Starting phenix.real_space_refine on Fri Mar 6 20:28:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lex_23293/03_2026/7lex_23293.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lex_23293/03_2026/7lex_23293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lex_23293/03_2026/7lex_23293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lex_23293/03_2026/7lex_23293.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lex_23293/03_2026/7lex_23293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lex_23293/03_2026/7lex_23293.map" } resolution = 3.6 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= 0.053 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 21822 2.51 5 N 5856 2.21 5 O 6792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34596 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "D" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1717 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Restraints were copied for chains: B, C, J, M, N, F, G, K, Q, R, H, I, L, O, P Time building chain proxies: 4.51, per 1000 atoms: 0.13 Number of scatterers: 34596 At special positions: 0 Unit cell: (121.68, 115.44, 246.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 6792 8.00 N 5856 7.00 C 21822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 207 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 152 " - pdb=" SG CYS Q 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 152 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 194 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 194 " distance=2.03 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: 2.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8280 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 72 sheets defined 20.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.737A pdb=" N VAL A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.811A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 103 through 113 removed outlier: 4.059A pdb=" N HIS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.610A pdb=" N PHE A 147 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 200 through 221 removed outlier: 7.068A pdb=" N ILE A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N GLY A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 285 through 304 removed outlier: 3.554A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.057A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 183 through 189 removed outlier: 4.177A pdb=" N HIS E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.737A pdb=" N VAL B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 69 through 90 removed outlier: 3.809A pdb=" N VAL B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 103 through 113 removed outlier: 4.060A pdb=" N HIS B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.611A pdb=" N PHE B 147 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 200 through 221 removed outlier: 7.068A pdb=" N ILE B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLY B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 285 through 304 removed outlier: 3.553A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 25 No H-bonds generated for 'chain 'C' and resid 23 through 25' Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.735A pdb=" N VAL C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 69 through 90 removed outlier: 3.810A pdb=" N VAL C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 113 removed outlier: 4.060A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.610A pdb=" N PHE C 147 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 200 through 221 removed outlier: 7.068A pdb=" N ILE C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLY C 209 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 285 through 304 removed outlier: 3.554A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.057A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 183 through 189 removed outlier: 4.177A pdb=" N HIS H 189 " --> pdb=" O GLU H 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.058A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 126 Processing helix chain 'I' and resid 183 through 189 removed outlier: 4.176A pdb=" N HIS I 189 " --> pdb=" O GLU I 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 34 removed outlier: 3.736A pdb=" N VAL J 30 " --> pdb=" O GLU J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 41 Processing helix chain 'J' and resid 69 through 90 removed outlier: 3.810A pdb=" N VAL J 73 " --> pdb=" O ASN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 102 No H-bonds generated for 'chain 'J' and resid 100 through 102' Processing helix chain 'J' and resid 103 through 113 removed outlier: 4.060A pdb=" N HIS J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 148 removed outlier: 3.611A pdb=" N PHE J 147 " --> pdb=" O PRO J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing helix chain 'J' and resid 183 through 193 Processing helix chain 'J' and resid 200 through 221 removed outlier: 7.068A pdb=" N ILE J 208 " --> pdb=" O ASP J 204 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLY J 209 " --> pdb=" O ARG J 205 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS J 210 " --> pdb=" O LEU J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 266 Processing helix chain 'J' and resid 285 through 304 removed outlier: 3.554A pdb=" N VAL J 289 " --> pdb=" O THR J 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.057A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 189 removed outlier: 4.177A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 25 No H-bonds generated for 'chain 'M' and resid 23 through 25' Processing helix chain 'M' and resid 26 through 34 removed outlier: 3.737A pdb=" N VAL M 30 " --> pdb=" O GLU M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 41 Processing helix chain 'M' and resid 69 through 90 removed outlier: 3.810A pdb=" N VAL M 73 " --> pdb=" O ASN M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 103 through 113 removed outlier: 4.060A pdb=" N HIS M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 148 removed outlier: 3.610A pdb=" N PHE M 147 " --> pdb=" O PRO M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 153 Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 183 through 193 Processing helix chain 'M' and resid 200 through 221 removed outlier: 7.068A pdb=" N ILE M 208 " --> pdb=" O ASP M 204 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N GLY M 209 " --> pdb=" O ARG M 205 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS M 210 " --> pdb=" O LEU M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 266 Processing helix chain 'M' and resid 285 through 304 removed outlier: 3.556A pdb=" N VAL M 289 " --> pdb=" O THR M 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 25 No H-bonds generated for 'chain 'N' and resid 23 through 25' Processing helix chain 'N' and resid 26 through 34 removed outlier: 3.737A pdb=" N VAL N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 41 Processing helix chain 'N' and resid 69 through 90 removed outlier: 3.809A pdb=" N VAL N 73 " --> pdb=" O ASN N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 102 No H-bonds generated for 'chain 'N' and resid 100 through 102' Processing helix chain 'N' and resid 103 through 113 removed outlier: 4.059A pdb=" N HIS N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 148 removed outlier: 3.611A pdb=" N PHE N 147 " --> pdb=" O PRO N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 153 Processing helix chain 'N' and resid 170 through 172 No H-bonds generated for 'chain 'N' and resid 170 through 172' Processing helix chain 'N' and resid 183 through 193 Processing helix chain 'N' and resid 200 through 221 removed outlier: 7.069A pdb=" N ILE N 208 " --> pdb=" O ASP N 204 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLY N 209 " --> pdb=" O ARG N 205 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS N 210 " --> pdb=" O LEU N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 266 Processing helix chain 'N' and resid 285 through 304 removed outlier: 3.553A pdb=" N VAL N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 4.056A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 126 Processing helix chain 'O' and resid 183 through 189 removed outlier: 4.177A pdb=" N HIS O 189 " --> pdb=" O GLU O 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.057A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 126 Processing helix chain 'P' and resid 183 through 189 removed outlier: 4.177A pdb=" N HIS P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.891A pdb=" N ILE A 8 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 94 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 227 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 273 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE A 275 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE A 198 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR A 176 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.688A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET D 81 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 46 through 50 removed outlier: 5.959A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.682A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.682A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 166 removed outlier: 3.587A pdb=" N THR D 165 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS D 207 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 21 through 24 removed outlier: 3.682A pdb=" N LEU E 73 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 48 removed outlier: 3.728A pdb=" N ARG E 45 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.594A pdb=" N ASN E 137 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 153 through 154 removed outlier: 3.601A pdb=" N ASN E 145 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS E 149 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.891A pdb=" N ILE B 8 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 94 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 227 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B 273 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU B 229 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE B 275 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE B 231 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE B 198 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR B 176 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.891A pdb=" N ILE C 8 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 94 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE C 227 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU C 273 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE C 275 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE C 231 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N PHE C 198 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR C 176 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'H' and resid 21 through 24 removed outlier: 3.682A pdb=" N LEU H 73 " --> pdb=" O LEU H 21 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 45 through 48 removed outlier: 3.729A pdb=" N ARG H 45 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.594A pdb=" N ASN H 137 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 153 through 154 removed outlier: 3.603A pdb=" N ASN H 145 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS H 149 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR H 193 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'I' and resid 21 through 24 removed outlier: 3.682A pdb=" N LEU I 73 " --> pdb=" O LEU I 21 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 45 through 48 removed outlier: 3.728A pdb=" N ARG I 45 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.594A pdb=" N ASN I 137 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 153 through 154 removed outlier: 3.602A pdb=" N ASN I 145 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS I 149 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR I 193 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 48 through 49 removed outlier: 6.891A pdb=" N ILE J 8 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER J 94 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE J 227 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU J 273 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU J 229 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE J 275 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE J 231 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY J 119 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER J 230 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE J 121 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP J 232 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL J 123 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE J 198 " --> pdb=" O ILE J 174 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR J 176 " --> pdb=" O PHE J 198 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'L' and resid 21 through 24 removed outlier: 3.683A pdb=" N LEU L 73 " --> pdb=" O LEU L 21 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 45 through 48 removed outlier: 3.730A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.594A pdb=" N ASN L 137 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.602A pdb=" N ASN L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS L 149 " --> pdb=" O THR L 193 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR L 193 " --> pdb=" O LYS L 149 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 48 through 49 removed outlier: 6.892A pdb=" N ILE M 8 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER M 94 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE M 227 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU M 273 " --> pdb=" O ILE M 227 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU M 229 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE M 275 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE M 231 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY M 119 " --> pdb=" O HIS M 228 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER M 230 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE M 121 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP M 232 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL M 123 " --> pdb=" O ASP M 232 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE M 198 " --> pdb=" O ILE M 174 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR M 176 " --> pdb=" O PHE M 198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 48 through 49 removed outlier: 6.891A pdb=" N ILE N 8 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER N 94 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE N 227 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU N 273 " --> pdb=" O ILE N 227 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU N 229 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE N 275 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE N 231 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY N 119 " --> pdb=" O HIS N 228 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER N 230 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE N 121 " --> pdb=" O SER N 230 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP N 232 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL N 123 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE N 198 " --> pdb=" O ILE N 174 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR N 176 " --> pdb=" O PHE N 198 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'O' and resid 21 through 24 removed outlier: 3.682A pdb=" N LEU O 73 " --> pdb=" O LEU O 21 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 45 through 48 removed outlier: 3.729A pdb=" N ARG O 45 " --> pdb=" O GLN O 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 114 through 118 removed outlier: 3.594A pdb=" N ASN O 137 " --> pdb=" O THR O 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL O 133 " --> pdb=" O PHE O 118 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR O 173 " --> pdb=" O ASN O 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 153 through 154 removed outlier: 3.603A pdb=" N ASN O 145 " --> pdb=" O THR O 197 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS O 149 " --> pdb=" O THR O 193 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR O 193 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'P' and resid 21 through 24 removed outlier: 3.682A pdb=" N LEU P 73 " --> pdb=" O LEU P 21 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 45 through 48 removed outlier: 3.727A pdb=" N ARG P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 114 through 118 removed outlier: 3.595A pdb=" N ASN P 137 " --> pdb=" O THR P 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL P 133 " --> pdb=" O PHE P 118 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR P 173 " --> pdb=" O ASN P 138 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 153 through 154 removed outlier: 3.601A pdb=" N ASN P 145 " --> pdb=" O THR P 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS P 149 " --> pdb=" O THR P 193 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR P 193 " --> pdb=" O LYS P 149 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.689A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET F 81 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 46 through 50 removed outlier: 5.959A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AF1, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.684A pdb=" N SER F 192 " --> pdb=" O CYS F 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR F 188 " --> pdb=" O GLY F 156 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.684A pdb=" N SER F 192 " --> pdb=" O CYS F 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR F 188 " --> pdb=" O GLY F 156 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 163 through 166 removed outlier: 3.587A pdb=" N THR F 165 " --> pdb=" O ASN F 208 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS F 207 " --> pdb=" O LYS F 220 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.689A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET G 81 " --> pdb=" O VAL G 20 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 46 through 50 removed outlier: 5.958A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AF7, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.684A pdb=" N SER G 192 " --> pdb=" O CYS G 152 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.684A pdb=" N SER G 192 " --> pdb=" O CYS G 152 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 163 through 166 removed outlier: 3.587A pdb=" N THR G 165 " --> pdb=" O ASN G 208 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.689A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET K 81 " --> pdb=" O VAL K 20 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 46 through 50 removed outlier: 5.957A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 92 through 93 Processing sheet with id=AG4, first strand: chain 'K' and resid 132 through 133 removed outlier: 3.683A pdb=" N SER K 192 " --> pdb=" O CYS K 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR K 188 " --> pdb=" O GLY K 156 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 132 through 133 removed outlier: 3.683A pdb=" N SER K 192 " --> pdb=" O CYS K 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR K 188 " --> pdb=" O GLY K 156 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 163 through 166 removed outlier: 3.586A pdb=" N THR K 165 " --> pdb=" O ASN K 208 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS K 207 " --> pdb=" O LYS K 220 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.689A pdb=" N SER Q 25 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET Q 81 " --> pdb=" O VAL Q 20 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 46 through 50 removed outlier: 5.959A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 92 through 93 Processing sheet with id=AH1, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.681A pdb=" N SER Q 192 " --> pdb=" O CYS Q 152 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.681A pdb=" N SER Q 192 " --> pdb=" O CYS Q 152 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 163 through 166 removed outlier: 3.587A pdb=" N THR Q 165 " --> pdb=" O ASN Q 208 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS Q 207 " --> pdb=" O LYS Q 220 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'R' and resid 3 through 7 removed outlier: 3.688A pdb=" N SER R 25 " --> pdb=" O GLN R 3 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET R 81 " --> pdb=" O VAL R 20 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 46 through 50 removed outlier: 5.958A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 92 through 93 Processing sheet with id=AH7, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.682A pdb=" N SER R 192 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.682A pdb=" N SER R 192 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 163 through 166 removed outlier: 3.587A pdb=" N THR R 165 " --> pdb=" O ASN R 208 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS R 207 " --> pdb=" O LYS R 220 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 2952 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: 6.69 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 14694 1.43 - 1.63: 20508 1.63 - 1.84: 174 1.84 - 2.04: 0 2.04 - 2.25: 6 Bond restraints: 35382 Sorted by residual: bond pdb=" C LYS P 107 " pdb=" N ARG P 108 " ideal model delta sigma weight residual 1.331 2.246 -0.916 1.39e-02 5.18e+03 4.34e+03 bond pdb=" C LYS I 107 " pdb=" N ARG I 108 " ideal model delta sigma weight residual 1.331 2.246 -0.916 1.39e-02 5.18e+03 4.34e+03 bond pdb=" C LYS O 107 " pdb=" N ARG O 108 " ideal model delta sigma weight residual 1.331 2.246 -0.915 1.39e-02 5.18e+03 4.34e+03 bond pdb=" C LYS L 107 " pdb=" N ARG L 108 " ideal model delta sigma weight residual 1.331 2.245 -0.915 1.39e-02 5.18e+03 4.33e+03 bond pdb=" C LYS H 107 " pdb=" N ARG H 108 " ideal model delta sigma weight residual 1.331 2.245 -0.915 1.39e-02 5.18e+03 4.33e+03 ... (remaining 35377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 47157 3.05 - 6.10: 819 6.10 - 9.15: 150 9.15 - 12.20: 12 12.20 - 15.24: 6 Bond angle restraints: 48144 Sorted by residual: angle pdb=" C GLN R 65 " pdb=" N GLY R 66 " pdb=" CA GLY R 66 " ideal model delta sigma weight residual 121.70 130.27 -8.57 1.80e+00 3.09e-01 2.27e+01 angle pdb=" C GLN Q 65 " pdb=" N GLY Q 66 " pdb=" CA GLY Q 66 " ideal model delta sigma weight residual 121.70 130.24 -8.54 1.80e+00 3.09e-01 2.25e+01 angle pdb=" C GLN G 65 " pdb=" N GLY G 66 " pdb=" CA GLY G 66 " ideal model delta sigma weight residual 121.70 130.22 -8.52 1.80e+00 3.09e-01 2.24e+01 angle pdb=" C GLN K 65 " pdb=" N GLY K 66 " pdb=" CA GLY K 66 " ideal model delta sigma weight residual 121.70 130.15 -8.45 1.80e+00 3.09e-01 2.20e+01 angle pdb=" C GLN F 65 " pdb=" N GLY F 66 " pdb=" CA GLY F 66 " ideal model delta sigma weight residual 121.70 130.14 -8.44 1.80e+00 3.09e-01 2.20e+01 ... (remaining 48139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.01: 19314 12.01 - 24.02: 1387 24.02 - 36.03: 347 36.03 - 48.05: 96 48.05 - 60.06: 12 Dihedral angle restraints: 21156 sinusoidal: 8172 harmonic: 12984 Sorted by residual: dihedral pdb=" CA LYS G 13 " pdb=" C LYS G 13 " pdb=" N PRO G 14 " pdb=" CA PRO G 14 " ideal model delta harmonic sigma weight residual 180.00 134.49 45.51 0 5.00e+00 4.00e-02 8.28e+01 dihedral pdb=" CA LYS K 13 " pdb=" C LYS K 13 " pdb=" N PRO K 14 " pdb=" CA PRO K 14 " ideal model delta harmonic sigma weight residual 180.00 134.50 45.50 0 5.00e+00 4.00e-02 8.28e+01 dihedral pdb=" CA LYS D 13 " pdb=" C LYS D 13 " pdb=" N PRO D 14 " pdb=" CA PRO D 14 " ideal model delta harmonic sigma weight residual 180.00 134.53 45.47 0 5.00e+00 4.00e-02 8.27e+01 ... (remaining 21153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3382 0.043 - 0.086: 1317 0.086 - 0.129: 595 0.129 - 0.171: 141 0.171 - 0.214: 43 Chirality restraints: 5478 Sorted by residual: chirality pdb=" CA TYR P 49 " pdb=" N TYR P 49 " pdb=" C TYR P 49 " pdb=" CB TYR P 49 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA TYR E 49 " pdb=" N TYR E 49 " pdb=" C TYR E 49 " pdb=" CB TYR E 49 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA TYR O 49 " pdb=" N TYR O 49 " pdb=" C TYR O 49 " pdb=" CB TYR O 49 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 5475 not shown) Planarity restraints: 6168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Q 13 " -0.078 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO Q 14 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO Q 14 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO Q 14 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS R 13 " 0.078 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO R 14 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO R 14 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO R 14 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 13 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO G 14 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO G 14 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO G 14 " -0.065 5.00e-02 4.00e+02 ... (remaining 6165 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 8773 2.80 - 3.32: 31061 3.32 - 3.85: 61102 3.85 - 4.37: 70092 4.37 - 4.90: 117972 Nonbonded interactions: 289000 Sorted by model distance: nonbonded pdb=" O ARG M 32 " pdb=" OG SER Q 75 " model vdw 2.269 3.040 nonbonded pdb=" O ARG B 32 " pdb=" OG SER F 75 " model vdw 2.269 3.040 nonbonded pdb=" O ALA Q 101 " pdb=" OG SER Q 106 " model vdw 2.276 3.040 nonbonded pdb=" O ALA R 101 " pdb=" OG SER R 106 " model vdw 2.276 3.040 nonbonded pdb=" O ALA F 101 " pdb=" OG SER F 106 " model vdw 2.276 3.040 ... (remaining 288995 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'P' } 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 group one per residue 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: 3.120 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: 0.040 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.810 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5446 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 : 0.013 0.916 35406 Z= 0.899 Angle : 1.032 15.244 48192 Z= 0.553 Chirality : 0.057 0.214 5478 Planarity : 0.009 0.120 6168 Dihedral : 9.442 60.058 12804 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.70 % Favored : 90.40 % Rotamer: Outliers : 0.31 % Allowed : 3.12 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 2.13 % Twisted General : 0.57 % 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: -4.14 (0.11), residues: 4470 helix: -2.46 (0.13), residues: 786 sheet: -2.91 (0.13), residues: 1350 loop : -2.72 (0.11), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 180 TYR 0.044 0.003 TYR L 49 PHE 0.051 0.004 PHE E 71 TRP 0.031 0.004 TRP Q 115 HIS 0.013 0.003 HIS R 109 Details of bonding type rmsd covalent geometry : bond 0.01344 (35382) covalent geometry : angle 1.03186 (48144) SS BOND : bond 0.00257 ( 24) SS BOND : angle 1.20897 ( 48) hydrogen bonds : bond 0.22370 ( 1050) hydrogen bonds : angle 10.50240 ( 2952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 367 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.5829 (m-30) cc_final: 0.4927 (p0) REVERT: P 187 GLU cc_start: 0.0354 (mm-30) cc_final: -0.0350 (mm-30) REVERT: G 168 SER cc_start: 0.6787 (m) cc_final: 0.6584 (p) REVERT: R 73 ASP cc_start: 0.7681 (t70) cc_final: 0.6919 (t70) outliers start: 12 outliers final: 3 residues processed: 375 average time/residue: 0.2688 time to fit residues: 149.6615 Evaluate side-chains 148 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 83 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 40.0000 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 40.0000 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 30.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 319 ASN D 6 GLN D 31 ASN D 39 GLN D 59 ASN D 110 ASN D 183 GLN E 38 GLN E 89 GLN ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS B 319 ASN C 141 HIS C 319 ASN H 38 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** I 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS J 141 HIS J 319 ASN L 137 ASN L 138 ASN M 126 HIS M 141 HIS ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 HIS N 141 HIS N 319 ASN O 90 GLN O 137 ASN P 137 ASN F 6 GLN F 31 ASN F 39 GLN F 59 ASN G 6 GLN G 31 ASN G 39 GLN G 59 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN Q 6 GLN Q 31 ASN Q 109 HIS R 6 GLN R 31 ASN R 59 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.085074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.061358 restraints weight = 290398.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.063190 restraints weight = 120554.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.063251 restraints weight = 60048.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.063681 restraints weight = 43104.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.063591 restraints weight = 42119.119| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 35406 Z= 0.257 Angle : 0.819 10.436 48192 Z= 0.413 Chirality : 0.047 0.214 5478 Planarity : 0.007 0.121 6168 Dihedral : 7.118 45.625 4884 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.95 % Favored : 89.78 % Rotamer: Outliers : 1.74 % Allowed : 6.34 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 2.13 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.12), residues: 4482 helix: -0.36 (0.17), residues: 810 sheet: -2.34 (0.13), residues: 1314 loop : -2.21 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 71 TYR 0.032 0.002 TYR H 49 PHE 0.022 0.002 PHE N 64 TRP 0.046 0.002 TRP O 163 HIS 0.010 0.002 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00569 (35382) covalent geometry : angle 0.81864 (48144) SS BOND : bond 0.00354 ( 24) SS BOND : angle 0.99151 ( 48) hydrogen bonds : bond 0.03674 ( 1050) hydrogen bonds : angle 6.60675 ( 2952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 159 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.7336 (t0) cc_final: 0.6503 (t0) REVERT: E 183 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7643 (tppt) REVERT: B 212 MET cc_start: 0.9329 (tpt) cc_final: 0.9128 (tpt) REVERT: C 212 MET cc_start: 0.9349 (mmm) cc_final: 0.9013 (mmm) REVERT: C 276 MET cc_start: 0.8989 (mmm) cc_final: 0.8644 (mmm) REVERT: I 175 MET cc_start: 0.7439 (tmm) cc_final: 0.7207 (tmm) REVERT: J 158 ASP cc_start: 0.8703 (m-30) cc_final: 0.8418 (p0) REVERT: L 38 GLN cc_start: 0.8581 (tt0) cc_final: 0.8104 (tp-100) REVERT: L 58 ILE cc_start: 0.3726 (OUTLIER) cc_final: 0.3115 (mp) REVERT: N 101 HIS cc_start: 0.3736 (OUTLIER) cc_final: 0.3046 (m170) REVERT: P 54 ARG cc_start: 0.5812 (mmp80) cc_final: 0.5322 (mmp80) REVERT: P 58 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6619 (tp) REVERT: F 48 MET cc_start: 0.9019 (ptp) cc_final: 0.8591 (ptp) REVERT: F 81 MET cc_start: 0.8830 (tmm) cc_final: 0.8575 (tmm) REVERT: G 48 MET cc_start: 0.9075 (ptm) cc_final: 0.8658 (ppp) REVERT: K 46 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9306 (tm-30) REVERT: K 48 MET cc_start: 0.6768 (ptt) cc_final: 0.6530 (ptt) REVERT: K 68 VAL cc_start: 0.5405 (OUTLIER) cc_final: 0.4988 (p) REVERT: Q 48 MET cc_start: 0.6396 (ptt) cc_final: 0.5888 (ptt) REVERT: R 48 MET cc_start: 0.6374 (ptt) cc_final: 0.6082 (ptt) outliers start: 67 outliers final: 21 residues processed: 224 average time/residue: 0.2176 time to fit residues: 78.9543 Evaluate side-chains 143 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 65 optimal weight: 3.9990 chunk 398 optimal weight: 40.0000 chunk 411 optimal weight: 30.0000 chunk 431 optimal weight: 30.0000 chunk 124 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 312 optimal weight: 4.9990 chunk 300 optimal weight: 8.9990 chunk 395 optimal weight: 20.0000 chunk 420 optimal weight: 20.0000 chunk 376 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN D 39 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN H 212 ASN I 137 ASN I 212 ASN J 90 ASN M 90 ASN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 39 GLN G 109 HIS K 6 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.084744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.060794 restraints weight = 292380.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.062330 restraints weight = 109880.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.063172 restraints weight = 55380.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.063678 restraints weight = 33167.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.063938 restraints weight = 23077.965| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35406 Z= 0.196 Angle : 0.740 11.363 48192 Z= 0.369 Chirality : 0.046 0.179 5478 Planarity : 0.006 0.124 6168 Dihedral : 6.639 44.388 4884 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.91 % Favored : 89.89 % Rotamer: Outliers : 1.59 % Allowed : 7.31 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 2.13 % 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: -2.42 (0.12), residues: 4482 helix: 0.37 (0.18), residues: 810 sheet: -2.14 (0.13), residues: 1314 loop : -1.98 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 24 TYR 0.030 0.002 TYR H 49 PHE 0.046 0.002 PHE C 64 TRP 0.019 0.002 TRP Q 50 HIS 0.007 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00441 (35382) covalent geometry : angle 0.73957 (48144) SS BOND : bond 0.00287 ( 24) SS BOND : angle 0.77669 ( 48) hydrogen bonds : bond 0.03093 ( 1050) hydrogen bonds : angle 5.93231 ( 2952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.8977 (mmm) cc_final: 0.8758 (mmm) REVERT: E 183 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7080 (mmmt) REVERT: B 212 MET cc_start: 0.9357 (tpt) cc_final: 0.9051 (tpt) REVERT: B 276 MET cc_start: 0.8671 (mmm) cc_final: 0.8333 (mmm) REVERT: H 11 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8840 (tt) REVERT: I 102 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7794 (p) REVERT: J 158 ASP cc_start: 0.8703 (m-30) cc_final: 0.8436 (p0) REVERT: N 101 HIS cc_start: 0.3701 (OUTLIER) cc_final: 0.2742 (m170) REVERT: O 75 ILE cc_start: 0.5856 (OUTLIER) cc_final: 0.5422 (tp) REVERT: P 58 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6904 (tp) REVERT: F 48 MET cc_start: 0.8983 (ptp) cc_final: 0.8536 (ptp) REVERT: F 81 MET cc_start: 0.8832 (tmm) cc_final: 0.8570 (tmm) REVERT: K 13 LYS cc_start: 0.9194 (mmtm) cc_final: 0.8976 (mmtt) REVERT: R 48 MET cc_start: 0.6746 (ptt) cc_final: 0.6478 (ptt) outliers start: 61 outliers final: 28 residues processed: 185 average time/residue: 0.2074 time to fit residues: 62.3094 Evaluate side-chains 144 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain P residue 165 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 89 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 314 optimal weight: 0.6980 chunk 415 optimal weight: 50.0000 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 232 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN E 156 GLN B 126 HIS J 101 HIS N 143 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 HIS Q 183 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.084738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.060673 restraints weight = 290211.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.062236 restraints weight = 108967.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.063079 restraints weight = 54815.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.063593 restraints weight = 32956.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.063789 restraints weight = 22946.044| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35406 Z= 0.162 Angle : 0.700 10.750 48192 Z= 0.349 Chirality : 0.045 0.178 5478 Planarity : 0.006 0.112 6168 Dihedral : 6.338 49.310 4884 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.22 % Favored : 89.69 % Rotamer: Outliers : 1.72 % Allowed : 8.14 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 2.13 % 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: -2.15 (0.13), residues: 4482 helix: 0.76 (0.19), residues: 804 sheet: -2.02 (0.13), residues: 1398 loop : -1.81 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 108 TYR 0.029 0.002 TYR E 49 PHE 0.024 0.002 PHE C 64 TRP 0.018 0.002 TRP Q 50 HIS 0.006 0.001 HIS E 91 Details of bonding type rmsd covalent geometry : bond 0.00370 (35382) covalent geometry : angle 0.70029 (48144) SS BOND : bond 0.00276 ( 24) SS BOND : angle 0.71468 ( 48) hydrogen bonds : bond 0.02754 ( 1050) hydrogen bonds : angle 5.51355 ( 2952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 122 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.7419 (t0) cc_final: 0.6809 (t0) REVERT: D 81 MET cc_start: 0.9332 (tmm) cc_final: 0.8916 (tmm) REVERT: D 187 TYR cc_start: 0.8924 (m-80) cc_final: 0.8390 (m-80) REVERT: B 212 MET cc_start: 0.9347 (tpt) cc_final: 0.9059 (tpt) REVERT: B 276 MET cc_start: 0.8592 (mmm) cc_final: 0.8212 (mmm) REVERT: H 11 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8809 (tt) REVERT: I 102 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7828 (p) REVERT: J 158 ASP cc_start: 0.8727 (m-30) cc_final: 0.8467 (p0) REVERT: N 101 HIS cc_start: 0.3235 (OUTLIER) cc_final: 0.2505 (m170) REVERT: O 75 ILE cc_start: 0.5403 (OUTLIER) cc_final: 0.5036 (tp) REVERT: O 163 TRP cc_start: 0.8710 (m-10) cc_final: 0.8469 (m-10) REVERT: P 54 ARG cc_start: 0.5884 (mmp80) cc_final: 0.5218 (mmp80) REVERT: F 48 MET cc_start: 0.8919 (ptp) cc_final: 0.8546 (ptp) REVERT: G 81 MET cc_start: 0.8925 (tmm) cc_final: 0.8604 (tmm) REVERT: K 222 ILE cc_start: -0.0523 (OUTLIER) cc_final: -0.0808 (mt) outliers start: 66 outliers final: 31 residues processed: 184 average time/residue: 0.2052 time to fit residues: 62.5127 Evaluate side-chains 148 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 31 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 429 optimal weight: 20.0000 chunk 326 optimal weight: 30.0000 chunk 231 optimal weight: 0.4980 chunk 213 optimal weight: 30.0000 chunk 324 optimal weight: 40.0000 chunk 169 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 HIS ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.083431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.058868 restraints weight = 289880.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.060336 restraints weight = 110349.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.061148 restraints weight = 56102.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.061623 restraints weight = 33820.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.061873 restraints weight = 23855.118| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 35406 Z= 0.212 Angle : 0.733 10.770 48192 Z= 0.365 Chirality : 0.046 0.173 5478 Planarity : 0.005 0.112 6168 Dihedral : 6.296 51.546 4882 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.58 % Favored : 89.31 % Rotamer: Outliers : 1.79 % Allowed : 8.32 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 1.77 % 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: -1.97 (0.13), residues: 4482 helix: 0.94 (0.19), residues: 804 sheet: -1.78 (0.14), residues: 1332 loop : -1.82 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 24 TYR 0.030 0.002 TYR E 49 PHE 0.015 0.002 PHE B 162 TRP 0.019 0.002 TRP E 163 HIS 0.012 0.002 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00475 (35382) covalent geometry : angle 0.73325 (48144) SS BOND : bond 0.00297 ( 24) SS BOND : angle 0.80294 ( 48) hydrogen bonds : bond 0.02884 ( 1050) hydrogen bonds : angle 5.46178 ( 2952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 124 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.7496 (t0) cc_final: 0.6912 (t0) REVERT: D 81 MET cc_start: 0.9354 (tmm) cc_final: 0.9046 (tmm) REVERT: D 83 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8152 (mm) REVERT: B 212 MET cc_start: 0.9417 (tpt) cc_final: 0.9022 (tpt) REVERT: B 276 MET cc_start: 0.8690 (mmm) cc_final: 0.8278 (mmm) REVERT: I 187 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9127 (mm-30) REVERT: J 32 ARG cc_start: 0.8693 (mtt180) cc_final: 0.8217 (tpt170) REVERT: J 101 HIS cc_start: 0.5448 (OUTLIER) cc_final: 0.3756 (t-170) REVERT: J 158 ASP cc_start: 0.8749 (m-30) cc_final: 0.8513 (p0) REVERT: J 276 MET cc_start: 0.7798 (ttm) cc_final: 0.7100 (tmm) REVERT: L 110 ASP cc_start: 0.6170 (m-30) cc_final: 0.5937 (m-30) REVERT: M 97 LEU cc_start: 0.9280 (mp) cc_final: 0.9075 (pt) REVERT: N 101 HIS cc_start: 0.3297 (OUTLIER) cc_final: 0.2544 (m170) REVERT: O 75 ILE cc_start: 0.5259 (OUTLIER) cc_final: 0.5003 (tp) REVERT: P 154 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7748 (tm-30) REVERT: F 48 MET cc_start: 0.8916 (ptp) cc_final: 0.8521 (ptp) REVERT: G 81 MET cc_start: 0.8950 (tmm) cc_final: 0.8522 (tmm) REVERT: K 222 ILE cc_start: -0.0860 (OUTLIER) cc_final: -0.1069 (mt) outliers start: 69 outliers final: 44 residues processed: 190 average time/residue: 0.2055 time to fit residues: 64.1739 Evaluate side-chains 157 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 108 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 68 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 394 optimal weight: 40.0000 chunk 325 optimal weight: 8.9990 chunk 278 optimal weight: 20.0000 chunk 427 optimal weight: 40.0000 chunk 353 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 274 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 227 optimal weight: 30.0000 overall best weight: 7.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 126 HIS M 60 ASN M 69 ASN ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN Q 39 GLN Q 59 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.081038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.056336 restraints weight = 290401.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.057733 restraints weight = 112471.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.058506 restraints weight = 57720.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.058976 restraints weight = 35380.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.059170 restraints weight = 24915.157| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.130 35406 Z= 0.363 Angle : 0.884 15.627 48192 Z= 0.440 Chirality : 0.049 0.232 5478 Planarity : 0.006 0.118 6168 Dihedral : 6.741 49.446 4880 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.94 % Favored : 87.91 % Rotamer: Outliers : 2.11 % Allowed : 9.00 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 1.77 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.13), residues: 4482 helix: 0.58 (0.18), residues: 804 sheet: -1.85 (0.13), residues: 1404 loop : -1.98 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 61 TYR 0.040 0.003 TYR E 49 PHE 0.024 0.003 PHE B 162 TRP 0.026 0.003 TRP O 163 HIS 0.010 0.002 HIS E 91 Details of bonding type rmsd covalent geometry : bond 0.00801 (35382) covalent geometry : angle 0.88363 (48144) SS BOND : bond 0.00490 ( 24) SS BOND : angle 0.95280 ( 48) hydrogen bonds : bond 0.03637 ( 1050) hydrogen bonds : angle 6.07974 ( 2952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 128 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.8861 (mmm) cc_final: 0.8611 (mmm) REVERT: E 175 MET cc_start: 0.7538 (mmp) cc_final: 0.7311 (mmp) REVERT: B 212 MET cc_start: 0.9455 (tpt) cc_final: 0.9009 (tpt) REVERT: B 276 MET cc_start: 0.8843 (mmm) cc_final: 0.8515 (mmm) REVERT: I 77 SER cc_start: 0.8904 (t) cc_final: 0.8602 (p) REVERT: J 32 ARG cc_start: 0.8780 (mtt180) cc_final: 0.7973 (tpt170) REVERT: J 158 ASP cc_start: 0.8920 (m-30) cc_final: 0.8644 (p0) REVERT: J 276 MET cc_start: 0.7509 (ttm) cc_final: 0.7287 (ttt) REVERT: L 4 MET cc_start: 0.4543 (ptp) cc_final: 0.4309 (ptp) REVERT: M 97 LEU cc_start: 0.9306 (mp) cc_final: 0.8986 (pt) REVERT: N 101 HIS cc_start: 0.3552 (OUTLIER) cc_final: 0.2714 (m170) REVERT: O 75 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5765 (tp) REVERT: P 58 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5251 (pt) REVERT: F 48 MET cc_start: 0.8886 (ptp) cc_final: 0.8592 (ptp) REVERT: F 81 MET cc_start: 0.8936 (tmm) cc_final: 0.8557 (tmm) REVERT: G 81 MET cc_start: 0.9032 (tmm) cc_final: 0.8566 (tmm) REVERT: K 222 ILE cc_start: -0.0756 (OUTLIER) cc_final: -0.1246 (mp) outliers start: 81 outliers final: 51 residues processed: 206 average time/residue: 0.2103 time to fit residues: 71.2811 Evaluate side-chains 169 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 169 LYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 81 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 81 optimal weight: 3.9990 chunk 316 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 425 optimal weight: 40.0000 chunk 321 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 399 optimal weight: 0.5980 chunk 416 optimal weight: 30.0000 chunk 275 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN J 115 HIS L 27 GLN ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.083212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.059048 restraints weight = 291776.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.060473 restraints weight = 112236.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.061272 restraints weight = 57220.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.061757 restraints weight = 35034.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.061956 restraints weight = 24499.131| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35406 Z= 0.140 Angle : 0.716 10.694 48192 Z= 0.354 Chirality : 0.046 0.223 5478 Planarity : 0.005 0.105 6168 Dihedral : 6.211 45.288 4880 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.55 % Favored : 90.34 % Rotamer: Outliers : 1.46 % Allowed : 10.09 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 0.71 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.13), residues: 4482 helix: 0.69 (0.18), residues: 840 sheet: -1.85 (0.14), residues: 1338 loop : -1.68 (0.14), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 24 TYR 0.031 0.002 TYR H 49 PHE 0.015 0.001 PHE O 62 TRP 0.020 0.002 TRP O 148 HIS 0.009 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00320 (35382) covalent geometry : angle 0.71615 (48144) SS BOND : bond 0.00371 ( 24) SS BOND : angle 0.79075 ( 48) hydrogen bonds : bond 0.02649 ( 1050) hydrogen bonds : angle 5.41247 ( 2952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 127 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.7768 (t0) cc_final: 0.7153 (t0) REVERT: E 4 MET cc_start: 0.9037 (mmm) cc_final: 0.8668 (mmm) REVERT: E 105 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8116 (mp0) REVERT: E 175 MET cc_start: 0.7569 (mmp) cc_final: 0.7208 (mmp) REVERT: B 212 MET cc_start: 0.9339 (tpt) cc_final: 0.9077 (tpt) REVERT: B 276 MET cc_start: 0.8497 (mmm) cc_final: 0.8096 (mmm) REVERT: H 24 ARG cc_start: 0.9004 (ttp80) cc_final: 0.8476 (ttp-110) REVERT: H 183 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6433 (tppt) REVERT: I 70 ASP cc_start: 0.9342 (p0) cc_final: 0.9114 (p0) REVERT: I 102 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7701 (p) REVERT: J 158 ASP cc_start: 0.8893 (m-30) cc_final: 0.8593 (p0) REVERT: L 4 MET cc_start: 0.4469 (ptp) cc_final: 0.4171 (ptp) REVERT: N 101 HIS cc_start: 0.3215 (OUTLIER) cc_final: 0.2501 (m170) REVERT: O 75 ILE cc_start: 0.5295 (OUTLIER) cc_final: 0.5063 (tp) REVERT: F 48 MET cc_start: 0.8813 (ptp) cc_final: 0.8586 (ptp) REVERT: F 81 MET cc_start: 0.8798 (tmm) cc_final: 0.8394 (tmm) REVERT: G 81 MET cc_start: 0.9027 (tmm) cc_final: 0.8662 (tmm) REVERT: K 222 ILE cc_start: -0.1073 (OUTLIER) cc_final: -0.1300 (mt) REVERT: R 23 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8766 (mmtm) outliers start: 56 outliers final: 32 residues processed: 178 average time/residue: 0.2145 time to fit residues: 61.6639 Evaluate side-chains 148 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain R residue 18 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 69 optimal weight: 5.9990 chunk 211 optimal weight: 40.0000 chunk 400 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 404 optimal weight: 1.9990 chunk 370 optimal weight: 40.0000 chunk 387 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 339 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 HIS ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.081980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.057629 restraints weight = 292580.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.058999 restraints weight = 113753.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.059769 restraints weight = 58375.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.060235 restraints weight = 36004.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.060404 restraints weight = 25504.305| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 35406 Z= 0.223 Angle : 0.751 10.357 48192 Z= 0.372 Chirality : 0.046 0.200 5478 Planarity : 0.005 0.110 6168 Dihedral : 6.236 45.031 4880 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.27 % Favored : 88.62 % Rotamer: Outliers : 1.35 % Allowed : 10.45 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 1.06 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.13), residues: 4482 helix: 1.03 (0.19), residues: 792 sheet: -1.90 (0.14), residues: 1368 loop : -1.64 (0.14), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 108 TYR 0.034 0.002 TYR H 49 PHE 0.015 0.002 PHE O 62 TRP 0.028 0.002 TRP L 148 HIS 0.017 0.002 HIS O 91 Details of bonding type rmsd covalent geometry : bond 0.00501 (35382) covalent geometry : angle 0.75067 (48144) SS BOND : bond 0.00319 ( 24) SS BOND : angle 0.80270 ( 48) hydrogen bonds : bond 0.02914 ( 1050) hydrogen bonds : angle 5.46884 ( 2952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.7792 (t0) cc_final: 0.7203 (t0) REVERT: E 49 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.8094 (p90) REVERT: E 175 MET cc_start: 0.7680 (mmp) cc_final: 0.7374 (mmp) REVERT: B 212 MET cc_start: 0.9404 (tpt) cc_final: 0.9014 (tpt) REVERT: B 276 MET cc_start: 0.8619 (mmm) cc_final: 0.8198 (mmm) REVERT: H 183 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6403 (tppt) REVERT: J 32 ARG cc_start: 0.8723 (mtt180) cc_final: 0.8019 (tpt170) REVERT: J 101 HIS cc_start: 0.5585 (OUTLIER) cc_final: 0.4768 (t-170) REVERT: J 158 ASP cc_start: 0.8927 (m-30) cc_final: 0.8685 (p0) REVERT: J 276 MET cc_start: 0.7738 (ttm) cc_final: 0.7360 (tmm) REVERT: L 4 MET cc_start: 0.4681 (ptp) cc_final: 0.4414 (ptp) REVERT: N 101 HIS cc_start: 0.3268 (OUTLIER) cc_final: 0.2611 (m170) REVERT: P 1 GLU cc_start: 0.7582 (mm-30) cc_final: 0.6677 (tp30) REVERT: F 48 MET cc_start: 0.8760 (ptp) cc_final: 0.8550 (ptp) REVERT: F 81 MET cc_start: 0.8844 (tmm) cc_final: 0.8465 (tmm) REVERT: G 81 MET cc_start: 0.8973 (tmm) cc_final: 0.8554 (tmm) REVERT: K 222 ILE cc_start: -0.0935 (OUTLIER) cc_final: -0.1435 (mp) outliers start: 52 outliers final: 37 residues processed: 168 average time/residue: 0.2088 time to fit residues: 58.0044 Evaluate side-chains 154 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 223 LYS Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain R residue 18 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 141 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 317 optimal weight: 30.0000 chunk 238 optimal weight: 30.0000 chunk 341 optimal weight: 5.9990 chunk 286 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN L 124 GLN M 19 GLN M 69 ASN ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.081911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.057548 restraints weight = 290950.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.058928 restraints weight = 113038.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.059715 restraints weight = 58027.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.060129 restraints weight = 35576.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.060457 restraints weight = 25401.458| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 35406 Z= 0.210 Angle : 0.745 12.727 48192 Z= 0.369 Chirality : 0.046 0.211 5478 Planarity : 0.005 0.108 6168 Dihedral : 6.208 50.935 4880 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.58 % Favored : 89.31 % Rotamer: Outliers : 1.53 % Allowed : 10.63 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 1.06 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.13), residues: 4482 helix: 1.08 (0.18), residues: 792 sheet: -1.88 (0.13), residues: 1404 loop : -1.61 (0.14), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 61 TYR 0.033 0.002 TYR E 49 PHE 0.015 0.002 PHE P 118 TRP 0.028 0.002 TRP D 47 HIS 0.009 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00474 (35382) covalent geometry : angle 0.74491 (48144) SS BOND : bond 0.00286 ( 24) SS BOND : angle 0.78643 ( 48) hydrogen bonds : bond 0.02829 ( 1050) hydrogen bonds : angle 5.43883 ( 2952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 119 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.7839 (t0) cc_final: 0.7240 (t0) REVERT: E 105 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8105 (mp0) REVERT: E 175 MET cc_start: 0.7766 (mmp) cc_final: 0.7464 (mmp) REVERT: B 212 MET cc_start: 0.9410 (tpt) cc_final: 0.9019 (tpt) REVERT: B 276 MET cc_start: 0.8578 (mmm) cc_final: 0.8154 (mmm) REVERT: H 24 ARG cc_start: 0.9056 (ttp80) cc_final: 0.8631 (ttp-110) REVERT: H 183 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.6427 (tppt) REVERT: J 32 ARG cc_start: 0.8731 (mtt180) cc_final: 0.7999 (tpt170) REVERT: J 158 ASP cc_start: 0.8923 (m-30) cc_final: 0.8693 (p0) REVERT: L 58 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6323 (mp) REVERT: N 101 HIS cc_start: 0.3174 (OUTLIER) cc_final: 0.2599 (m170) REVERT: N 212 MET cc_start: 0.0131 (tmm) cc_final: -0.0201 (mmm) REVERT: F 81 MET cc_start: 0.8802 (tmm) cc_final: 0.8429 (tmm) REVERT: G 81 MET cc_start: 0.9008 (tmm) cc_final: 0.8606 (tmm) REVERT: K 68 VAL cc_start: 0.5987 (OUTLIER) cc_final: 0.5704 (p) REVERT: K 222 ILE cc_start: -0.0968 (OUTLIER) cc_final: -0.1458 (mp) REVERT: R 39 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8806 (tp-100) outliers start: 59 outliers final: 36 residues processed: 176 average time/residue: 0.2169 time to fit residues: 61.9663 Evaluate side-chains 154 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 223 LYS Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain R residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 398 optimal weight: 8.9990 chunk 273 optimal weight: 30.0000 chunk 417 optimal weight: 5.9990 chunk 305 optimal weight: 8.9990 chunk 425 optimal weight: 6.9990 chunk 435 optimal weight: 50.0000 chunk 428 optimal weight: 30.0000 chunk 342 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.080876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.056315 restraints weight = 292773.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.057681 restraints weight = 114520.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.058459 restraints weight = 59082.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.058928 restraints weight = 36384.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.059096 restraints weight = 25714.974| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 35406 Z= 0.272 Angle : 0.812 11.038 48192 Z= 0.402 Chirality : 0.048 0.191 5478 Planarity : 0.006 0.112 6168 Dihedral : 6.446 67.091 4878 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.14 % Favored : 87.75 % Rotamer: Outliers : 1.35 % Allowed : 10.92 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 0.71 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.13), residues: 4482 helix: 0.99 (0.18), residues: 792 sheet: -1.80 (0.13), residues: 1404 loop : -1.75 (0.14), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 61 TYR 0.045 0.002 TYR E 49 PHE 0.026 0.002 PHE O 62 TRP 0.023 0.002 TRP O 163 HIS 0.011 0.002 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00608 (35382) covalent geometry : angle 0.81166 (48144) SS BOND : bond 0.00394 ( 24) SS BOND : angle 0.94445 ( 48) hydrogen bonds : bond 0.03210 ( 1050) hydrogen bonds : angle 5.68737 ( 2952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 116 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.7829 (t0) cc_final: 0.7374 (t0) REVERT: E 49 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7595 (p90) REVERT: E 157 ASN cc_start: 0.7962 (m110) cc_final: 0.7755 (p0) REVERT: E 175 MET cc_start: 0.7829 (mmp) cc_final: 0.7566 (mmp) REVERT: B 212 MET cc_start: 0.9430 (tpt) cc_final: 0.9008 (tpt) REVERT: B 276 MET cc_start: 0.8672 (mmm) cc_final: 0.8243 (mmm) REVERT: H 24 ARG cc_start: 0.9072 (ttp80) cc_final: 0.8630 (ttp-110) REVERT: H 183 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7126 (tptp) REVERT: I 77 SER cc_start: 0.8884 (t) cc_final: 0.8667 (m) REVERT: J 158 ASP cc_start: 0.8900 (m-30) cc_final: 0.8641 (p0) REVERT: J 276 MET cc_start: 0.7440 (ttt) cc_final: 0.6808 (tmm) REVERT: L 58 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6452 (mp) REVERT: N 101 HIS cc_start: 0.3256 (OUTLIER) cc_final: 0.2592 (m170) REVERT: N 212 MET cc_start: 0.0993 (tmm) cc_final: 0.0650 (mmm) REVERT: O 1 GLU cc_start: 0.6960 (tt0) cc_final: 0.6702 (tm-30) REVERT: P 54 ARG cc_start: 0.4750 (mmp80) cc_final: 0.4214 (mmp80) REVERT: P 81 GLU cc_start: 0.5277 (pp20) cc_final: 0.5067 (pp20) REVERT: F 81 MET cc_start: 0.8861 (tmm) cc_final: 0.8506 (tmm) REVERT: G 81 MET cc_start: 0.8974 (tmm) cc_final: 0.8534 (tmm) REVERT: K 68 VAL cc_start: 0.6366 (OUTLIER) cc_final: 0.6074 (p) REVERT: K 222 ILE cc_start: -0.0600 (OUTLIER) cc_final: -0.1853 (mm) REVERT: R 39 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8814 (tp-100) outliers start: 52 outliers final: 39 residues processed: 165 average time/residue: 0.2116 time to fit residues: 57.2498 Evaluate side-chains 158 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 223 LYS Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 86 TYR Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain R residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 328 optimal weight: 5.9990 chunk 413 optimal weight: 20.0000 chunk 43 optimal weight: 0.5980 chunk 324 optimal weight: 30.0000 chunk 139 optimal weight: 4.9990 chunk 381 optimal weight: 30.0000 chunk 23 optimal weight: 1.9990 chunk 442 optimal weight: 30.0000 chunk 76 optimal weight: 0.7980 chunk 354 optimal weight: 7.9990 chunk 421 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 126 HIS L 89 GLN L 91 HIS ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.081846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.057683 restraints weight = 289438.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.059075 restraints weight = 112118.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.059852 restraints weight = 57526.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.060335 restraints weight = 35209.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.060536 restraints weight = 24800.260| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.6808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35406 Z= 0.171 Angle : 0.745 14.346 48192 Z= 0.366 Chirality : 0.046 0.203 5478 Planarity : 0.006 0.138 6168 Dihedral : 6.246 80.013 4878 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.24 % Favored : 89.65 % Rotamer: Outliers : 1.35 % Allowed : 11.02 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 1.06 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.13), residues: 4482 helix: 1.18 (0.19), residues: 792 sheet: -1.78 (0.14), residues: 1392 loop : -1.64 (0.14), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 61 TYR 0.041 0.002 TYR L 86 PHE 0.023 0.002 PHE O 62 TRP 0.020 0.002 TRP D 47 HIS 0.018 0.002 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00392 (35382) covalent geometry : angle 0.74487 (48144) SS BOND : bond 0.00386 ( 24) SS BOND : angle 0.78455 ( 48) hydrogen bonds : bond 0.02751 ( 1050) hydrogen bonds : angle 5.37829 ( 2952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8384.90 seconds wall clock time: 145 minutes 34.88 seconds (8734.88 seconds total)