: E 17 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.7802 (m-40) outliers start: 62 outliers final: 20 residues processed: 266 average time/residue: 0.6802 time to fit residues: 200.0828 Evaluate side-chains 242 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain E residue 17 ASN 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 141 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 216 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN J 221 GLN K 214 GLN N 252 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.200130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158793 restraints weight = 17656.739| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.55 r_work: 0.3359 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18914 Z= 0.131 Angle : 0.477 6.321 25896 Z= 0.273 Chirality : 0.041 0.153 2852 Planarity : 0.003 0.038 3012 Dihedral : 18.228 86.384 3258 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.09 % Allowed : 15.79 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 2032 helix: 2.71 (0.16), residues: 974 sheet: 1.17 (0.23), residues: 434 loop : -2.55 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 166 TYR 0.011 0.001 TYR B 83 PHE 0.012 0.001 PHE E 1 TRP 0.010 0.001 TRP E 19 HIS 0.004 0.001 HIS M 12 Details of bonding type rmsd covalent geometry : bond 0.00282 (18882) covalent geometry : angle 0.47419 (25886) hydrogen bonds : bond 0.05005 ( 1062) hydrogen bonds : angle 4.34622 ( 3014) metal coordination : bond 0.01183 ( 32) metal coordination : angle 2.57476 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: B 87 GLU cc_start: 0.7955 (tt0) cc_final: 0.7690 (tt0) REVERT: B 112 HIS cc_start: 0.8669 (t70) cc_final: 0.8184 (m90) REVERT: B 273 ARG cc_start: 0.7833 (mpt180) cc_final: 0.7532 (mmt90) REVERT: C 62 GLN cc_start: 0.7645 (mt0) cc_final: 0.7177 (mt0) REVERT: C 154 MET cc_start: 0.8242 (mmm) cc_final: 0.7436 (mmt) REVERT: D 68 LEU cc_start: 0.7337 (tp) cc_final: 0.7083 (tt) REVERT: D 73 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7461 (mm) REVERT: D 150 VAL cc_start: 0.6132 (t) cc_final: 0.5905 (t) REVERT: D 234 GLN cc_start: 0.8612 (mt0) cc_final: 0.8238 (mp10) REVERT: F 252 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: M 7 LYS cc_start: 0.7864 (mttt) cc_final: 0.7261 (mtmt) REVERT: M 17 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.7738 (m-40) REVERT: I 11 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: I 264 LYS cc_start: 0.7179 (mttt) cc_final: 0.6766 (mtpp) REVERT: J 87 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: J 112 HIS cc_start: 0.8710 (t70) cc_final: 0.8196 (m90) REVERT: J 136 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: J 273 ARG cc_start: 0.7842 (mpt180) cc_final: 0.7434 (mmt90) REVERT: K 62 GLN cc_start: 0.7724 (mt0) cc_final: 0.7241 (mt0) REVERT: L 68 LEU cc_start: 0.7096 (tp) cc_final: 0.6790 (tt) REVERT: L 234 GLN cc_start: 0.8582 (mt0) cc_final: 0.8186 (mp10) REVERT: N 252 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8804 (tp-100) REVERT: E 7 LYS cc_start: 0.7854 (mttt) cc_final: 0.7250 (mtmt) REVERT: E 17 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.7787 (m-40) outliers start: 54 outliers final: 31 residues processed: 248 average time/residue: 0.6649 time to fit residues: 182.5301 Evaluate side-chains 250 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 62 optimal weight: 0.0050 chunk 22 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN N 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.199545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158324 restraints weight = 17522.764| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.54 r_work: 0.3333 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18914 Z= 0.137 Angle : 0.486 6.623 25896 Z= 0.278 Chirality : 0.041 0.145 2852 Planarity : 0.004 0.041 3012 Dihedral : 18.230 86.498 3257 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.32 % Allowed : 16.02 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 2032 helix: 2.69 (0.16), residues: 974 sheet: 1.19 (0.23), residues: 434 loop : -2.51 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 166 TYR 0.010 0.001 TYR B 83 PHE 0.013 0.001 PHE E 1 TRP 0.010 0.001 TRP E 19 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00298 (18882) covalent geometry : angle 0.48391 (25886) hydrogen bonds : bond 0.05190 ( 1062) hydrogen bonds : angle 4.37858 ( 3014) metal coordination : bond 0.01263 ( 32) metal coordination : angle 2.56292 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: A 264 LYS cc_start: 0.7213 (mttt) cc_final: 0.6762 (mtpp) REVERT: B 22 MET cc_start: 0.8662 (mtm) cc_final: 0.8342 (mtm) REVERT: B 87 GLU cc_start: 0.7974 (tt0) cc_final: 0.7719 (tt0) REVERT: B 112 HIS cc_start: 0.8710 (t70) cc_final: 0.8197 (m90) REVERT: B 273 ARG cc_start: 0.7794 (mpt180) cc_final: 0.7480 (mmt90) REVERT: C 62 GLN cc_start: 0.7675 (mt0) cc_final: 0.7215 (mt0) REVERT: D 68 LEU cc_start: 0.7245 (tp) cc_final: 0.7034 (tt) REVERT: D 73 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7412 (mm) REVERT: D 234 GLN cc_start: 0.8619 (mt0) cc_final: 0.8233 (mp10) REVERT: F 252 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: M 7 LYS cc_start: 0.7872 (mttt) cc_final: 0.7266 (mtmt) REVERT: M 17 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.7758 (m-40) REVERT: I 11 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7899 (mm-30) REVERT: I 264 LYS cc_start: 0.7185 (mttt) cc_final: 0.6715 (mtpp) REVERT: J 87 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: J 112 HIS cc_start: 0.8743 (t70) cc_final: 0.8207 (m90) REVERT: J 136 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: K 62 GLN cc_start: 0.7718 (mt0) cc_final: 0.7225 (mt0) REVERT: L 68 LEU cc_start: 0.7048 (tp) cc_final: 0.6746 (tt) REVERT: L 234 GLN cc_start: 0.8603 (mt0) cc_final: 0.8200 (mp10) REVERT: N 252 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8641 (tp-100) REVERT: E 7 LYS cc_start: 0.7864 (mttt) cc_final: 0.7256 (mtmt) REVERT: E 17 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.7792 (m-40) outliers start: 58 outliers final: 38 residues processed: 244 average time/residue: 0.6457 time to fit residues: 174.5315 Evaluate side-chains 254 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 186 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 221 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN N 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.199616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158461 restraints weight = 17587.690| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.62 r_work: 0.3330 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18914 Z= 0.137 Angle : 0.487 6.848 25896 Z= 0.278 Chirality : 0.041 0.145 2852 Planarity : 0.004 0.040 3012 Dihedral : 18.231 86.422 3257 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.26 % Allowed : 16.48 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.19), residues: 2032 helix: 2.70 (0.16), residues: 974 sheet: 1.20 (0.23), residues: 434 loop : -2.49 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 166 TYR 0.010 0.001 TYR B 83 PHE 0.013 0.001 PHE E 1 TRP 0.011 0.001 TRP M 19 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00298 (18882) covalent geometry : angle 0.48458 (25886) hydrogen bonds : bond 0.05196 ( 1062) hydrogen bonds : angle 4.38087 ( 3014) metal coordination : bond 0.01279 ( 32) metal coordination : angle 2.58207 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: A 264 LYS cc_start: 0.7246 (mttt) cc_final: 0.6800 (mtpp) REVERT: B 22 MET cc_start: 0.8686 (mtm) cc_final: 0.8351 (mtm) REVERT: B 87 GLU cc_start: 0.7994 (tt0) cc_final: 0.7755 (tt0) REVERT: B 112 HIS cc_start: 0.8724 (t70) cc_final: 0.8217 (m90) REVERT: B 273 ARG cc_start: 0.7780 (mpt180) cc_final: 0.7468 (mmt90) REVERT: C 62 GLN cc_start: 0.7643 (mt0) cc_final: 0.7173 (mt0) REVERT: D 68 LEU cc_start: 0.7258 (tp) cc_final: 0.7042 (tt) REVERT: D 73 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7427 (mm) REVERT: D 234 GLN cc_start: 0.8569 (mt0) cc_final: 0.8187 (mp10) REVERT: F 252 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: M 7 LYS cc_start: 0.7860 (mttt) cc_final: 0.7255 (mtmt) REVERT: M 17 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.7757 (m-40) REVERT: I 11 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: I 264 LYS cc_start: 0.7213 (mttt) cc_final: 0.6746 (mtpp) REVERT: J 87 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: J 112 HIS cc_start: 0.8760 (t70) cc_final: 0.8220 (m90) REVERT: J 136 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: K 62 GLN cc_start: 0.7731 (mt0) cc_final: 0.7244 (mt0) REVERT: L 68 LEU cc_start: 0.7044 (tp) cc_final: 0.6779 (tt) REVERT: L 234 GLN cc_start: 0.8552 (mt0) cc_final: 0.8151 (mp10) REVERT: N 229 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7343 (pp20) REVERT: N 252 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8779 (tp-100) REVERT: E 7 LYS cc_start: 0.7861 (mttt) cc_final: 0.7253 (mtmt) REVERT: E 17 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.7794 (m-40) outliers start: 57 outliers final: 39 residues processed: 243 average time/residue: 0.6748 time to fit residues: 181.6002 Evaluate side-chains 256 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 130 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 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 216 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN N 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.198053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157024 restraints weight = 17571.638| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.61 r_work: 0.3313 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18914 Z= 0.161 Angle : 0.519 7.093 25896 Z= 0.296 Chirality : 0.043 0.146 2852 Planarity : 0.004 0.042 3012 Dihedral : 18.312 85.990 3257 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.97 % Allowed : 16.76 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.19), residues: 2032 helix: 2.62 (0.16), residues: 972 sheet: 1.17 (0.23), residues: 434 loop : -2.50 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 166 TYR 0.010 0.001 TYR C 83 PHE 0.015 0.001 PHE E 1 TRP 0.010 0.001 TRP M 19 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00361 (18882) covalent geometry : angle 0.51676 (25886) hydrogen bonds : bond 0.05815 ( 1062) hydrogen bonds : angle 4.43784 ( 3014) metal coordination : bond 0.01404 ( 32) metal coordination : angle 2.59114 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: A 264 LYS cc_start: 0.7191 (mttt) cc_final: 0.6743 (mtpp) REVERT: B 87 GLU cc_start: 0.7996 (tt0) cc_final: 0.7730 (tt0) REVERT: B 112 HIS cc_start: 0.8734 (t70) cc_final: 0.8222 (m90) REVERT: B 273 ARG cc_start: 0.7698 (mpt180) cc_final: 0.7357 (mmt90) REVERT: C 62 GLN cc_start: 0.7673 (mt0) cc_final: 0.7139 (mt0) REVERT: D 68 LEU cc_start: 0.7225 (tp) cc_final: 0.7015 (tt) REVERT: D 73 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7397 (mm) REVERT: D 213 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6480 (tp) REVERT: D 234 GLN cc_start: 0.8621 (mt0) cc_final: 0.8231 (mp10) REVERT: F 252 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: M 7 LYS cc_start: 0.7911 (mttt) cc_final: 0.7315 (mtmt) REVERT: M 17 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.7908 (m110) REVERT: I 11 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7944 (mm-30) REVERT: I 264 LYS cc_start: 0.7221 (mttt) cc_final: 0.6742 (mtpp) REVERT: J 87 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: J 112 HIS cc_start: 0.8769 (t70) cc_final: 0.8227 (m90) REVERT: J 136 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: K 62 GLN cc_start: 0.7731 (mt0) cc_final: 0.7245 (mt0) REVERT: L 68 LEU cc_start: 0.7015 (tp) cc_final: 0.6756 (tt) REVERT: L 213 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6462 (tp) REVERT: L 234 GLN cc_start: 0.8606 (mt0) cc_final: 0.8199 (mp10) REVERT: N 229 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7356 (pp20) REVERT: E 7 LYS cc_start: 0.7923 (mttt) cc_final: 0.7327 (mtmt) REVERT: E 17 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.7849 (m110) outliers start: 52 outliers final: 36 residues processed: 239 average time/residue: 0.6455 time to fit residues: 171.2715 Evaluate side-chains 256 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 133 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 148 optimal weight: 0.0030 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.196331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.155073 restraints weight = 17597.304| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.64 r_work: 0.3273 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18914 Z= 0.199 Angle : 0.567 7.081 25896 Z= 0.323 Chirality : 0.045 0.152 2852 Planarity : 0.004 0.045 3012 Dihedral : 18.430 85.112 3257 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.92 % Allowed : 17.11 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 2032 helix: 2.43 (0.16), residues: 966 sheet: 1.05 (0.23), residues: 436 loop : -2.57 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 166 TYR 0.011 0.002 TYR C 83 PHE 0.018 0.002 PHE E 1 TRP 0.011 0.001 TRP M 19 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00461 (18882) covalent geometry : angle 0.56520 (25886) hydrogen bonds : bond 0.06705 ( 1062) hydrogen bonds : angle 4.54085 ( 3014) metal coordination : bond 0.01606 ( 32) metal coordination : angle 2.59734 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6006.02 seconds wall clock time: 103 minutes 34.34 seconds (6214.34 seconds total)