Starting phenix.real_space_refine on Sat Jul 4 17:52:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s4m_24831/07_2026/7s4m_24831_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s4m_24831/07_2026/7s4m_24831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s4m_24831/07_2026/7s4m_24831_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s4m_24831/07_2026/7s4m_24831_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s4m_24831/07_2026/7s4m_24831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s4m_24831/07_2026/7s4m_24831.map" } resolution = 2.42 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= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cu 6 5.60 5 P 12 5.49 5 S 72 5.16 5 C 14364 2.51 5 N 3498 2.21 5 O 3777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21729 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3026 Classifications: {'peptide': 388} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 20, 'TRANS': 361} Chain: "F" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1974 Classifications: {'peptide': 244} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 231} Chain: "B" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1974 Classifications: {'peptide': 244} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 231} Chain: "J" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1974 Classifications: {'peptide': 244} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 231} Chain: "G" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1982 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "C" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1982 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1982 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "N" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3026 Classifications: {'peptide': 388} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 20, 'TRANS': 361} Chain: "I" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3026 Classifications: {'peptide': 388} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 20, 'TRANS': 361} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CU': 1} Chain breaks: 1 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'D10': 1, 'HXG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'D10': 1, 'HXG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'D10': 1, 'HXG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'D12': 1, 'HXG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'D12': 1, 'HXG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Chain: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'D12': 1, 'HXG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CU': 1} Chain breaks: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CU': 1} Chain breaks: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} 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: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} 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: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 5.33, per 1000 atoms: 0.25 Number of scatterers: 21729 At special positions: 0 Unit cell: (110.24, 107.64, 119.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 6 28.99 S 72 16.00 P 12 15.00 O 3777 8.00 N 3498 7.00 C 14364 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: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4878 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 21 sheets defined 56.2% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 180 through 206 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 207 through 217 Processing helix chain 'A' and resid 227 through 253 Processing helix chain 'A' and resid 369 through 375 removed outlier: 4.045A pdb=" N ASP A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.945A pdb=" N ALA A 381 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 50 removed outlier: 4.681A pdb=" N ALA F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLY F 40 " --> pdb=" O PHE F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 63 through 89 Proline residue: F 70 - end of helix removed outlier: 4.342A pdb=" N THR F 75 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N PHE F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 112 Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 129 through 143 Processing helix chain 'F' and resid 145 through 160 removed outlier: 3.940A pdb=" N SER F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 170 Proline residue: F 167 - end of helix Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 185 through 193 Processing helix chain 'F' and resid 216 through 244 removed outlier: 3.815A pdb=" N MET F 230 " --> pdb=" O GLY F 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 50 removed outlier: 4.566A pdb=" N ALA B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLY B 40 " --> pdb=" O PHE B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 64 through 89 Proline residue: B 70 - end of helix removed outlier: 4.178A pdb=" N THR B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 112 Processing helix chain 'B' and resid 120 through 125 removed outlier: 3.506A pdb=" N VAL B 124 " --> pdb=" O PRO B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 143 Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.791A pdb=" N SER B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 170 Proline residue: B 167 - end of helix Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 199 through 204 removed outlier: 4.417A pdb=" N MET B 204 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 244 removed outlier: 4.561A pdb=" N MET B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N MET B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 50 removed outlier: 4.612A pdb=" N ALA J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY J 40 " --> pdb=" O PHE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 Processing helix chain 'J' and resid 64 through 89 Proline residue: J 70 - end of helix removed outlier: 4.374A pdb=" N THR J 75 " --> pdb=" O ILE J 71 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N PHE J 76 " --> pdb=" O LEU J 72 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 112 Processing helix chain 'J' and resid 120 through 125 Processing helix chain 'J' and resid 129 through 143 Processing helix chain 'J' and resid 145 through 160 removed outlier: 3.614A pdb=" N SER J 154 " --> pdb=" O ALA J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 170 Proline residue: J 167 - end of helix Processing helix chain 'J' and resid 171 through 173 No H-bonds generated for 'chain 'J' and resid 171 through 173' Processing helix chain 'J' and resid 185 through 193 Processing helix chain 'J' and resid 216 through 244 removed outlier: 4.311A pdb=" N MET J 230 " --> pdb=" O GLY J 226 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N MET J 231 " --> pdb=" O PHE J 227 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL J 232 " --> pdb=" O VAL J 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 46 Processing helix chain 'G' and resid 55 through 62 removed outlier: 3.670A pdb=" N GLN G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 87 removed outlier: 3.796A pdb=" N ILE G 70 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Proline residue: G 71 - end of helix Processing helix chain 'G' and resid 91 through 95 Processing helix chain 'G' and resid 96 through 123 Processing helix chain 'G' and resid 123 through 134 removed outlier: 3.762A pdb=" N GLY G 130 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET G 134 " --> pdb=" O GLY G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 152 through 172 Processing helix chain 'G' and resid 172 through 177 Processing helix chain 'G' and resid 181 through 189 Processing helix chain 'G' and resid 190 through 194 removed outlier: 4.144A pdb=" N ILE G 194 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.621A pdb=" N LEU G 199 " --> pdb=" O PRO G 195 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU G 201 " --> pdb=" O VAL G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 218 through 226 removed outlier: 3.523A pdb=" N VAL G 222 " --> pdb=" O HIS G 218 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 229 No H-bonds generated for 'chain 'G' and resid 227 through 229' Processing helix chain 'G' and resid 230 through 246 Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.518A pdb=" N LYS G 252 " --> pdb=" O LYS G 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 46 Processing helix chain 'C' and resid 55 through 62 removed outlier: 3.666A pdb=" N GLN C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 87 removed outlier: 3.700A pdb=" N ILE C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 96 through 123 Processing helix chain 'C' and resid 123 through 133 removed outlier: 3.925A pdb=" N GLY C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 152 through 172 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 181 through 189 Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.588A pdb=" N ILE C 193 " --> pdb=" O PRO C 190 " (cutoff:3.500A) Proline residue: C 195 - end of helix Processing helix chain 'C' and resid 196 through 206 removed outlier: 4.128A pdb=" N ASN C 200 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 removed outlier: 4.117A pdb=" N GLY C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 230 through 246 Processing helix chain 'C' and resid 247 through 252 Processing helix chain 'D' and resid 4 through 19 removed outlier: 3.573A pdb=" N UNK D 11 " --> pdb=" O UNK D 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 46 Processing helix chain 'K' and resid 55 through 62 removed outlier: 3.650A pdb=" N GLN K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 87 removed outlier: 3.850A pdb=" N ILE K 70 " --> pdb=" O LEU K 66 " (cutoff:3.500A) Proline residue: K 71 - end of helix Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'K' and resid 96 through 123 Processing helix chain 'K' and resid 123 through 133 removed outlier: 3.707A pdb=" N GLY K 130 " --> pdb=" O THR K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 150 Processing helix chain 'K' and resid 152 through 172 Processing helix chain 'K' and resid 172 through 177 Processing helix chain 'K' and resid 181 through 189 Processing helix chain 'K' and resid 195 through 202 removed outlier: 4.199A pdb=" N LEU K 199 " --> pdb=" O PRO K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 226 Processing helix chain 'K' and resid 227 through 229 No H-bonds generated for 'chain 'K' and resid 227 through 229' Processing helix chain 'K' and resid 230 through 246 Processing helix chain 'K' and resid 247 through 253 removed outlier: 3.513A pdb=" N LYS K 252 " --> pdb=" O LYS K 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 19 Processing helix chain 'H' and resid 4 through 19 removed outlier: 3.807A pdb=" N UNK H 11 " --> pdb=" O UNK H 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'E' and resid 180 through 206 Proline residue: E 190 - end of helix Processing helix chain 'E' and resid 207 through 217 Processing helix chain 'E' and resid 227 through 253 Processing helix chain 'E' and resid 369 through 375 removed outlier: 4.045A pdb=" N ASP E 373 " --> pdb=" O ASP E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 383 removed outlier: 3.944A pdb=" N ALA E 381 " --> pdb=" O SER E 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 34 Processing helix chain 'I' and resid 35 through 41 Processing helix chain 'I' and resid 158 through 162 Processing helix chain 'I' and resid 180 through 206 Proline residue: I 190 - end of helix Processing helix chain 'I' and resid 207 through 217 Processing helix chain 'I' and resid 227 through 253 Processing helix chain 'I' and resid 369 through 375 removed outlier: 4.046A pdb=" N ASP I 373 " --> pdb=" O ASP I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 383 removed outlier: 3.944A pdb=" N ALA I 381 " --> pdb=" O SER I 378 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 50 removed outlier: 5.394A pdb=" N TRP A 45 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS A 68 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP A 47 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS A 66 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 98 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG A 125 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG A 96 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.449A pdb=" N VAL A 140 " --> pdb=" O PRO A 145 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE A 147 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 138 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 167 Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 368 removed outlier: 6.741A pdb=" N GLU A 299 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR A 293 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR A 301 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY A 291 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN A 303 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ILE A 411 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLY A 291 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS A 413 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR A 293 " --> pdb=" O LYS A 413 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.815A pdb=" N PHE A 393 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR A 319 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 391 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 175 through 177 Processing sheet with id=AA7, first strand: chain 'F' and resid 248 through 249 Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AA9, first strand: chain 'B' and resid 248 through 249 Processing sheet with id=AB1, first strand: chain 'J' and resid 175 through 177 Processing sheet with id=AB2, first strand: chain 'J' and resid 248 through 249 Processing sheet with id=AB3, first strand: chain 'E' and resid 43 through 50 removed outlier: 5.394A pdb=" N TRP E 45 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS E 68 " --> pdb=" O TRP E 45 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP E 47 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS E 66 " --> pdb=" O ASP E 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA E 98 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG E 125 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG E 96 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 54 through 56 removed outlier: 6.449A pdb=" N VAL E 140 " --> pdb=" O PRO E 145 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE E 147 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE E 138 " --> pdb=" O ILE E 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AB6, first strand: chain 'E' and resid 360 through 368 removed outlier: 6.741A pdb=" N GLU E 299 " --> pdb=" O TYR E 293 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR E 293 " --> pdb=" O GLU E 299 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR E 301 " --> pdb=" O GLY E 291 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY E 291 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN E 303 " --> pdb=" O ASN E 289 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ILE E 411 " --> pdb=" O ASN E 289 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLY E 291 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS E 413 " --> pdb=" O GLY E 291 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR E 293 " --> pdb=" O LYS E 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 325 through 327 removed outlier: 6.815A pdb=" N PHE E 393 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR E 319 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU E 391 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 43 through 50 removed outlier: 5.394A pdb=" N TRP I 45 " --> pdb=" O HIS I 68 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS I 68 " --> pdb=" O TRP I 45 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP I 47 " --> pdb=" O LYS I 66 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS I 66 " --> pdb=" O ASP I 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA I 98 " --> pdb=" O ASN I 123 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG I 125 " --> pdb=" O ARG I 96 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG I 96 " --> pdb=" O ARG I 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 54 through 56 removed outlier: 6.449A pdb=" N VAL I 140 " --> pdb=" O PRO I 145 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE I 147 " --> pdb=" O ILE I 138 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE I 138 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 166 through 167 Processing sheet with id=AC2, first strand: chain 'I' and resid 360 through 368 removed outlier: 6.740A pdb=" N GLU I 299 " --> pdb=" O TYR I 293 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR I 293 " --> pdb=" O GLU I 299 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR I 301 " --> pdb=" O GLY I 291 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY I 291 " --> pdb=" O THR I 301 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN I 303 " --> pdb=" O ASN I 289 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N ILE I 411 " --> pdb=" O ASN I 289 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLY I 291 " --> pdb=" O ILE I 411 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS I 413 " --> pdb=" O GLY I 291 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR I 293 " --> pdb=" O LYS I 413 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 325 through 327 removed outlier: 6.815A pdb=" N PHE I 393 " --> pdb=" O GLY I 317 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR I 319 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU I 391 " --> pdb=" O TYR I 319 " (cutoff:3.500A) 1151 hydrogen bonds defined for protein. 3276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3514 1.32 - 1.45: 6467 1.45 - 1.57: 12183 1.57 - 1.69: 36 1.69 - 1.82: 138 Bond restraints: 22338 Sorted by residual: bond pdb=" N VAL A 295 " pdb=" CA VAL A 295 " ideal model delta sigma weight residual 1.456 1.494 -0.037 8.70e-03 1.32e+04 1.85e+01 bond pdb=" N VAL I 295 " pdb=" CA VAL I 295 " ideal model delta sigma weight residual 1.456 1.494 -0.037 8.70e-03 1.32e+04 1.84e+01 bond pdb=" N VAL E 295 " pdb=" CA VAL E 295 " ideal model delta sigma weight residual 1.456 1.493 -0.037 8.70e-03 1.32e+04 1.81e+01 bond pdb=" N PHE K 208 " pdb=" CA PHE K 208 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.22e-02 6.72e+03 1.09e+01 bond pdb=" N ILE K 194 " pdb=" CA ILE K 194 " ideal model delta sigma weight residual 1.463 1.502 -0.039 1.20e-02 6.94e+03 1.04e+01 ... (remaining 22333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 29827 2.97 - 5.94: 539 5.94 - 8.91: 48 8.91 - 11.87: 19 11.87 - 14.84: 5 Bond angle restraints: 30438 Sorted by residual: angle pdb=" C PHE K 208 " pdb=" CA PHE K 208 " pdb=" CB PHE K 208 " ideal model delta sigma weight residual 109.65 124.12 -14.47 1.71e+00 3.42e-01 7.16e+01 angle pdb=" C PRO K 195 " pdb=" CA PRO K 195 " pdb=" CB PRO K 195 " ideal model delta sigma weight residual 111.56 99.19 12.37 1.65e+00 3.67e-01 5.62e+01 angle pdb=" N PRO K 195 " pdb=" CA PRO K 195 " pdb=" CB PRO K 195 " ideal model delta sigma weight residual 103.25 97.11 6.14 1.05e+00 9.07e-01 3.42e+01 angle pdb=" N MET K 209 " pdb=" CA MET K 209 " pdb=" C MET K 209 " ideal model delta sigma weight residual 112.59 119.42 -6.83 1.22e+00 6.72e-01 3.14e+01 angle pdb=" N LEU E 377 " pdb=" CA LEU E 377 " pdb=" C LEU E 377 " ideal model delta sigma weight residual 113.23 106.63 6.60 1.24e+00 6.50e-01 2.83e+01 ... (remaining 30433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.05: 11755 28.05 - 56.09: 803 56.09 - 84.14: 136 84.14 - 112.18: 22 112.18 - 140.23: 10 Dihedral angle restraints: 12726 sinusoidal: 5091 harmonic: 7635 Sorted by residual: dihedral pdb=" CA ASP E 226 " pdb=" C ASP E 226 " pdb=" N ASP E 227 " pdb=" CA ASP E 227 " ideal model delta harmonic sigma weight residual 180.00 54.22 125.78 0 5.00e+00 4.00e-02 6.33e+02 dihedral pdb=" CA ASP A 226 " pdb=" C ASP A 226 " pdb=" N ASP A 227 " pdb=" CA ASP A 227 " ideal model delta harmonic sigma weight residual 180.00 54.27 125.73 0 5.00e+00 4.00e-02 6.32e+02 dihedral pdb=" CA ASP I 226 " pdb=" C ASP I 226 " pdb=" N ASP I 227 " pdb=" CA ASP I 227 " ideal model delta harmonic sigma weight residual 180.00 54.28 125.72 0 5.00e+00 4.00e-02 6.32e+02 ... (remaining 12723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2543 0.061 - 0.121: 635 0.121 - 0.182: 89 0.182 - 0.242: 27 0.242 - 0.303: 3 Chirality restraints: 3297 Sorted by residual: chirality pdb=" CA PHE K 208 " pdb=" N PHE K 208 " pdb=" C PHE K 208 " pdb=" CB PHE K 208 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB VAL G 92 " pdb=" CA VAL G 92 " pdb=" CG1 VAL G 92 " pdb=" CG2 VAL G 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE C 194 " pdb=" CA ILE C 194 " pdb=" CG1 ILE C 194 " pdb=" CG2 ILE C 194 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3294 not shown) Planarity restraints: 3759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 194 " -0.079 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO G 195 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO G 195 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 195 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 37 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ALA J 37 " 0.068 2.00e-02 2.50e+03 pdb=" O ALA J 37 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL J 38 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 37 " -0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ALA B 37 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA B 37 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL B 38 " -0.023 2.00e-02 2.50e+03 ... (remaining 3756 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 257 2.59 - 3.17: 18742 3.17 - 3.75: 37194 3.75 - 4.32: 53475 4.32 - 4.90: 87182 Nonbonded interactions: 196850 Sorted by model distance: nonbonded pdb=" O PRO C 195 " pdb=" O HOH C 401 " model vdw 2.015 3.040 nonbonded pdb=" NE2 HIS C 146 " pdb="CU CU C 301 " model vdw 2.026 3.060 nonbonded pdb=" OD2 ASP K 129 " pdb="CU CU K 301 " model vdw 2.029 2.980 nonbonded pdb=" NE2 HIS K 146 " pdb="CU CU K 301 " model vdw 2.032 3.060 nonbonded pdb=" NE2 HIS G 146 " pdb="CU CU G 301 " model vdw 2.047 3.060 ... (remaining 196845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.420 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 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 : 0.007 0.064 22338 Z= 0.421 Angle : 0.934 14.842 30438 Z= 0.552 Chirality : 0.055 0.303 3297 Planarity : 0.005 0.117 3759 Dihedral : 19.358 140.225 7848 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.54 % Favored : 94.04 % Rotamer: Outliers : 6.06 % Allowed : 19.93 % Favored : 74.01 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.17 (0.17), residues: 2601 helix: 1.03 (0.15), residues: 1248 sheet: -0.25 (0.27), residues: 390 loop : -1.57 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 376 TYR 0.022 0.002 TYR J 42 PHE 0.040 0.002 PHE J 227 TRP 0.021 0.001 TRP B 56 HIS 0.010 0.001 HIS K 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.42 (22338) covalent geometry : angle 0.93425 / 0.55 (30438) hydrogen bonds : bond 0.16833 / 11.21 ( 1151) hydrogen bonds : angle 7.64632 / 5.39 ( 3276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 224 time to evaluate : 0.815 Fit side-chains REVERT: A 205 ARG cc_start: 0.6607 (mmm-85) cc_final: 0.5882 (ttm-80) REVERT: A 285 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6546 (p) REVERT: A 295 VAL cc_start: 0.6833 (OUTLIER) cc_final: 0.6620 (m) REVERT: A 299 GLU cc_start: 0.6128 (mp0) cc_final: 0.5894 (tt0) REVERT: A 305 LYS cc_start: 0.6102 (OUTLIER) cc_final: 0.5860 (mttt) REVERT: A 315 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5211 (ptm-80) REVERT: A 346 ARG cc_start: 0.3891 (OUTLIER) cc_final: 0.2658 (ttm-80) REVERT: F 64 MET cc_start: 0.5265 (mmm) cc_final: 0.4875 (mmt) REVERT: F 230 MET cc_start: 0.6735 (mtt) cc_final: 0.6529 (mtt) REVERT: F 247 LYS cc_start: 0.5725 (ttmt) cc_final: 0.5322 (ttmt) REVERT: B 64 MET cc_start: 0.4925 (mmm) cc_final: 0.4674 (mmt) REVERT: B 247 LYS cc_start: 0.5641 (ttmt) cc_final: 0.5333 (ttmt) REVERT: J 247 LYS cc_start: 0.5642 (ttmt) cc_final: 0.5338 (ttmt) REVERT: G 151 TYR cc_start: 0.6828 (m-80) cc_final: 0.6452 (m-80) REVERT: G 209 MET cc_start: 0.3553 (OUTLIER) cc_final: 0.0477 (mmp) REVERT: C 101 MET cc_start: 0.5701 (tpp) cc_final: 0.5490 (mmm) REVERT: C 192 MET cc_start: 0.6567 (tpp) cc_final: 0.6333 (tpp) REVERT: C 201 GLU cc_start: 0.4251 (OUTLIER) cc_final: 0.3732 (mm-30) REVERT: K 47 TRP cc_start: 0.5630 (OUTLIER) cc_final: 0.5089 (p90) REVERT: K 211 GLU cc_start: 0.4459 (OUTLIER) cc_final: 0.4069 (mp0) REVERT: E 103 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7975 (mt-10) REVERT: E 205 ARG cc_start: 0.6452 (mmm-85) cc_final: 0.5773 (ttm-80) REVERT: E 282 GLU cc_start: 0.6116 (mt-10) cc_final: 0.5765 (mt-10) REVERT: E 298 ARG cc_start: 0.5957 (ptp90) cc_final: 0.5532 (mtp180) REVERT: E 305 LYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5909 (mttt) REVERT: E 345 ASP cc_start: 0.5865 (OUTLIER) cc_final: 0.5268 (m-30) REVERT: E 346 ARG cc_start: 0.3937 (OUTLIER) cc_final: 0.2774 (ttm-80) REVERT: E 373 ASP cc_start: 0.7446 (t70) cc_final: 0.7156 (t0) REVERT: E 413 LYS cc_start: 0.4568 (OUTLIER) cc_final: 0.4187 (ttmt) REVERT: I 128 ARG cc_start: 0.6450 (mtp180) cc_final: 0.6201 (mtp180) REVERT: I 205 ARG cc_start: 0.6467 (mmm-85) cc_final: 0.5787 (ttm-80) REVERT: I 230 ARG cc_start: 0.5216 (mtm-85) cc_final: 0.4749 (mmt180) REVERT: I 282 GLU cc_start: 0.6228 (mt-10) cc_final: 0.5877 (mt-10) REVERT: I 295 VAL cc_start: 0.6756 (OUTLIER) cc_final: 0.6527 (m) REVERT: I 298 ARG cc_start: 0.5993 (ptp90) cc_final: 0.5369 (mtp180) REVERT: I 299 GLU cc_start: 0.6088 (mp0) cc_final: 0.5813 (tt0) REVERT: I 327 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5951 (mp) REVERT: I 345 ASP cc_start: 0.5845 (OUTLIER) cc_final: 0.5237 (m-30) REVERT: I 346 ARG cc_start: 0.3966 (OUTLIER) cc_final: 0.2724 (ttm-80) outliers start: 132 outliers final: 33 residues processed: 327 average time/residue: 0.7043 time to fit residues: 260.8165 Evaluate side-chains 203 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 209 MET Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 210 GLU Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain I residue 224 ILE Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 327 LEU Chi-restraints excluded: chain I residue 337 ASP Chi-restraints excluded: chain I residue 345 ASP Chi-restraints excluded: chain I residue 346 ARG Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 398 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 258 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 HIS A 137 GLN A 139 ASN A 387 GLN F 87 ASN B 87 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 218 HIS K 243 HIS E 133 HIS E 137 GLN E 139 ASN E 387 GLN I 133 HIS I 137 GLN I 139 ASN I 387 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.162746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123778 restraints weight = 22105.162| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.72 r_work: 0.3438 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 22338 Z= 0.283 Angle : 0.775 11.355 30438 Z= 0.409 Chirality : 0.051 0.284 3297 Planarity : 0.006 0.097 3759 Dihedral : 14.538 141.266 3348 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.27 % Favored : 94.50 % Rotamer: Outliers : 5.42 % Allowed : 21.35 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.55 (0.17), residues: 2601 helix: 0.64 (0.15), residues: 1245 sheet: -0.35 (0.28), residues: 363 loop : -1.63 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG I 315 TYR 0.023 0.002 TYR K 174 PHE 0.036 0.003 PHE K 208 TRP 0.020 0.002 TRP J 236 HIS 0.009 0.002 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.28 (22338) covalent geometry : angle 0.77539 / 0.41 (30438) hydrogen bonds : bond 0.04979 / 3.37 ( 1151) hydrogen bonds : angle 5.76330 / 4.03 ( 3276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 190 time to evaluate : 0.789 Fit side-chains REVERT: A 205 ARG cc_start: 0.6893 (mmm-85) cc_final: 0.6134 (ttm-80) REVERT: A 298 ARG cc_start: 0.6364 (ptp90) cc_final: 0.5837 (mtp180) REVERT: A 299 GLU cc_start: 0.6379 (mp0) cc_final: 0.6022 (tt0) REVERT: A 373 ASP cc_start: 0.7886 (t70) cc_final: 0.7430 (t0) REVERT: F 64 MET cc_start: 0.6550 (mmm) cc_final: 0.5983 (mmt) REVERT: F 247 LYS cc_start: 0.6531 (ttmt) cc_final: 0.6080 (tttt) REVERT: B 64 MET cc_start: 0.6652 (mmm) cc_final: 0.6158 (mmt) REVERT: B 227 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6467 (t80) REVERT: B 234 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6783 (t80) REVERT: B 247 LYS cc_start: 0.6507 (ttmt) cc_final: 0.6058 (ttmt) REVERT: J 24 GLN cc_start: 0.5332 (OUTLIER) cc_final: 0.4826 (tp40) REVERT: J 227 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.6469 (t80) REVERT: J 234 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6799 (t80) REVERT: J 247 LYS cc_start: 0.6493 (ttmt) cc_final: 0.6042 (ttmt) REVERT: G 207 TRP cc_start: 0.3487 (OUTLIER) cc_final: 0.1426 (t60) REVERT: G 211 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5101 (mm-30) REVERT: C 209 MET cc_start: 0.4458 (mmm) cc_final: 0.3031 (mmm) REVERT: K 48 ARG cc_start: 0.7215 (ttm170) cc_final: 0.6696 (ttt180) REVERT: K 211 GLU cc_start: 0.4602 (OUTLIER) cc_final: 0.3938 (tp30) REVERT: E 103 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8177 (mt-10) REVERT: E 205 ARG cc_start: 0.6873 (mmm-85) cc_final: 0.6222 (ttm-80) REVERT: E 298 ARG cc_start: 0.6302 (ptp90) cc_final: 0.5803 (mtp180) REVERT: E 315 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.4870 (ptt-90) REVERT: E 373 ASP cc_start: 0.7809 (t70) cc_final: 0.7305 (t0) REVERT: E 413 LYS cc_start: 0.5158 (OUTLIER) cc_final: 0.4749 (tttp) REVERT: I 205 ARG cc_start: 0.6747 (mmm-85) cc_final: 0.6074 (ttm-80) REVERT: I 230 ARG cc_start: 0.5607 (mtm-85) cc_final: 0.4941 (mmt180) REVERT: I 295 VAL cc_start: 0.7228 (OUTLIER) cc_final: 0.7014 (m) REVERT: I 298 ARG cc_start: 0.6422 (ptp90) cc_final: 0.5886 (mtp180) REVERT: I 299 GLU cc_start: 0.6351 (mp0) cc_final: 0.6096 (tt0) REVERT: I 373 ASP cc_start: 0.7878 (t70) cc_final: 0.7480 (t0) outliers start: 118 outliers final: 37 residues processed: 294 average time/residue: 0.5862 time to fit residues: 199.7544 Evaluate side-chains 200 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 137 ASP Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 234 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 207 TRP Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 240 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 210 GLU Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 115 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 190 optimal weight: 0.0770 chunk 237 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN B 108 ASN B 112 ASN C 128 GLN ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN I 328 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.190474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.152803 restraints weight = 22110.188| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.83 r_work: 0.3944 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22338 Z= 0.141 Angle : 0.636 12.273 30438 Z= 0.334 Chirality : 0.045 0.225 3297 Planarity : 0.005 0.088 3759 Dihedral : 13.176 140.712 3275 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.19 % Rotamer: Outliers : 3.63 % Allowed : 23.46 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.30 (0.17), residues: 2601 helix: 0.91 (0.15), residues: 1230 sheet: -0.26 (0.29), residues: 339 loop : -1.53 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 315 TYR 0.023 0.001 TYR C 157 PHE 0.026 0.001 PHE J 227 TRP 0.017 0.001 TRP I 198 HIS 0.004 0.001 HIS I 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (22338) covalent geometry : angle 0.63641 / 0.33 (30438) hydrogen bonds : bond 0.04212 / 2.85 ( 1151) hydrogen bonds : angle 5.35650 / 3.75 ( 3276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 163 time to evaluate : 0.826 Fit side-chains REVERT: A 205 ARG cc_start: 0.6394 (mmm-85) cc_final: 0.5676 (ttm-80) REVERT: A 298 ARG cc_start: 0.5622 (ptp90) cc_final: 0.5187 (mtp180) REVERT: A 299 GLU cc_start: 0.6019 (mp0) cc_final: 0.5655 (tt0) REVERT: A 373 ASP cc_start: 0.7405 (t70) cc_final: 0.7083 (t0) REVERT: F 64 MET cc_start: 0.5745 (mmm) cc_final: 0.5354 (mmt) REVERT: F 247 LYS cc_start: 0.5944 (ttmt) cc_final: 0.5557 (tttt) REVERT: B 64 MET cc_start: 0.5960 (mmm) cc_final: 0.5411 (mmt) REVERT: B 227 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.6315 (t80) REVERT: B 234 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.6243 (t80) REVERT: B 247 LYS cc_start: 0.5911 (ttmt) cc_final: 0.5536 (ttmt) REVERT: J 227 PHE cc_start: 0.6462 (OUTLIER) cc_final: 0.6203 (t80) REVERT: J 234 PHE cc_start: 0.6653 (OUTLIER) cc_final: 0.6313 (t80) REVERT: J 247 LYS cc_start: 0.5989 (ttmt) cc_final: 0.5591 (ttmt) REVERT: G 207 TRP cc_start: 0.3311 (OUTLIER) cc_final: 0.1478 (t60) REVERT: G 211 GLU cc_start: 0.5638 (OUTLIER) cc_final: 0.4679 (mp0) REVERT: C 209 MET cc_start: 0.4339 (mmm) cc_final: 0.3135 (mmm) REVERT: C 240 MET cc_start: 0.5884 (ttp) cc_final: 0.5654 (mtp) REVERT: K 48 ARG cc_start: 0.6816 (ttm170) cc_final: 0.6374 (ttt180) REVERT: K 184 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5630 (mp) REVERT: K 211 GLU cc_start: 0.4317 (OUTLIER) cc_final: 0.3522 (tm-30) REVERT: E 103 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8057 (mt-10) REVERT: E 205 ARG cc_start: 0.6365 (mmm-85) cc_final: 0.5736 (ttm-80) REVERT: E 298 ARG cc_start: 0.5678 (ptp90) cc_final: 0.5179 (mtp180) REVERT: E 373 ASP cc_start: 0.7405 (t70) cc_final: 0.6997 (t0) REVERT: E 413 LYS cc_start: 0.4638 (OUTLIER) cc_final: 0.4274 (tttp) REVERT: I 205 ARG cc_start: 0.6194 (mmm-85) cc_final: 0.5579 (ttm-80) REVERT: I 230 ARG cc_start: 0.5219 (mtm-85) cc_final: 0.4658 (mmt180) REVERT: I 298 ARG cc_start: 0.5796 (ptp90) cc_final: 0.5308 (mtp180) REVERT: I 299 GLU cc_start: 0.6040 (mp0) cc_final: 0.5734 (tt0) REVERT: I 373 ASP cc_start: 0.7505 (t70) cc_final: 0.7191 (t0) outliers start: 79 outliers final: 28 residues processed: 229 average time/residue: 0.6418 time to fit residues: 168.8507 Evaluate side-chains 190 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 234 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 207 TRP Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 259 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 224 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 196 ASN C 200 ASN C 218 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.189023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.151428 restraints weight = 22229.698| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.83 r_work: 0.3923 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22338 Z= 0.155 Angle : 0.621 9.294 30438 Z= 0.326 Chirality : 0.045 0.233 3297 Planarity : 0.005 0.081 3759 Dihedral : 12.533 142.440 3269 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.18 % Allowed : 23.69 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.26 (0.17), residues: 2601 helix: 0.98 (0.15), residues: 1230 sheet: -0.33 (0.29), residues: 339 loop : -1.52 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 211 TYR 0.021 0.001 TYR K 157 PHE 0.027 0.002 PHE K 208 TRP 0.018 0.001 TRP I 198 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (22338) covalent geometry : angle 0.62065 / 0.33 (30438) hydrogen bonds : bond 0.04074 / 2.76 ( 1151) hydrogen bonds : angle 5.22682 / 3.66 ( 3276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 167 time to evaluate : 0.808 Fit side-chains REVERT: A 205 ARG cc_start: 0.6338 (mmm-85) cc_final: 0.5627 (ttm-80) REVERT: A 298 ARG cc_start: 0.5430 (ptp90) cc_final: 0.5014 (mtp180) REVERT: A 299 GLU cc_start: 0.5967 (mp0) cc_final: 0.5609 (tt0) REVERT: A 373 ASP cc_start: 0.7319 (t70) cc_final: 0.7005 (t0) REVERT: F 52 ASP cc_start: 0.7361 (t70) cc_final: 0.6576 (t70) REVERT: F 58 ASP cc_start: 0.7535 (p0) cc_final: 0.7334 (p0) REVERT: F 64 MET cc_start: 0.5583 (mmm) cc_final: 0.5299 (mmt) REVERT: F 202 ILE cc_start: 0.6059 (OUTLIER) cc_final: 0.5799 (tp) REVERT: F 247 LYS cc_start: 0.5741 (ttmt) cc_final: 0.5380 (tttt) REVERT: B 64 MET cc_start: 0.5885 (mmm) cc_final: 0.5285 (mmt) REVERT: B 227 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.6035 (t80) REVERT: B 234 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6182 (t80) REVERT: B 247 LYS cc_start: 0.5710 (ttmt) cc_final: 0.5231 (tttt) REVERT: J 202 ILE cc_start: 0.6148 (OUTLIER) cc_final: 0.5901 (tp) REVERT: J 227 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.6118 (t80) REVERT: J 234 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.6187 (t80) REVERT: J 247 LYS cc_start: 0.5795 (ttmt) cc_final: 0.5455 (ttmt) REVERT: G 16 GLU cc_start: 0.3685 (OUTLIER) cc_final: 0.3412 (pp20) REVERT: G 207 TRP cc_start: 0.3283 (OUTLIER) cc_final: 0.1463 (t60) REVERT: G 211 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.4489 (mp0) REVERT: C 184 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5616 (mp) REVERT: C 209 MET cc_start: 0.4477 (mmm) cc_final: 0.3548 (mmm) REVERT: K 184 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5450 (mp) REVERT: K 211 GLU cc_start: 0.4148 (OUTLIER) cc_final: 0.3240 (tm-30) REVERT: E 103 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8013 (mt-10) REVERT: E 141 GLU cc_start: 0.6587 (tp30) cc_final: 0.6336 (tp30) REVERT: E 205 ARG cc_start: 0.6295 (mmm-85) cc_final: 0.5659 (ttm-80) REVERT: E 298 ARG cc_start: 0.5547 (ptp90) cc_final: 0.5133 (mtp180) REVERT: E 373 ASP cc_start: 0.7334 (t70) cc_final: 0.6957 (t0) REVERT: E 413 LYS cc_start: 0.4570 (OUTLIER) cc_final: 0.4236 (tttp) REVERT: I 103 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7761 (pt0) REVERT: I 205 ARG cc_start: 0.6219 (mmm-85) cc_final: 0.5535 (ttm-80) REVERT: I 230 ARG cc_start: 0.5041 (mtm-85) cc_final: 0.4542 (mmt180) REVERT: I 298 ARG cc_start: 0.5654 (ptp90) cc_final: 0.5223 (mtp180) REVERT: I 299 GLU cc_start: 0.5978 (mp0) cc_final: 0.5681 (tt0) REVERT: I 373 ASP cc_start: 0.7413 (t70) cc_final: 0.7116 (t0) outliers start: 91 outliers final: 38 residues processed: 241 average time/residue: 0.6123 time to fit residues: 170.3724 Evaluate side-chains 205 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 234 PHE Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 207 TRP Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 240 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 174 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 125 optimal weight: 0.1980 chunk 24 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.185659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.148224 restraints weight = 22336.215| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.82 r_work: 0.3888 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22338 Z= 0.200 Angle : 0.650 9.384 30438 Z= 0.341 Chirality : 0.046 0.228 3297 Planarity : 0.005 0.075 3759 Dihedral : 11.886 145.339 3267 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.78 % Allowed : 23.37 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.41 (0.17), residues: 2601 helix: 0.80 (0.15), residues: 1248 sheet: -0.68 (0.28), residues: 351 loop : -1.45 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 211 TYR 0.021 0.002 TYR C 157 PHE 0.026 0.002 PHE J 227 TRP 0.018 0.001 TRP A 198 HIS 0.005 0.001 HIS F 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (22338) covalent geometry : angle 0.64973 / 0.34 (30438) hydrogen bonds : bond 0.04241 / 2.86 ( 1151) hydrogen bonds : angle 5.26419 / 3.69 ( 3276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 160 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.6486 (mmm160) cc_final: 0.5804 (ttm-80) REVERT: A 298 ARG cc_start: 0.5522 (ptp90) cc_final: 0.5065 (mtp180) REVERT: A 299 GLU cc_start: 0.6139 (mp0) cc_final: 0.5777 (tt0) REVERT: A 373 ASP cc_start: 0.7354 (t70) cc_final: 0.7004 (t0) REVERT: F 52 ASP cc_start: 0.7582 (t70) cc_final: 0.6887 (t70) REVERT: F 64 MET cc_start: 0.5664 (mmm) cc_final: 0.5345 (mmt) REVERT: F 202 ILE cc_start: 0.6147 (OUTLIER) cc_final: 0.5872 (tp) REVERT: F 247 LYS cc_start: 0.5821 (ttmt) cc_final: 0.5435 (tttt) REVERT: B 58 ASP cc_start: 0.7662 (p0) cc_final: 0.7387 (p0) REVERT: B 64 MET cc_start: 0.5979 (mmm) cc_final: 0.5309 (mmt) REVERT: B 234 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.6322 (t80) REVERT: B 247 LYS cc_start: 0.5818 (ttmt) cc_final: 0.5342 (tttt) REVERT: J 202 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5980 (tp) REVERT: J 204 MET cc_start: 0.6895 (ttm) cc_final: 0.6601 (ttm) REVERT: J 234 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6296 (t80) REVERT: J 247 LYS cc_start: 0.5849 (ttmt) cc_final: 0.5466 (ttmt) REVERT: G 16 GLU cc_start: 0.3688 (OUTLIER) cc_final: 0.3481 (pp20) REVERT: G 207 TRP cc_start: 0.3245 (OUTLIER) cc_final: 0.1509 (t60) REVERT: G 211 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.4492 (mp0) REVERT: C 209 MET cc_start: 0.4519 (mmm) cc_final: 0.3825 (mmm) REVERT: K 48 ARG cc_start: 0.6705 (ttm170) cc_final: 0.6415 (ttt180) REVERT: K 184 LEU cc_start: 0.5843 (OUTLIER) cc_final: 0.5557 (mp) REVERT: K 211 GLU cc_start: 0.4683 (OUTLIER) cc_final: 0.4136 (mp0) REVERT: E 103 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8025 (mt-10) REVERT: E 141 GLU cc_start: 0.6677 (tp30) cc_final: 0.6149 (tp30) REVERT: E 205 ARG cc_start: 0.6463 (mmm-85) cc_final: 0.5765 (ttm-80) REVERT: E 298 ARG cc_start: 0.5627 (ptp90) cc_final: 0.5088 (mtp180) REVERT: E 373 ASP cc_start: 0.7398 (t70) cc_final: 0.6998 (t0) REVERT: E 413 LYS cc_start: 0.4751 (OUTLIER) cc_final: 0.4403 (tttp) REVERT: I 141 GLU cc_start: 0.6698 (tp30) cc_final: 0.6084 (tp30) REVERT: I 170 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.6124 (p0) REVERT: I 205 ARG cc_start: 0.6377 (mmm160) cc_final: 0.5726 (ttm-80) REVERT: I 230 ARG cc_start: 0.5074 (mtm-85) cc_final: 0.4574 (mmt180) REVERT: I 298 ARG cc_start: 0.5689 (ptp90) cc_final: 0.5304 (mtp180) REVERT: I 299 GLU cc_start: 0.6075 (mp0) cc_final: 0.5784 (tt0) REVERT: I 373 ASP cc_start: 0.7450 (t70) cc_final: 0.7149 (t0) REVERT: I 383 ASP cc_start: 0.7758 (t0) cc_final: 0.7535 (t0) outliers start: 104 outliers final: 54 residues processed: 249 average time/residue: 0.5768 time to fit residues: 166.9655 Evaluate side-chains 213 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 148 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 137 ASP Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 234 PHE Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 207 TRP Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 240 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 chunk 232 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.186501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.149468 restraints weight = 22239.282| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.80 r_work: 0.3906 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22338 Z= 0.167 Angle : 0.616 9.211 30438 Z= 0.322 Chirality : 0.045 0.223 3297 Planarity : 0.005 0.068 3759 Dihedral : 11.485 148.253 3267 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.59 % Allowed : 23.60 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2601 helix: 0.92 (0.15), residues: 1233 sheet: -0.69 (0.28), residues: 351 loop : -1.52 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 211 TYR 0.022 0.001 TYR C 157 PHE 0.024 0.002 PHE J 227 TRP 0.018 0.001 TRP A 198 HIS 0.004 0.001 HIS I 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (22338) covalent geometry : angle 0.61593 / 0.32 (30438) hydrogen bonds : bond 0.04027 / 2.71 ( 1151) hydrogen bonds : angle 5.18208 / 3.63 ( 3276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 153 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.6397 (mmm160) cc_final: 0.5708 (ttm-80) REVERT: A 298 ARG cc_start: 0.5446 (ptp90) cc_final: 0.4977 (mtp180) REVERT: A 299 GLU cc_start: 0.6163 (mp0) cc_final: 0.5779 (tt0) REVERT: A 373 ASP cc_start: 0.7326 (t70) cc_final: 0.6972 (t0) REVERT: F 52 ASP cc_start: 0.7526 (t70) cc_final: 0.6818 (t70) REVERT: F 64 MET cc_start: 0.5569 (mmm) cc_final: 0.5335 (mmt) REVERT: F 202 ILE cc_start: 0.6072 (OUTLIER) cc_final: 0.5803 (tp) REVERT: F 230 MET cc_start: 0.7186 (mtt) cc_final: 0.6904 (mtp) REVERT: F 247 LYS cc_start: 0.5754 (ttmt) cc_final: 0.5386 (tttt) REVERT: B 58 ASP cc_start: 0.7545 (p0) cc_final: 0.7269 (p0) REVERT: B 64 MET cc_start: 0.5942 (mmm) cc_final: 0.5388 (mmt) REVERT: B 234 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.6265 (t80) REVERT: B 247 LYS cc_start: 0.5764 (ttmt) cc_final: 0.5292 (tttt) REVERT: J 202 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5883 (tp) REVERT: J 204 MET cc_start: 0.6823 (ttm) cc_final: 0.6562 (ttm) REVERT: J 234 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.6280 (t80) REVERT: J 247 LYS cc_start: 0.5723 (ttmt) cc_final: 0.5340 (ttmt) REVERT: G 211 GLU cc_start: 0.5594 (OUTLIER) cc_final: 0.4449 (mp0) REVERT: C 209 MET cc_start: 0.4440 (mmm) cc_final: 0.3838 (mmm) REVERT: K 48 ARG cc_start: 0.6679 (ttm170) cc_final: 0.6409 (ttt180) REVERT: K 184 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5448 (mp) REVERT: K 211 GLU cc_start: 0.4207 (OUTLIER) cc_final: 0.3782 (mp0) REVERT: E 103 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8014 (mt-10) REVERT: E 141 GLU cc_start: 0.6617 (tp30) cc_final: 0.6133 (tp30) REVERT: E 205 ARG cc_start: 0.6429 (mmm160) cc_final: 0.5733 (ttm-80) REVERT: E 298 ARG cc_start: 0.5497 (ptp90) cc_final: 0.4972 (mtp180) REVERT: E 373 ASP cc_start: 0.7371 (t70) cc_final: 0.6977 (t0) REVERT: E 413 LYS cc_start: 0.4639 (OUTLIER) cc_final: 0.4306 (tttp) REVERT: I 103 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7789 (pt0) REVERT: I 141 GLU cc_start: 0.6626 (tp30) cc_final: 0.6058 (tp30) REVERT: I 205 ARG cc_start: 0.6315 (mmm160) cc_final: 0.5767 (ttm-80) REVERT: I 230 ARG cc_start: 0.4958 (mtm-85) cc_final: 0.4507 (mmt180) REVERT: I 298 ARG cc_start: 0.5568 (ptp90) cc_final: 0.5176 (mtp180) REVERT: I 299 GLU cc_start: 0.6044 (mp0) cc_final: 0.5742 (tt0) REVERT: I 373 ASP cc_start: 0.7400 (t70) cc_final: 0.7103 (t0) REVERT: I 383 ASP cc_start: 0.7688 (t0) cc_final: 0.7172 (t0) outliers start: 100 outliers final: 58 residues processed: 241 average time/residue: 0.5671 time to fit residues: 159.3907 Evaluate side-chains 209 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 143 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 137 ASP Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 234 PHE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 240 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 48 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 49 optimal weight: 0.3980 chunk 216 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.187576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.150553 restraints weight = 22237.045| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.82 r_work: 0.3925 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22338 Z= 0.150 Angle : 0.617 9.679 30438 Z= 0.319 Chirality : 0.045 0.219 3297 Planarity : 0.005 0.069 3759 Dihedral : 11.191 152.095 3267 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.86 % Allowed : 24.47 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.29 (0.17), residues: 2601 helix: 0.99 (0.15), residues: 1233 sheet: -0.57 (0.27), residues: 378 loop : -1.52 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 211 TYR 0.022 0.001 TYR C 157 PHE 0.024 0.001 PHE J 227 TRP 0.018 0.001 TRP A 198 HIS 0.004 0.001 HIS J 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (22338) covalent geometry : angle 0.61708 / 0.32 (30438) hydrogen bonds : bond 0.03939 / 2.66 ( 1151) hydrogen bonds : angle 5.11006 / 3.58 ( 3276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 144 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.6431 (mmm160) cc_final: 0.5720 (ttm-80) REVERT: A 298 ARG cc_start: 0.5537 (ptp90) cc_final: 0.5066 (mtp180) REVERT: A 299 GLU cc_start: 0.6241 (mp0) cc_final: 0.5847 (tt0) REVERT: A 373 ASP cc_start: 0.7340 (t70) cc_final: 0.6973 (t0) REVERT: F 52 ASP cc_start: 0.7504 (t70) cc_final: 0.6791 (t70) REVERT: F 64 MET cc_start: 0.5638 (mmm) cc_final: 0.5389 (mmt) REVERT: F 202 ILE cc_start: 0.6086 (OUTLIER) cc_final: 0.5814 (tp) REVERT: F 230 MET cc_start: 0.7184 (mtt) cc_final: 0.6743 (mtt) REVERT: F 247 LYS cc_start: 0.5808 (ttmt) cc_final: 0.5449 (tttt) REVERT: B 58 ASP cc_start: 0.7518 (p0) cc_final: 0.7308 (p0) REVERT: B 64 MET cc_start: 0.6018 (mmm) cc_final: 0.5423 (mmt) REVERT: B 234 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.6259 (t80) REVERT: B 247 LYS cc_start: 0.5806 (ttmt) cc_final: 0.5320 (tttt) REVERT: J 137 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6309 (m-30) REVERT: J 202 ILE cc_start: 0.6137 (OUTLIER) cc_final: 0.5893 (tp) REVERT: J 204 MET cc_start: 0.6868 (ttm) cc_final: 0.6616 (ttm) REVERT: J 247 LYS cc_start: 0.5834 (ttmt) cc_final: 0.5452 (ttmt) REVERT: C 184 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5568 (mp) REVERT: C 209 MET cc_start: 0.4390 (mmm) cc_final: 0.3902 (mmm) REVERT: K 48 ARG cc_start: 0.6808 (ttm170) cc_final: 0.6588 (ptp-170) REVERT: K 184 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5560 (mp) REVERT: K 211 GLU cc_start: 0.4345 (OUTLIER) cc_final: 0.3903 (mp0) REVERT: E 103 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8009 (mt-10) REVERT: E 141 GLU cc_start: 0.6672 (tp30) cc_final: 0.6174 (tp30) REVERT: E 205 ARG cc_start: 0.6399 (mmm160) cc_final: 0.5709 (ttm-80) REVERT: E 298 ARG cc_start: 0.5576 (ptp90) cc_final: 0.4883 (mtp180) REVERT: E 373 ASP cc_start: 0.7392 (t70) cc_final: 0.6999 (t0) REVERT: I 141 GLU cc_start: 0.6696 (tp30) cc_final: 0.6156 (tp30) REVERT: I 205 ARG cc_start: 0.6344 (mmm160) cc_final: 0.5786 (ttm-80) REVERT: I 230 ARG cc_start: 0.5045 (mtm-85) cc_final: 0.4570 (mmt180) REVERT: I 298 ARG cc_start: 0.5667 (ptp90) cc_final: 0.5256 (mtp180) REVERT: I 299 GLU cc_start: 0.6088 (mp0) cc_final: 0.5802 (tt0) REVERT: I 373 ASP cc_start: 0.7412 (t70) cc_final: 0.7103 (t0) REVERT: I 383 ASP cc_start: 0.7480 (t0) cc_final: 0.7155 (t0) outliers start: 84 outliers final: 54 residues processed: 217 average time/residue: 0.5763 time to fit residues: 146.0685 Evaluate side-chains 201 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 140 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 137 ASP Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 162 optimal weight: 8.9990 chunk 243 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 103 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.179826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.142833 restraints weight = 22346.915| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.78 r_work: 0.3832 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 22338 Z= 0.293 Angle : 0.740 13.819 30438 Z= 0.382 Chirality : 0.050 0.241 3297 Planarity : 0.006 0.072 3759 Dihedral : 11.466 153.561 3263 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.45 % Allowed : 24.06 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.85 (0.16), residues: 2601 helix: 0.52 (0.15), residues: 1266 sheet: -1.19 (0.26), residues: 372 loop : -1.69 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 211 TYR 0.021 0.002 TYR G 157 PHE 0.029 0.003 PHE E 37 TRP 0.019 0.002 TRP A 198 HIS 0.007 0.001 HIS I 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.29 (22338) covalent geometry : angle 0.74020 / 0.38 (30438) hydrogen bonds : bond 0.04723 / 3.18 ( 1151) hydrogen bonds : angle 5.42703 / 3.80 ( 3276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 156 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.6590 (mmm160) cc_final: 0.5875 (ttm-80) REVERT: A 256 ARG cc_start: 0.6861 (mtp85) cc_final: 0.5694 (mtm110) REVERT: A 299 GLU cc_start: 0.6282 (mp0) cc_final: 0.5933 (tt0) REVERT: A 373 ASP cc_start: 0.7352 (t70) cc_final: 0.7044 (t0) REVERT: F 52 ASP cc_start: 0.7669 (t70) cc_final: 0.7204 (t70) REVERT: F 64 MET cc_start: 0.5669 (mmm) cc_final: 0.5249 (mmt) REVERT: F 202 ILE cc_start: 0.6138 (OUTLIER) cc_final: 0.5838 (tp) REVERT: F 247 LYS cc_start: 0.5800 (ttmt) cc_final: 0.5458 (tttt) REVERT: B 58 ASP cc_start: 0.7790 (p0) cc_final: 0.7549 (p0) REVERT: B 64 MET cc_start: 0.6203 (mmm) cc_final: 0.5428 (mmt) REVERT: B 234 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.6379 (t80) REVERT: B 247 LYS cc_start: 0.5836 (ttmt) cc_final: 0.5473 (tttt) REVERT: J 202 ILE cc_start: 0.6230 (OUTLIER) cc_final: 0.5967 (tp) REVERT: J 247 LYS cc_start: 0.5726 (ttmt) cc_final: 0.5296 (tttt) REVERT: G 134 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.7059 (mtm) REVERT: G 211 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.4322 (tm-30) REVERT: C 209 MET cc_start: 0.4354 (mmm) cc_final: 0.3845 (mmm) REVERT: K 184 LEU cc_start: 0.5881 (OUTLIER) cc_final: 0.5575 (mp) REVERT: E 141 GLU cc_start: 0.6603 (tp30) cc_final: 0.6235 (tp30) REVERT: E 205 ARG cc_start: 0.6615 (mmm160) cc_final: 0.5880 (ttm-80) REVERT: E 256 ARG cc_start: 0.6880 (mtp85) cc_final: 0.5691 (mtm110) REVERT: E 298 ARG cc_start: 0.5611 (ptp90) cc_final: 0.4936 (mtp180) REVERT: E 373 ASP cc_start: 0.7408 (t70) cc_final: 0.7012 (t0) REVERT: I 205 ARG cc_start: 0.6571 (mmm160) cc_final: 0.5970 (ttm-80) REVERT: I 230 ARG cc_start: 0.5068 (mtm-85) cc_final: 0.4591 (mmt180) REVERT: I 298 ARG cc_start: 0.5693 (ptp90) cc_final: 0.5332 (mtp180) REVERT: I 299 GLU cc_start: 0.6150 (mp0) cc_final: 0.5849 (tt0) REVERT: I 373 ASP cc_start: 0.7444 (t70) cc_final: 0.7142 (t0) REVERT: I 383 ASP cc_start: 0.7743 (t0) cc_final: 0.7445 (t0) outliers start: 97 outliers final: 62 residues processed: 239 average time/residue: 0.5578 time to fit residues: 155.9044 Evaluate side-chains 220 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 152 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 137 ASP Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 29 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 189 optimal weight: 0.6980 chunk 233 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.184835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.147974 restraints weight = 21985.794| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.79 r_work: 0.3892 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22338 Z= 0.164 Angle : 0.642 11.589 30438 Z= 0.331 Chirality : 0.045 0.216 3297 Planarity : 0.006 0.088 3759 Dihedral : 11.176 158.583 3260 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.63 % Allowed : 25.07 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.58 (0.16), residues: 2601 helix: 0.83 (0.15), residues: 1236 sheet: -0.87 (0.27), residues: 351 loop : -1.71 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 207 TYR 0.023 0.002 TYR C 157 PHE 0.025 0.001 PHE J 227 TRP 0.018 0.001 TRP A 198 HIS 0.004 0.001 HIS I 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (22338) covalent geometry : angle 0.64195 / 0.33 (30438) hydrogen bonds : bond 0.04064 / 2.75 ( 1151) hydrogen bonds : angle 5.21731 / 3.65 ( 3276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 146 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.6503 (mmm160) cc_final: 0.5773 (ttm-80) REVERT: A 256 ARG cc_start: 0.6801 (mtp85) cc_final: 0.5642 (mtm110) REVERT: A 299 GLU cc_start: 0.6221 (mp0) cc_final: 0.5866 (tt0) REVERT: A 373 ASP cc_start: 0.7335 (t70) cc_final: 0.7009 (t0) REVERT: F 52 ASP cc_start: 0.7595 (t70) cc_final: 0.7132 (t70) REVERT: F 64 MET cc_start: 0.5553 (mmm) cc_final: 0.5272 (mmt) REVERT: F 202 ILE cc_start: 0.6070 (OUTLIER) cc_final: 0.5806 (tp) REVERT: F 230 MET cc_start: 0.7145 (mtt) cc_final: 0.6867 (mtp) REVERT: F 247 LYS cc_start: 0.5699 (ttmt) cc_final: 0.5395 (tttt) REVERT: B 58 ASP cc_start: 0.7561 (p0) cc_final: 0.7263 (p0) REVERT: B 64 MET cc_start: 0.6100 (mmm) cc_final: 0.5440 (mmt) REVERT: B 234 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.6330 (t80) REVERT: B 247 LYS cc_start: 0.5751 (ttmt) cc_final: 0.5361 (tttt) REVERT: J 137 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6231 (m-30) REVERT: J 202 ILE cc_start: 0.6123 (OUTLIER) cc_final: 0.5837 (tp) REVERT: J 230 MET cc_start: 0.7179 (mmt) cc_final: 0.6966 (mmt) REVERT: J 247 LYS cc_start: 0.5683 (ttmt) cc_final: 0.5284 (tttt) REVERT: G 134 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6892 (mtm) REVERT: G 211 GLU cc_start: 0.5646 (OUTLIER) cc_final: 0.4232 (tm-30) REVERT: C 209 MET cc_start: 0.4152 (mmm) cc_final: 0.3860 (mmm) REVERT: K 184 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5522 (mp) REVERT: E 141 GLU cc_start: 0.6590 (tp30) cc_final: 0.6147 (tp30) REVERT: E 160 LYS cc_start: 0.6699 (mttm) cc_final: 0.6168 (mtpt) REVERT: E 205 ARG cc_start: 0.6487 (mmm160) cc_final: 0.5777 (ttm-80) REVERT: E 298 ARG cc_start: 0.5514 (ptp90) cc_final: 0.4833 (mtp180) REVERT: E 373 ASP cc_start: 0.7398 (t70) cc_final: 0.6993 (t0) REVERT: I 103 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7846 (pt0) REVERT: I 205 ARG cc_start: 0.6450 (mmm160) cc_final: 0.5858 (ttm-80) REVERT: I 230 ARG cc_start: 0.5037 (mtm-85) cc_final: 0.4556 (mmt180) REVERT: I 298 ARG cc_start: 0.5613 (ptp90) cc_final: 0.5268 (mtp180) REVERT: I 299 GLU cc_start: 0.6124 (mp0) cc_final: 0.5795 (tt0) REVERT: I 373 ASP cc_start: 0.7453 (t70) cc_final: 0.7151 (t0) REVERT: I 383 ASP cc_start: 0.7595 (t0) cc_final: 0.7316 (t0) outliers start: 79 outliers final: 58 residues processed: 214 average time/residue: 0.5454 time to fit residues: 136.2067 Evaluate side-chains 209 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 144 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 137 ASP Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 53 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 247 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.187819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.151132 restraints weight = 21841.369| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.79 r_work: 0.3930 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22338 Z= 0.137 Angle : 0.617 13.134 30438 Z= 0.317 Chirality : 0.044 0.216 3297 Planarity : 0.005 0.069 3759 Dihedral : 10.896 166.167 3260 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.80 % Allowed : 26.12 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.35 (0.17), residues: 2601 helix: 1.01 (0.15), residues: 1236 sheet: -0.65 (0.26), residues: 378 loop : -1.64 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.022 0.001 TYR C 157 PHE 0.023 0.001 PHE J 227 TRP 0.017 0.001 TRP A 198 HIS 0.003 0.001 HIS I 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (22338) covalent geometry : angle 0.61653 / 0.32 (30438) hydrogen bonds : bond 0.03829 / 2.59 ( 1151) hydrogen bonds : angle 5.08553 / 3.56 ( 3276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 145 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.6703 (mmm160) cc_final: 0.5938 (ttm-80) REVERT: A 256 ARG cc_start: 0.6936 (mtp85) cc_final: 0.5783 (mtm110) REVERT: A 299 GLU cc_start: 0.6444 (mp0) cc_final: 0.6066 (tt0) REVERT: A 373 ASP cc_start: 0.7523 (t70) cc_final: 0.7149 (t0) REVERT: F 52 ASP cc_start: 0.7714 (t70) cc_final: 0.7039 (t70) REVERT: F 64 MET cc_start: 0.5933 (mmm) cc_final: 0.5649 (mmt) REVERT: F 202 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.6048 (tp) REVERT: F 230 MET cc_start: 0.7292 (mtt) cc_final: 0.6990 (mtp) REVERT: F 247 LYS cc_start: 0.6046 (ttmt) cc_final: 0.5660 (tttt) REVERT: B 58 ASP cc_start: 0.7589 (p0) cc_final: 0.7384 (p0) REVERT: B 64 MET cc_start: 0.6484 (mmm) cc_final: 0.5781 (mmt) REVERT: B 234 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6537 (t80) REVERT: B 247 LYS cc_start: 0.6074 (ttmt) cc_final: 0.5646 (tttt) REVERT: J 137 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6278 (m-30) REVERT: J 202 ILE cc_start: 0.6395 (OUTLIER) cc_final: 0.6162 (tp) REVERT: J 204 MET cc_start: 0.7111 (ttm) cc_final: 0.6849 (ttm) REVERT: J 247 LYS cc_start: 0.6057 (ttmt) cc_final: 0.5701 (ttmt) REVERT: G 211 GLU cc_start: 0.5624 (OUTLIER) cc_final: 0.4586 (mp0) REVERT: K 184 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5883 (mp) REVERT: E 141 GLU cc_start: 0.6918 (tp30) cc_final: 0.6452 (tp30) REVERT: E 205 ARG cc_start: 0.6700 (mmm160) cc_final: 0.5922 (ttm-80) REVERT: E 298 ARG cc_start: 0.5875 (ptp90) cc_final: 0.5163 (mtp180) REVERT: E 373 ASP cc_start: 0.7550 (t70) cc_final: 0.7125 (t0) REVERT: I 103 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7950 (pt0) REVERT: I 205 ARG cc_start: 0.6599 (mmm160) cc_final: 0.5978 (ttm-80) REVERT: I 230 ARG cc_start: 0.5304 (mtm-85) cc_final: 0.4720 (mmt180) REVERT: I 298 ARG cc_start: 0.5962 (ptp90) cc_final: 0.5589 (mtp180) REVERT: I 299 GLU cc_start: 0.6352 (mp0) cc_final: 0.6040 (tt0) REVERT: I 373 ASP cc_start: 0.7628 (t70) cc_final: 0.7294 (t0) REVERT: I 383 ASP cc_start: 0.7654 (t0) cc_final: 0.7429 (t0) outliers start: 61 outliers final: 48 residues processed: 198 average time/residue: 0.6092 time to fit residues: 139.9154 Evaluate side-chains 192 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 138 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 137 ASP Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain K residue 47 TRP Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 21 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 238 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.180473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.143694 restraints weight = 22362.836| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.78 r_work: 0.3844 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 22338 Z= 0.268 Angle : 0.723 17.431 30438 Z= 0.372 Chirality : 0.049 0.237 3297 Planarity : 0.006 0.072 3759 Dihedral : 11.101 165.641 3259 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.12 % Allowed : 25.94 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.16), residues: 2601 helix: 0.68 (0.15), residues: 1251 sheet: -1.06 (0.27), residues: 360 loop : -1.72 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 203 TYR 0.021 0.002 TYR G 157 PHE 0.026 0.002 PHE J 227 TRP 0.021 0.002 TRP J 236 HIS 0.006 0.001 HIS I 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.27 (22338) covalent geometry : angle 0.72300 / 0.37 (30438) hydrogen bonds : bond 0.04534 / 3.05 ( 1151) hydrogen bonds : angle 5.35328 / 3.75 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7165.38 seconds wall clock time: 123 minutes 22.26 seconds (7402.26 seconds total)