Starting phenix.real_space_refine on Sun Jul 5 20:10:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vtr_65340/07_2026/9vtr_65340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vtr_65340/07_2026/9vtr_65340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vtr_65340/07_2026/9vtr_65340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vtr_65340/07_2026/9vtr_65340.map" model { file = "/net/cci-nas-00/data/ceres_data/9vtr_65340/07_2026/9vtr_65340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vtr_65340/07_2026/9vtr_65340.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 99 5.49 5 Mg 1 5.21 5 S 133 5.16 5 C 18320 2.51 5 N 5075 2.21 5 O 5704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29332 Number of models: 1 Model: "" Number of chains: 15 Chain: "1" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1221 Classifications: {'RNA': 57} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 7, 'rna3p_pur': 18, 'rna3p_pyr': 15} Link IDs: {'rna2p': 23, 'rna3p': 33} Chain breaks: 1 Chain: "2" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 759 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "3" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 123 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2725 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2745 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2752 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2756 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 326} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2727 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 19, 'TRANS': 320} Chain breaks: 1 Chain: "F" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2392 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 278} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 2045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2045 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 15, 'TRANS': 260} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 5, 'GLU:plan': 3, 'HIS:plan': 1, 'TRP:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2186 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'UNK:plan-1': 46} Unresolved non-hydrogen planarities: 46 Chain: "H" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1452 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2798 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 428 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'TYR:plan': 5, 'ASP:plan': 5, 'GLU:plan': 8, 'ASN:plan1': 6, 'HIS:plan': 3, 'TRP:plan': 1, 'PHE:plan': 4, 'ARG:plan': 7, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 199 Chain: "J" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2650 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 16, 'TRANS': 330} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 4, 'ASN:plan1': 6, 'GLU:plan': 5, 'ASP:plan': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 110 Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.06, per 1000 atoms: 0.17 Number of scatterers: 29332 At special positions: 0 Unit cell: (124.832, 188, 164.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 133 16.00 P 99 15.00 Mg 1 11.99 O 5704 8.00 N 5075 7.00 C 18320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6608 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 39 sheets defined 38.3% alpha, 9.1% beta 36 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.334A pdb=" N ALA A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.692A pdb=" N GLN A 67 " --> pdb=" O SER A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 322 through 339 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.508A pdb=" N SER B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.695A pdb=" N ALA B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 139 through 147 removed outlier: 6.328A pdb=" N ARG B 144 " --> pdb=" O TRP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.705A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 255 through 264 Processing helix chain 'B' and resid 300 through 307 removed outlier: 3.801A pdb=" N LYS B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 322 through 339 Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 105 through 123 Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 179 through 185 Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 300 through 307 removed outlier: 3.563A pdb=" N LEU C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 317 removed outlier: 3.533A pdb=" N ALA C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 339 Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 105 through 123 Processing helix chain 'D' and resid 125 through 138 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 144 through 149 removed outlier: 4.084A pdb=" N CYS D 148 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR D 149 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 179 through 185 removed outlier: 3.588A pdb=" N PHE D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 255 through 264 Processing helix chain 'D' and resid 300 through 307 Processing helix chain 'D' and resid 307 through 317 removed outlier: 3.647A pdb=" N ALA D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 105 through 123 Processing helix chain 'E' and resid 125 through 138 Processing helix chain 'E' and resid 179 through 185 Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 300 through 307 removed outlier: 3.590A pdb=" N LEU E 304 " --> pdb=" O ASP E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 318 Processing helix chain 'E' and resid 322 through 339 Processing helix chain 'F' and resid 105 through 123 removed outlier: 4.257A pdb=" N GLU F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 138 Processing helix chain 'F' and resid 139 through 147 removed outlier: 6.548A pdb=" N ARG F 144 " --> pdb=" O TRP F 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU F 147 " --> pdb=" O ARG F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 188 through 202 removed outlier: 3.572A pdb=" N ILE F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 264 Processing helix chain 'F' and resid 300 through 307 removed outlier: 4.020A pdb=" N LYS F 307 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 313 Processing helix chain 'F' and resid 322 through 339 Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 35 through 46 removed outlier: 4.415A pdb=" N ALA G 39 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 56 removed outlier: 3.863A pdb=" N GLN G 53 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYS G 54 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN G 55 " --> pdb=" O GLU G 52 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 56 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 68 removed outlier: 3.819A pdb=" N CYS G 62 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP G 68 " --> pdb=" O ASP G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 78 removed outlier: 3.983A pdb=" N THR G 78 " --> pdb=" O ASN G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 129 through 137 removed outlier: 3.746A pdb=" N PHE G 135 " --> pdb=" O ASN G 131 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU G 136 " --> pdb=" O LYS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 158 through 168 Processing helix chain 'G' and resid 170 through 184 removed outlier: 3.653A pdb=" N ALA G 174 " --> pdb=" O TYR G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 230 Processing helix chain 'G' and resid 232 through 236 Processing helix chain 'G' and resid 248 through 254 removed outlier: 3.893A pdb=" N CYS G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 281 through 291 Processing helix chain 'G' and resid 313 through 325 removed outlier: 4.840A pdb=" N UNK G 319 " --> pdb=" O UNK G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 348 Processing helix chain 'G' and resid 349 through 351 No H-bonds generated for 'chain 'G' and resid 349 through 351' Processing helix chain 'G' and resid 356 through 367 Processing helix chain 'G' and resid 415 through 432 removed outlier: 3.555A pdb=" N THR G 432 " --> pdb=" O ARG G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 503 Processing helix chain 'G' and resid 517 through 520 removed outlier: 3.517A pdb=" N ILE G 520 " --> pdb=" O ILE G 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 517 through 520' Processing helix chain 'G' and resid 528 through 535 Processing helix chain 'G' and resid 554 through 565 removed outlier: 3.610A pdb=" N VAL G 558 " --> pdb=" O SER G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 587 through 591 Processing helix chain 'H' and resid 16 through 36 removed outlier: 4.023A pdb=" N ILE H 20 " --> pdb=" O ASN H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 67 removed outlier: 3.773A pdb=" N LEU H 66 " --> pdb=" O ASN H 62 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 67' Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 104 through 110 removed outlier: 4.346A pdb=" N ASP H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 135 through 139 Processing helix chain 'I' and resid 17 through 29 removed outlier: 3.972A pdb=" N PHE I 21 " --> pdb=" O SER I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 47 Processing helix chain 'I' and resid 64 through 68 removed outlier: 4.034A pdb=" N SER I 68 " --> pdb=" O PRO I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 85 removed outlier: 4.138A pdb=" N LEU I 85 " --> pdb=" O HIS I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 140 removed outlier: 3.678A pdb=" N HIS I 139 " --> pdb=" O CYS I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 209 removed outlier: 4.038A pdb=" N SER I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 234 removed outlier: 3.597A pdb=" N ARG I 223 " --> pdb=" O PRO I 219 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP I 224 " --> pdb=" O LEU I 220 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY I 225 " --> pdb=" O SER I 221 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN I 232 " --> pdb=" O HIS I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 237 No H-bonds generated for 'chain 'I' and resid 235 through 237' Processing helix chain 'I' and resid 241 through 251 removed outlier: 3.509A pdb=" N PHE I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 270 removed outlier: 3.601A pdb=" N PHE I 256 " --> pdb=" O TRP I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 278 removed outlier: 3.915A pdb=" N LEU I 278 " --> pdb=" O LYS I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 289 Processing helix chain 'I' and resid 302 through 315 removed outlier: 3.575A pdb=" N LYS I 306 " --> pdb=" O ASN I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 337 removed outlier: 3.656A pdb=" N ILE I 333 " --> pdb=" O ASN I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 351 Processing helix chain 'I' and resid 373 through 384 Processing helix chain 'J' and resid 21 through 29 removed outlier: 3.717A pdb=" N VAL J 25 " --> pdb=" O PHE J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 47 Processing helix chain 'J' and resid 59 through 63 removed outlier: 3.610A pdb=" N CYS J 62 " --> pdb=" O ASP J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 68 removed outlier: 3.583A pdb=" N SER J 68 " --> pdb=" O PRO J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 84 removed outlier: 3.654A pdb=" N GLN J 84 " --> pdb=" O HIS J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 124 removed outlier: 3.832A pdb=" N LEU J 123 " --> pdb=" O PRO J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 138 Processing helix chain 'J' and resid 172 through 177 Processing helix chain 'J' and resid 197 through 207 removed outlier: 3.591A pdb=" N LEU J 207 " --> pdb=" O ILE J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 219 through 229 removed outlier: 3.661A pdb=" N TRP J 224 " --> pdb=" O LEU J 220 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY J 225 " --> pdb=" O SER J 221 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE J 226 " --> pdb=" O TYR J 222 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET J 227 " --> pdb=" O ARG J 223 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS J 228 " --> pdb=" O TRP J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 250 Processing helix chain 'J' and resid 251 through 271 removed outlier: 3.650A pdb=" N SER J 255 " --> pdb=" O HIS J 251 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE J 256 " --> pdb=" O TRP J 252 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N HIS J 257 " --> pdb=" O PRO J 253 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY J 261 " --> pdb=" O HIS J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 284 removed outlier: 4.174A pdb=" N ILE J 283 " --> pdb=" O ARG J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 289 removed outlier: 3.547A pdb=" N PHE J 289 " --> pdb=" O GLY J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 315 removed outlier: 4.261A pdb=" N LYS J 306 " --> pdb=" O ASN J 302 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN J 310 " --> pdb=" O LYS J 306 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR J 311 " --> pdb=" O GLU J 307 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS J 315 " --> pdb=" O TYR J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 332 through 336 removed outlier: 3.896A pdb=" N LEU J 336 " --> pdb=" O GLU J 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 332 through 336' Processing helix chain 'J' and resid 340 through 350 removed outlier: 3.781A pdb=" N THR J 345 " --> pdb=" O ARG J 341 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET J 347 " --> pdb=" O GLN J 343 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE J 348 " --> pdb=" O VAL J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 382 removed outlier: 3.616A pdb=" N TRP J 381 " --> pdb=" O VAL J 377 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 15 current: chain 'A' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 29 through 31 current: chain 'A' and resid 206 through 216 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 206 through 216 current: chain 'A' and resid 249 through 254 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 41 removed outlier: 3.587A pdb=" N GLY A 41 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.851A pdb=" N TYR A 290 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 15 current: chain 'B' and resid 28 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 28 through 31 current: chain 'B' and resid 170 through 171 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 170 through 171 current: chain 'B' and resid 249 through 254 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 42 Processing sheet with id=AA8, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.651A pdb=" N TYR B 290 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 15 current: chain 'C' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 29 through 31 current: chain 'C' and resid 206 through 216 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 206 through 216 current: chain 'C' and resid 249 through 254 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AB3, first strand: chain 'C' and resid 283 through 285 removed outlier: 3.859A pdb=" N TYR C 290 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 102 through 103 removed outlier: 3.618A pdb=" N LYS D 102 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 13 through 14 current: chain 'D' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 29 through 31 current: chain 'D' and resid 206 through 216 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 206 through 216 current: chain 'D' and resid 249 through 254 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 35 through 42 removed outlier: 3.571A pdb=" N GLY D 41 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 265 through 267 Processing sheet with id=AB8, first strand: chain 'D' and resid 283 through 284 Processing sheet with id=AB9, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AC1, first strand: chain 'E' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 13 through 14 current: chain 'E' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 29 through 31 current: chain 'E' and resid 206 through 216 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 206 through 216 current: chain 'E' and resid 249 through 254 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AC3, first strand: chain 'E' and resid 265 through 267 Processing sheet with id=AC4, first strand: chain 'E' and resid 284 through 285 removed outlier: 4.076A pdb=" N TYR E 290 " --> pdb=" O HIS E 285 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 8 through 9 Processing sheet with id=AC6, first strand: chain 'F' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 13 through 14 current: chain 'F' and resid 29 through 30 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 29 through 30 current: chain 'F' and resid 206 through 214 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AC8, first strand: chain 'F' and resid 243 through 246 Processing sheet with id=AC9, first strand: chain 'F' and resid 283 through 285 Processing sheet with id=AD1, first strand: chain 'G' and resid 82 through 83 removed outlier: 3.710A pdb=" N ALA G 122 " --> pdb=" O GLN G 83 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 85 through 86 current: chain 'G' and resid 210 through 218 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 210 through 218 current: chain 'G' and resid 478 through 488 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 478 through 488 current: chain 'G' and resid 593 through 606 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'G' and resid 97 through 99 Processing sheet with id=AD4, first strand: chain 'G' and resid 139 through 142 Processing sheet with id=AD5, first strand: chain 'G' and resid 237 through 239 removed outlier: 8.470A pdb=" N ILE G 411 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE G 261 " --> pdb=" O ILE G 411 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 461 through 462 Processing sheet with id=AD7, first strand: chain 'G' and resid 619 through 624 Processing sheet with id=AD8, first strand: chain 'H' and resid 41 through 43 removed outlier: 3.512A pdb=" N THR H 9 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AE1, first strand: chain 'H' and resid 150 through 155 Processing sheet with id=AE2, first strand: chain 'I' and resid 99 through 104 removed outlier: 4.478A pdb=" N ALA I 111 " --> pdb=" O ASN I 101 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 98 through 101 removed outlier: 3.599A pdb=" N ILE J 113 " --> pdb=" O ASN J 99 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN J 101 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA J 111 " --> pdb=" O ASN J 101 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2418 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7783 1.33 - 1.45: 6556 1.45 - 1.58: 15551 1.58 - 1.70: 195 1.70 - 1.82: 176 Bond restraints: 30261 Sorted by residual: bond pdb=" C3' DG 2 27 " pdb=" C2' DG 2 27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.48e+00 bond pdb=" C3' DG 2 39 " pdb=" C2' DG 2 39 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.10e+00 bond pdb=" C3' DA 2 26 " pdb=" C2' DA 2 26 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.06e+00 bond pdb=" C3' DG 2 33 " pdb=" C2' DG 2 33 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.98e+00 bond pdb=" C3' DT 2 32 " pdb=" C2' DT 2 32 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.78e+00 ... (remaining 30256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 41261 2.83 - 5.66: 246 5.66 - 8.49: 34 8.49 - 11.32: 7 11.32 - 14.15: 3 Bond angle restraints: 41551 Sorted by residual: angle pdb=" CA MET J 308 " pdb=" CB MET J 308 " pdb=" CG MET J 308 " ideal model delta sigma weight residual 114.10 125.97 -11.87 2.00e+00 2.50e-01 3.53e+01 angle pdb=" CB MET J 308 " pdb=" CG MET J 308 " pdb=" SD MET J 308 " ideal model delta sigma weight residual 112.70 126.85 -14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" O4' DC 2 50 " pdb=" C4' DC 2 50 " pdb=" C3' DC 2 50 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT 2 24 " pdb=" C4 DT 2 24 " pdb=" O4 DT 2 24 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT 3 3 " pdb=" C4 DT 3 3 " pdb=" O4 DT 3 3 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 ... (remaining 41546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.58: 15147 19.58 - 39.15: 2008 39.15 - 58.73: 574 58.73 - 78.31: 125 78.31 - 97.88: 29 Dihedral angle restraints: 17883 sinusoidal: 7652 harmonic: 10231 Sorted by residual: dihedral pdb=" CA SER J 106 " pdb=" C SER J 106 " pdb=" N PRO J 107 " pdb=" CA PRO J 107 " ideal model delta harmonic sigma weight residual -180.00 -144.80 -35.20 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" O4' C 1 15 " pdb=" C1' C 1 15 " pdb=" N1 C 1 15 " pdb=" C2 C 1 15 " ideal model delta sinusoidal sigma weight residual -128.00 -56.13 -71.87 1 1.70e+01 3.46e-03 2.29e+01 dihedral pdb=" O4' C 1 24 " pdb=" C1' C 1 24 " pdb=" N1 C 1 24 " pdb=" C2 C 1 24 " ideal model delta sinusoidal sigma weight residual -160.00 -101.06 -58.94 1 1.50e+01 4.44e-03 2.07e+01 ... (remaining 17880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4157 0.070 - 0.140: 404 0.140 - 0.210: 10 0.210 - 0.280: 0 0.280 - 0.350: 1 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CB ILE J 312 " pdb=" CA ILE J 312 " pdb=" CG1 ILE J 312 " pdb=" CG2 ILE J 312 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA GLU J 152 " pdb=" N GLU J 152 " pdb=" C GLU J 152 " pdb=" CB GLU J 152 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CA ASN G 55 " pdb=" N ASN G 55 " pdb=" C ASN G 55 " pdb=" CB ASN G 55 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 4569 not shown) Planarity restraints: 5000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 294 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO I 295 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO I 295 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO I 295 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 247 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" CG ASP E 247 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP E 247 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP E 247 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 6 " -0.030 2.00e-02 2.50e+03 1.38e-02 5.22e+00 pdb=" N9 A 1 6 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A 1 6 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A 1 6 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 1 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 1 6 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 1 6 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A 1 6 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 1 6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 1 6 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A 1 6 " 0.005 2.00e-02 2.50e+03 ... (remaining 4997 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 11455 2.90 - 3.40: 28892 3.40 - 3.90: 50432 3.90 - 4.40: 58229 4.40 - 4.90: 94424 Nonbonded interactions: 243432 Sorted by model distance: nonbonded pdb=" OP2 A 1 6 " pdb="MG MG 1 101 " model vdw 2.394 2.170 nonbonded pdb=" O ASN G 55 " pdb=" OD1 ASN G 55 " model vdw 2.408 3.040 nonbonded pdb=" O ASP E 247 " pdb=" OD1 ASP E 247 " model vdw 2.447 3.040 nonbonded pdb=" O VAL A 246 " pdb=" OD1 ASP A 247 " model vdw 2.495 3.040 nonbonded pdb=" O PRO A 271 " pdb=" OD1 ASP A 272 " model vdw 2.495 3.040 ... (remaining 243427 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 236 through 238 and (name N or name CA or name C or \ name O or name CB )) or resid 239 through 317 or (resid 318 through 320 and (na \ me N or name CA or name C or name O or name CB )) or resid 321 through 345)) selection = (chain 'B' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 236 through 238 and (name N or name CA or name C or \ name O or name CB )) or resid 239 through 345)) selection = (chain 'C' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 236 through 238 and (name N or name CA or name C or \ name O or name CB )) or resid 239 through 317 or (resid 318 through 320 and (na \ me N or name CA or name C or name O or name CB )) or resid 321 through 345)) selection = (chain 'D' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 236 through 238 and (name N or name CA or name C or \ name O or name CB )) or resid 239 through 317 or (resid 318 through 320 and (na \ me N or name CA or name C or name O or name CB )) or resid 321 through 345)) selection = (chain 'E' and (resid 1 through 38 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 161 or resid 169 through 178 or res \ id 183 through 231 or (resid 236 through 238 and (name N or name CA or name C or \ name O or name CB )) or resid 239 through 317 or (resid 318 through 320 and (na \ me N or name CA or name C or name O or name CB )) or resid 321 through 345)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 14 through 88 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 209 or (resid 210 through 219 and \ (name N or name CA or name C or name O or name CB )) or resid 220 through 234 or \ resid 241 through 251 or (resid 252 through 260 and (name N or name CA or name \ C or name O or name CB )) or resid 261 or (resid 262 through 279 and (name N or \ name CA or name C or name O or name CB )) or resid 280 through 319 or (resid 331 \ through 333 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 34 through 346 or (resid 347 through 350 and (name N or name CA or name C or nam \ e O or name CB )) or resid 351 or (resid 352 through 355 and (name N or name CA \ or name C or name O or name CB )) or resid 375 through 395)) selection = (chain 'J' and ((resid 14 through 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 through 31 or (resid 32 through 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 66 or (resid 67 throug \ h 74 and (name N or name CA or name C or name O or name CB )) or resid 75 throug \ h 88 or resid 92 through 159 or (resid 160 through 167 and (name N or name CA or \ name C or name O or name CB )) or resid 168 through 170 or (resid 171 and (name \ N or name CA or name C or name O or name CB )) or resid 172 or (resid 173 throu \ gh 176 and (name N or name CA or name C or name O or name CB )) or resid 177 or \ (resid 178 through 179 and (name N or name CA or name C or name O or name CB )) \ or resid 180 or (resid 181 through 185 and (name N or name CA or name C or name \ O or name CB )) or resid 186 or (resid 187 through 202 and (name N or name CA or \ name C or name O or name CB )) or resid 203 through 230 or (resid 231 through 2 \ 42 and (name N or name CA or name C or name O or name CB )) or resid 243 or (res \ id 244 and (name N or name CA or name C or name O or name CB )) or resid 245 thr \ ough 395)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 25.770 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 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 : 0.003 0.057 30261 Z= 0.182 Angle : 0.619 14.148 41551 Z= 0.364 Chirality : 0.041 0.350 4572 Planarity : 0.004 0.064 5000 Dihedral : 19.207 97.882 11275 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.84 % Allowed : 34.79 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 3407 helix: 1.02 (0.16), residues: 1098 sheet: 0.06 (0.24), residues: 507 loop : -0.92 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 110 TYR 0.021 0.001 TYR I 222 PHE 0.021 0.001 PHE G 135 TRP 0.031 0.001 TRP J 229 HIS 0.006 0.001 HIS J 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.18 (30261) covalent geometry : angle 0.61949 / 0.36 (41551) hydrogen bonds : bond 0.13757 / 13.28 ( 972) hydrogen bonds : angle 5.67429 / 7.51 ( 2594) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 276 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.7888 (p0) REVERT: A 212 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8392 (p) REVERT: A 236 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: A 325 MET cc_start: 0.8507 (tpp) cc_final: 0.8269 (tpt) REVERT: C 1 MET cc_start: 0.7795 (ttm) cc_final: 0.7414 (ptp) REVERT: C 342 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8885 (mt) REVERT: C 344 GLN cc_start: 0.8438 (pt0) cc_final: 0.7630 (pp30) REVERT: C 345 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7965 (ttmm) REVERT: D 99 LYS cc_start: 0.8660 (ptmm) cc_final: 0.8232 (ttmt) REVERT: D 107 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: D 198 ASP cc_start: 0.8886 (m-30) cc_final: 0.8487 (m-30) REVERT: E 286 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8477 (ttt90) REVERT: E 314 GLN cc_start: 0.8899 (tp40) cc_final: 0.8642 (tp-100) REVERT: F 1 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.6172 (pmt) REVERT: F 174 ARG cc_start: 0.8555 (ptm160) cc_final: 0.8177 (tmm-80) REVERT: G 539 GLU cc_start: 0.8326 (tp30) cc_final: 0.7931 (tp30) REVERT: H 27 GLU cc_start: 0.6805 (tp30) cc_final: 0.6510 (tp30) REVERT: H 36 GLU cc_start: 0.7691 (mm-30) cc_final: 0.6839 (pm20) REVERT: I 147 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.6237 (p-80) REVERT: I 153 TYR cc_start: 0.3667 (OUTLIER) cc_final: 0.3389 (t80) REVERT: I 258 LYS cc_start: 0.8284 (mmpt) cc_final: 0.7825 (mtmt) REVERT: I 276 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.6977 (t0) REVERT: I 286 LYS cc_start: 0.7319 (tppp) cc_final: 0.7015 (pttp) REVERT: J 281 LYS cc_start: 0.6381 (OUTLIER) cc_final: 0.5898 (mtmt) REVERT: J 286 LYS cc_start: 0.8277 (tptt) cc_final: 0.7920 (tptm) outliers start: 108 outliers final: 76 residues processed: 372 average time/residue: 0.5788 time to fit residues: 261.4538 Evaluate side-chains 344 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 256 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 286 ARG Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 559 ILE Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 153 TYR Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 268 PHE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain J residue 175 TYR Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 230 TRP Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 281 LYS Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 382 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 386 GLN ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.111930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.078339 restraints weight = 62375.142| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.60 r_work: 0.3060 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30261 Z= 0.125 Angle : 0.536 8.197 41551 Z= 0.285 Chirality : 0.040 0.153 4572 Planarity : 0.004 0.064 5000 Dihedral : 15.465 98.405 5227 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 6.79 % Allowed : 31.27 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 3407 helix: 1.18 (0.16), residues: 1125 sheet: 0.14 (0.24), residues: 505 loop : -0.96 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 110 TYR 0.012 0.001 TYR G 420 PHE 0.014 0.001 PHE J 248 TRP 0.031 0.001 TRP J 229 HIS 0.006 0.001 HIS D 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (30261) covalent geometry : angle 0.53558 / 0.29 (41551) hydrogen bonds : bond 0.04277 / 4.20 ( 972) hydrogen bonds : angle 4.77310 / 6.34 ( 2594) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 288 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7208 (tp30) REVERT: A 138 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7849 (p0) REVERT: C 1 MET cc_start: 0.7887 (ttm) cc_final: 0.7493 (ptp) REVERT: C 325 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8647 (ttm) REVERT: D 99 LYS cc_start: 0.8642 (ptmm) cc_final: 0.8210 (ttmt) REVERT: D 310 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8321 (pp30) REVERT: E 247 ASP cc_start: 0.8160 (t0) cc_final: 0.7867 (t0) REVERT: E 314 GLN cc_start: 0.8926 (tp40) cc_final: 0.8647 (tp-100) REVERT: F 88 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: F 174 ARG cc_start: 0.8607 (ptm160) cc_final: 0.8148 (tmm-80) REVERT: G 53 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6148 (mt0) REVERT: G 220 SER cc_start: 0.9077 (OUTLIER) cc_final: 0.8795 (m) REVERT: G 539 GLU cc_start: 0.8316 (tp30) cc_final: 0.7894 (tp30) REVERT: H 27 GLU cc_start: 0.7641 (tp30) cc_final: 0.7223 (tp30) REVERT: H 36 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7191 (pm20) REVERT: H 40 ILE cc_start: 0.6320 (OUTLIER) cc_final: 0.5977 (tp) REVERT: H 149 TYR cc_start: 0.7686 (p90) cc_final: 0.7406 (p90) REVERT: I 121 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6994 (ttp-110) REVERT: I 153 TYR cc_start: 0.3249 (OUTLIER) cc_final: 0.2914 (t80) REVERT: I 275 LYS cc_start: 0.8551 (tppt) cc_final: 0.8350 (mmmt) REVERT: I 286 LYS cc_start: 0.8015 (tppp) cc_final: 0.7312 (pttm) REVERT: I 310 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7435 (mt0) REVERT: I 322 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8152 (ttmm) REVERT: I 330 MET cc_start: 0.7589 (tmm) cc_final: 0.7259 (tmt) REVERT: I 343 GLN cc_start: 0.8013 (tm130) cc_final: 0.7807 (tm130) REVERT: J 42 LYS cc_start: 0.9163 (tttt) cc_final: 0.8530 (tptt) REVERT: J 104 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7845 (mm-40) REVERT: J 151 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.6177 (t80) REVERT: J 197 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: J 281 LYS cc_start: 0.6077 (OUTLIER) cc_final: 0.5717 (mtmt) REVERT: J 312 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.7809 (pp) outliers start: 191 outliers final: 78 residues processed: 446 average time/residue: 0.5251 time to fit residues: 288.9164 Evaluate side-chains 347 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 253 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 438 LYS Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 105 PHE Chi-restraints excluded: chain I residue 121 ARG Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 153 TYR Chi-restraints excluded: chain I residue 268 PHE Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 296 ASP Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 334 CYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 104 GLN Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 281 LYS Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 312 ILE Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 382 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 0.8980 chunk 259 optimal weight: 9.9990 chunk 321 optimal weight: 2.9990 chunk 128 optimal weight: 0.3980 chunk 338 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN I 350 GLN I 386 GLN J 386 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.112052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.078637 restraints weight = 62372.009| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.60 r_work: 0.3067 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30261 Z= 0.120 Angle : 0.531 11.039 41551 Z= 0.280 Chirality : 0.040 0.198 4572 Planarity : 0.004 0.077 5000 Dihedral : 15.232 98.318 5139 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 6.97 % Allowed : 31.49 % Favored : 61.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 3407 helix: 1.21 (0.16), residues: 1123 sheet: 0.15 (0.24), residues: 505 loop : -0.97 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 110 TYR 0.023 0.001 TYR I 222 PHE 0.014 0.001 PHE I 299 TRP 0.029 0.001 TRP J 229 HIS 0.005 0.001 HIS D 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (30261) covalent geometry : angle 0.53145 / 0.28 (41551) hydrogen bonds : bond 0.03954 / 3.90 ( 972) hydrogen bonds : angle 4.61017 / 6.13 ( 2594) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 272 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8327 (p0) REVERT: A 138 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7791 (p0) REVERT: A 202 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: C 1 MET cc_start: 0.7919 (ttm) cc_final: 0.7543 (ptp) REVERT: C 325 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8645 (ttm) REVERT: D 1 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8132 (tpt) REVERT: D 99 LYS cc_start: 0.8621 (ptmm) cc_final: 0.8180 (ttmt) REVERT: D 310 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8330 (pp30) REVERT: E 247 ASP cc_start: 0.8265 (t0) cc_final: 0.7932 (t0) REVERT: E 314 GLN cc_start: 0.8917 (tp40) cc_final: 0.8618 (tp-100) REVERT: F 88 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: F 174 ARG cc_start: 0.8596 (ptm160) cc_final: 0.8170 (tmm-80) REVERT: G 220 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8755 (m) REVERT: G 268 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8973 (pm20) REVERT: G 539 GLU cc_start: 0.8299 (tp30) cc_final: 0.7900 (tp30) REVERT: H 27 GLU cc_start: 0.7614 (tp30) cc_final: 0.7186 (tp30) REVERT: H 36 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7172 (pm20) REVERT: H 40 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.5986 (tp) REVERT: H 118 GLU cc_start: 0.8011 (pp20) cc_final: 0.7775 (pp20) REVERT: H 149 TYR cc_start: 0.7788 (p90) cc_final: 0.7381 (p90) REVERT: I 105 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.5985 (m-80) REVERT: I 153 TYR cc_start: 0.3284 (OUTLIER) cc_final: 0.2929 (t80) REVERT: I 281 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6659 (pmtt) REVERT: I 286 LYS cc_start: 0.7968 (tppp) cc_final: 0.7257 (pttm) REVERT: I 308 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8741 (mmp) REVERT: I 310 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: I 322 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8045 (ttmm) REVERT: I 330 MET cc_start: 0.7614 (tmm) cc_final: 0.7215 (tmt) REVERT: I 343 GLN cc_start: 0.7999 (tm130) cc_final: 0.7773 (tm130) REVERT: I 384 GLU cc_start: 0.8849 (mp0) cc_final: 0.8506 (mp0) REVERT: J 104 GLN cc_start: 0.8012 (mt0) cc_final: 0.7678 (mm-40) REVERT: J 197 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: J 379 CYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8033 (m) outliers start: 196 outliers final: 89 residues processed: 431 average time/residue: 0.5405 time to fit residues: 286.3746 Evaluate side-chains 369 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 263 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain G residue 438 LYS Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain I residue 105 PHE Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 153 TYR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 332 GLU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 334 CYS Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain J residue 175 TYR Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 379 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 269 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 238 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 340 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 73 optimal weight: 0.0670 chunk 321 optimal weight: 0.9990 chunk 207 optimal weight: 0.5980 chunk 216 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN E 67 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN I 386 GLN J 386 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.112836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079378 restraints weight = 62103.128| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.60 r_work: 0.3081 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30261 Z= 0.107 Angle : 0.525 9.598 41551 Z= 0.278 Chirality : 0.039 0.181 4572 Planarity : 0.004 0.077 5000 Dihedral : 15.177 99.130 5126 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 6.82 % Allowed : 31.49 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3407 helix: 1.23 (0.16), residues: 1128 sheet: 0.15 (0.24), residues: 507 loop : -0.95 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 110 TYR 0.014 0.001 TYR I 222 PHE 0.019 0.001 PHE J 248 TRP 0.028 0.001 TRP J 229 HIS 0.006 0.001 HIS D 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (30261) covalent geometry : angle 0.52516 / 0.28 (41551) hydrogen bonds : bond 0.03679 / 3.62 ( 972) hydrogen bonds : angle 4.49510 / 5.98 ( 2594) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 284 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8290 (p0) REVERT: A 138 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7687 (p0) REVERT: B 236 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: C 1 MET cc_start: 0.7936 (ttm) cc_final: 0.7575 (ptp) REVERT: C 325 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8653 (ttm) REVERT: C 344 GLN cc_start: 0.8439 (pt0) cc_final: 0.7731 (pp30) REVERT: D 310 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8314 (pp30) REVERT: E 247 ASP cc_start: 0.8342 (t0) cc_final: 0.8013 (t0) REVERT: E 275 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8638 (pmtt) REVERT: E 314 GLN cc_start: 0.8904 (tp40) cc_final: 0.8620 (tp-100) REVERT: F 2 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8410 (tptp) REVERT: F 88 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: F 174 ARG cc_start: 0.8587 (ptm160) cc_final: 0.8152 (tmm-80) REVERT: F 202 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: G 55 ASN cc_start: 0.7200 (p0) cc_final: 0.6997 (p0) REVERT: G 220 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8704 (m) REVERT: G 264 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8175 (mt) REVERT: G 539 GLU cc_start: 0.8293 (tp30) cc_final: 0.7905 (tp30) REVERT: G 585 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.7999 (mmm-85) REVERT: H 27 GLU cc_start: 0.7615 (tp30) cc_final: 0.7113 (tp30) REVERT: H 36 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7194 (pm20) REVERT: H 40 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.5964 (tp) REVERT: H 74 TYR cc_start: 0.7129 (t80) cc_final: 0.6812 (t80) REVERT: H 118 GLU cc_start: 0.8078 (pp20) cc_final: 0.7818 (pp20) REVERT: H 129 ARG cc_start: 0.5836 (OUTLIER) cc_final: 0.4895 (ppt170) REVERT: H 149 TYR cc_start: 0.7857 (p90) cc_final: 0.7384 (p90) REVERT: I 105 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.6124 (m-80) REVERT: I 153 TYR cc_start: 0.3284 (OUTLIER) cc_final: 0.2921 (t80) REVERT: I 281 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6707 (pmtt) REVERT: I 286 LYS cc_start: 0.7913 (tppp) cc_final: 0.7227 (pttm) REVERT: I 308 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8755 (mmp) REVERT: I 310 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: I 322 LYS cc_start: 0.8558 (ttpp) cc_final: 0.8059 (ttmm) REVERT: I 330 MET cc_start: 0.7629 (tmm) cc_final: 0.7221 (tmt) REVERT: I 343 GLN cc_start: 0.7979 (tm130) cc_final: 0.7742 (tm130) REVERT: I 384 GLU cc_start: 0.8849 (mp0) cc_final: 0.8536 (mp0) REVERT: J 42 LYS cc_start: 0.9181 (tttt) cc_final: 0.8967 (tttt) REVERT: J 104 GLN cc_start: 0.7918 (mt0) cc_final: 0.7608 (mm-40) REVERT: J 120 PRO cc_start: 0.8408 (Cg_endo) cc_final: 0.8046 (Cg_exo) REVERT: J 197 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: J 281 LYS cc_start: 0.6001 (OUTLIER) cc_final: 0.5618 (mtmm) outliers start: 192 outliers final: 84 residues processed: 438 average time/residue: 0.5655 time to fit residues: 303.1090 Evaluate side-chains 366 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 262 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 335 ASN Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 438 LYS Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 559 ILE Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 129 ARG Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 105 PHE Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 153 TYR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 268 PHE Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 296 ASP Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 334 CYS Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 281 LYS Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 293 optimal weight: 0.7980 chunk 222 optimal weight: 8.9990 chunk 248 optimal weight: 0.0770 chunk 23 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 344 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 319 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN I 386 GLN J 386 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.112679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079460 restraints weight = 62198.503| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.61 r_work: 0.3074 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30261 Z= 0.110 Angle : 0.536 9.837 41551 Z= 0.280 Chirality : 0.039 0.175 4572 Planarity : 0.004 0.080 5000 Dihedral : 15.134 99.750 5120 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 6.86 % Allowed : 31.59 % Favored : 61.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3407 helix: 1.19 (0.16), residues: 1145 sheet: 0.18 (0.24), residues: 507 loop : -0.90 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 341 TYR 0.032 0.001 TYR I 270 PHE 0.013 0.001 PHE I 299 TRP 0.031 0.001 TRP J 229 HIS 0.006 0.001 HIS D 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (30261) covalent geometry : angle 0.53633 / 0.28 (41551) hydrogen bonds : bond 0.03575 / 3.52 ( 972) hydrogen bonds : angle 4.42884 / 5.89 ( 2594) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 276 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7570 (p0) REVERT: B 236 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: C 1 MET cc_start: 0.8023 (ttm) cc_final: 0.7687 (ptp) REVERT: C 325 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8614 (ttm) REVERT: C 344 GLN cc_start: 0.8414 (pt0) cc_final: 0.7725 (pp30) REVERT: D 310 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8311 (pp30) REVERT: E 149 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8683 (m) REVERT: E 247 ASP cc_start: 0.8448 (t0) cc_final: 0.8105 (t0) REVERT: E 275 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8658 (pmtt) REVERT: E 314 GLN cc_start: 0.8936 (tp40) cc_final: 0.8656 (tp-100) REVERT: F 174 ARG cc_start: 0.8602 (ptm160) cc_final: 0.8168 (tmm-80) REVERT: F 175 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8736 (ptmm) REVERT: F 202 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: G 55 ASN cc_start: 0.7484 (p0) cc_final: 0.7284 (p0) REVERT: G 220 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8660 (m) REVERT: G 247 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8446 (tpt) REVERT: G 264 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8158 (mt) REVERT: G 539 GLU cc_start: 0.8316 (tp30) cc_final: 0.7906 (tp30) REVERT: G 585 ARG cc_start: 0.8418 (mmm-85) cc_final: 0.8037 (mmm-85) REVERT: H 27 GLU cc_start: 0.7609 (tp30) cc_final: 0.7132 (tp30) REVERT: H 36 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7205 (pm20) REVERT: H 40 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.5989 (tp) REVERT: H 74 TYR cc_start: 0.7026 (t80) cc_final: 0.6668 (t80) REVERT: H 118 GLU cc_start: 0.8095 (pp20) cc_final: 0.7786 (pp20) REVERT: H 149 TYR cc_start: 0.7931 (p90) cc_final: 0.7391 (p90) REVERT: I 153 TYR cc_start: 0.3354 (OUTLIER) cc_final: 0.2944 (t80) REVERT: I 258 LYS cc_start: 0.8490 (mmpt) cc_final: 0.7820 (mtmt) REVERT: I 276 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.6949 (t0) REVERT: I 281 LYS cc_start: 0.7097 (pttt) cc_final: 0.6751 (pmtt) REVERT: I 286 LYS cc_start: 0.7907 (tppp) cc_final: 0.7223 (pttm) REVERT: I 308 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8755 (mmp) REVERT: I 310 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: I 322 LYS cc_start: 0.8543 (ttpp) cc_final: 0.8031 (ttmm) REVERT: I 330 MET cc_start: 0.7695 (tmm) cc_final: 0.7220 (tmt) REVERT: I 343 GLN cc_start: 0.7986 (tm130) cc_final: 0.7777 (tm130) REVERT: I 384 GLU cc_start: 0.8854 (mp0) cc_final: 0.8529 (mp0) REVERT: J 104 GLN cc_start: 0.7934 (mt0) cc_final: 0.7442 (mm-40) REVERT: J 120 PRO cc_start: 0.8391 (Cg_endo) cc_final: 0.8095 (Cg_exo) REVERT: J 281 LYS cc_start: 0.6000 (OUTLIER) cc_final: 0.5609 (mtmt) outliers start: 193 outliers final: 98 residues processed: 428 average time/residue: 0.5272 time to fit residues: 277.9877 Evaluate side-chains 383 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 268 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 335 ASN Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 438 LYS Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 559 ILE Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 153 TYR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 268 PHE Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 332 GLU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 281 LYS Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 89 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 275 optimal weight: 5.9990 chunk 324 optimal weight: 0.0470 overall best weight: 2.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN E 67 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 ASN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.111117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077494 restraints weight = 62063.316| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.59 r_work: 0.3042 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30261 Z= 0.169 Angle : 0.559 9.222 41551 Z= 0.293 Chirality : 0.041 0.170 4572 Planarity : 0.004 0.093 5000 Dihedral : 15.091 97.714 5117 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 6.86 % Allowed : 31.95 % Favored : 61.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3407 helix: 1.29 (0.16), residues: 1128 sheet: 0.12 (0.23), residues: 519 loop : -0.94 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 341 TYR 0.030 0.001 TYR I 270 PHE 0.020 0.001 PHE G 135 TRP 0.032 0.001 TRP J 229 HIS 0.005 0.001 HIS D 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (30261) covalent geometry : angle 0.55885 / 0.29 (41551) hydrogen bonds : bond 0.03847 / 3.79 ( 972) hydrogen bonds : angle 4.45007 / 5.90 ( 2594) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 273 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7807 (p0) REVERT: A 236 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: B 236 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: C 1 MET cc_start: 0.7975 (ttm) cc_final: 0.7623 (ptp) REVERT: C 325 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8615 (ttm) REVERT: C 344 GLN cc_start: 0.8465 (pt0) cc_final: 0.7763 (pp30) REVERT: D 99 LYS cc_start: 0.8557 (ptmm) cc_final: 0.8169 (ttmt) REVERT: D 310 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8317 (pp30) REVERT: E 247 ASP cc_start: 0.8534 (t0) cc_final: 0.8238 (t0) REVERT: E 275 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8660 (pmtt) REVERT: F 1 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.6347 (pmt) REVERT: F 88 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: F 174 ARG cc_start: 0.8626 (ptm160) cc_final: 0.8199 (tmm-80) REVERT: F 175 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8803 (ptmm) REVERT: F 202 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8536 (pm20) REVERT: G 220 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8706 (m) REVERT: G 247 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8356 (tpt) REVERT: G 264 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8172 (mt) REVERT: G 539 GLU cc_start: 0.8350 (tp30) cc_final: 0.7899 (tp30) REVERT: G 585 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.8033 (mmm-85) REVERT: H 27 GLU cc_start: 0.7594 (tp30) cc_final: 0.7115 (tp30) REVERT: H 36 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7221 (pm20) REVERT: H 74 TYR cc_start: 0.7223 (t80) cc_final: 0.6936 (t80) REVERT: H 118 GLU cc_start: 0.8115 (pp20) cc_final: 0.7791 (pp20) REVERT: H 149 TYR cc_start: 0.8073 (p90) cc_final: 0.7543 (p90) REVERT: I 153 TYR cc_start: 0.3307 (OUTLIER) cc_final: 0.2866 (t80) REVERT: I 276 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7093 (t0) REVERT: I 286 LYS cc_start: 0.7957 (tppp) cc_final: 0.7251 (pttm) REVERT: I 308 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8775 (mmp) REVERT: I 310 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: I 313 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: I 322 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8078 (ttmm) REVERT: I 330 MET cc_start: 0.7705 (tmm) cc_final: 0.7207 (tmt) REVERT: I 343 GLN cc_start: 0.7974 (tm130) cc_final: 0.7762 (tm130) REVERT: I 350 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: I 384 GLU cc_start: 0.8850 (mp0) cc_final: 0.8522 (mp0) REVERT: I 390 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7446 (t80) REVERT: J 42 LYS cc_start: 0.9182 (tttt) cc_final: 0.8541 (tttt) REVERT: J 104 GLN cc_start: 0.8009 (mt0) cc_final: 0.7502 (mm-40) REVERT: J 281 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5547 (mtmt) REVERT: J 308 MET cc_start: 0.7531 (tmm) cc_final: 0.6803 (mmp) REVERT: J 312 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8095 (tt) REVERT: J 379 CYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7776 (m) outliers start: 193 outliers final: 112 residues processed: 423 average time/residue: 0.5587 time to fit residues: 287.2055 Evaluate side-chains 394 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 259 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 438 LYS Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 559 ILE Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 190 ASN Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 153 TYR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 268 PHE Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 300 ARG Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain I residue 313 GLU Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 332 GLU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 334 CYS Chi-restraints excluded: chain I residue 347 MET Chi-restraints excluded: chain I residue 350 GLN Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 390 PHE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain J residue 230 TRP Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 281 LYS Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 312 ILE Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 379 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 158 optimal weight: 1.9990 chunk 235 optimal weight: 30.0000 chunk 305 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 194 optimal weight: 0.0170 chunk 312 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 67 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 386 GLN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.110502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.076871 restraints weight = 62522.126| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.59 r_work: 0.3027 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30261 Z= 0.187 Angle : 0.575 10.097 41551 Z= 0.301 Chirality : 0.041 0.169 4572 Planarity : 0.004 0.094 5000 Dihedral : 15.097 95.926 5117 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 7.04 % Allowed : 31.91 % Favored : 61.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3407 helix: 1.25 (0.16), residues: 1123 sheet: 0.09 (0.24), residues: 519 loop : -0.95 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 110 TYR 0.023 0.001 TYR I 270 PHE 0.017 0.001 PHE G 135 TRP 0.033 0.001 TRP I 206 HIS 0.006 0.001 HIS J 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (30261) covalent geometry : angle 0.57488 / 0.30 (41551) hydrogen bonds : bond 0.03944 / 3.85 ( 972) hydrogen bonds : angle 4.47431 / 5.92 ( 2594) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 261 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.7857 (p0) REVERT: A 236 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: B 167 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8208 (pp) REVERT: B 236 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: C 325 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8617 (ttm) REVERT: C 344 GLN cc_start: 0.8487 (pt0) cc_final: 0.7708 (pp30) REVERT: D 99 LYS cc_start: 0.8599 (ptmm) cc_final: 0.8204 (ttmt) REVERT: D 310 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8307 (pp30) REVERT: E 247 ASP cc_start: 0.8569 (t0) cc_final: 0.8304 (t0) REVERT: E 249 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: E 275 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8645 (pmtt) REVERT: F 1 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.6236 (pmt) REVERT: F 88 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: F 174 ARG cc_start: 0.8646 (ptm160) cc_final: 0.8222 (tmm-80) REVERT: F 175 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8819 (ptmm) REVERT: F 202 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8515 (pm20) REVERT: F 314 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: G 220 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8738 (t) REVERT: G 221 MET cc_start: 0.9004 (mmm) cc_final: 0.8776 (tpp) REVERT: G 247 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8343 (tpt) REVERT: G 539 GLU cc_start: 0.8336 (tp30) cc_final: 0.7882 (tp30) REVERT: G 585 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.8031 (mmm-85) REVERT: H 27 GLU cc_start: 0.7611 (tp30) cc_final: 0.7148 (tp30) REVERT: H 36 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7233 (pm20) REVERT: H 74 TYR cc_start: 0.7314 (t80) cc_final: 0.7112 (t80) REVERT: H 118 GLU cc_start: 0.8139 (pp20) cc_final: 0.7799 (pp20) REVERT: H 149 TYR cc_start: 0.8142 (p90) cc_final: 0.7565 (p90) REVERT: I 153 TYR cc_start: 0.3295 (OUTLIER) cc_final: 0.2661 (t80) REVERT: I 156 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: I 258 LYS cc_start: 0.8464 (mmpt) cc_final: 0.7785 (mtmt) REVERT: I 276 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7093 (t0) REVERT: I 281 LYS cc_start: 0.7051 (pttt) cc_final: 0.6507 (pmtt) REVERT: I 286 LYS cc_start: 0.7983 (tppp) cc_final: 0.7770 (tmtt) REVERT: I 308 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8771 (mmp) REVERT: I 310 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: I 313 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: I 322 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8093 (ttmm) REVERT: I 330 MET cc_start: 0.7676 (tmm) cc_final: 0.7167 (tmt) REVERT: I 350 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: I 384 GLU cc_start: 0.8894 (mp0) cc_final: 0.8467 (mp0) REVERT: J 104 GLN cc_start: 0.7968 (mt0) cc_final: 0.7650 (mm-40) REVERT: J 120 PRO cc_start: 0.8363 (Cg_endo) cc_final: 0.8005 (Cg_exo) REVERT: J 281 LYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5509 (mtmt) REVERT: J 379 CYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7742 (m) outliers start: 198 outliers final: 121 residues processed: 417 average time/residue: 0.5090 time to fit residues: 259.9113 Evaluate side-chains 402 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 257 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain G residue 438 LYS Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 190 ASN Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 153 TYR Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 268 PHE Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain I residue 313 GLU Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 332 GLU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 334 CYS Chi-restraints excluded: chain I residue 350 GLN Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain J residue 230 TRP Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 281 LYS Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 379 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 344 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 312 optimal weight: 8.9990 chunk 138 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 316 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN E 67 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** 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 = 0.3732 r_free = 0.3732 target = 0.111319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.077622 restraints weight = 62090.459| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.60 r_work: 0.3048 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30261 Z= 0.139 Angle : 0.565 10.477 41551 Z= 0.295 Chirality : 0.041 0.178 4572 Planarity : 0.004 0.098 5000 Dihedral : 15.091 97.087 5117 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.25 % Allowed : 32.91 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3407 helix: 1.23 (0.16), residues: 1130 sheet: 0.13 (0.24), residues: 511 loop : -0.95 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 110 TYR 0.021 0.001 TYR I 270 PHE 0.020 0.001 PHE H 162 TRP 0.040 0.001 TRP I 206 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (30261) covalent geometry : angle 0.56498 / 0.30 (41551) hydrogen bonds : bond 0.03715 / 3.63 ( 972) hydrogen bonds : angle 4.41645 / 5.85 ( 2594) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 270 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7836 (p0) REVERT: A 236 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: B 236 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: C 342 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8902 (mt) REVERT: C 344 GLN cc_start: 0.8492 (pt0) cc_final: 0.7739 (pp30) REVERT: D 99 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8192 (ttmt) REVERT: D 310 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8319 (pp30) REVERT: E 247 ASP cc_start: 0.8589 (t0) cc_final: 0.8346 (t0) REVERT: E 249 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: E 275 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8653 (pmtt) REVERT: F 1 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.6262 (pmt) REVERT: F 88 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8475 (pm20) REVERT: F 174 ARG cc_start: 0.8634 (ptm160) cc_final: 0.8191 (tmm-80) REVERT: F 175 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8774 (ptmm) REVERT: F 202 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8509 (pm20) REVERT: F 314 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: G 220 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8745 (t) REVERT: G 247 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8404 (tpt) REVERT: G 539 GLU cc_start: 0.8327 (tp30) cc_final: 0.7876 (tp30) REVERT: G 585 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8005 (mmm-85) REVERT: H 27 GLU cc_start: 0.7559 (tp30) cc_final: 0.7118 (tp30) REVERT: H 36 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7202 (pm20) REVERT: H 118 GLU cc_start: 0.8186 (pp20) cc_final: 0.7857 (pp20) REVERT: H 149 TYR cc_start: 0.8211 (p90) cc_final: 0.7633 (p90) REVERT: H 154 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7942 (pp20) REVERT: I 153 TYR cc_start: 0.3308 (OUTLIER) cc_final: 0.2645 (t80) REVERT: I 276 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7078 (t0) REVERT: I 281 LYS cc_start: 0.7059 (pttt) cc_final: 0.6588 (pmtt) REVERT: I 286 LYS cc_start: 0.7981 (tppp) cc_final: 0.7760 (tmtt) REVERT: I 308 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8761 (mmp) REVERT: I 310 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: I 313 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: I 322 LYS cc_start: 0.8585 (ttpp) cc_final: 0.8073 (ttmm) REVERT: I 330 MET cc_start: 0.7640 (tmm) cc_final: 0.7127 (tmt) REVERT: I 350 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: I 384 GLU cc_start: 0.8865 (mp0) cc_final: 0.8458 (mp0) REVERT: J 104 GLN cc_start: 0.7954 (mt0) cc_final: 0.7656 (mm-40) REVERT: J 120 PRO cc_start: 0.8394 (Cg_endo) cc_final: 0.8055 (Cg_exo) REVERT: J 281 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5441 (mtmt) REVERT: J 308 MET cc_start: 0.7580 (tmm) cc_final: 0.6896 (mmp) outliers start: 176 outliers final: 109 residues processed: 413 average time/residue: 0.5151 time to fit residues: 260.9173 Evaluate side-chains 385 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 255 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain G residue 438 LYS Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 153 TYR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 268 PHE Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 296 ASP Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain I residue 313 GLU Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 332 GLU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 334 CYS Chi-restraints excluded: chain I residue 350 GLN Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain J residue 230 TRP Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 281 LYS Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 270 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 236 optimal weight: 30.0000 chunk 214 optimal weight: 0.1980 chunk 138 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 148 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 252 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 67 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** I 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.078012 restraints weight = 62187.642| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.60 r_work: 0.3050 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30261 Z= 0.133 Angle : 0.570 11.275 41551 Z= 0.296 Chirality : 0.040 0.175 4572 Planarity : 0.004 0.098 5000 Dihedral : 15.076 97.383 5117 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.65 % Allowed : 33.72 % Favored : 60.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3407 helix: 1.26 (0.16), residues: 1124 sheet: 0.18 (0.24), residues: 501 loop : -0.95 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 110 TYR 0.017 0.001 TYR I 270 PHE 0.017 0.001 PHE H 162 TRP 0.046 0.001 TRP I 206 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (30261) covalent geometry : angle 0.56979 / 0.30 (41551) hydrogen bonds : bond 0.03663 / 3.57 ( 972) hydrogen bonds : angle 4.40600 / 5.82 ( 2594) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 257 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.7795 (p0) REVERT: A 236 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: B 236 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: C 325 MET cc_start: 0.8810 (tmm) cc_final: 0.8520 (ttm) REVERT: C 342 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8886 (mt) REVERT: C 344 GLN cc_start: 0.8494 (pt0) cc_final: 0.7731 (pp30) REVERT: D 99 LYS cc_start: 0.8600 (ptmm) cc_final: 0.8193 (ttmt) REVERT: D 310 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8321 (pp30) REVERT: E 247 ASP cc_start: 0.8597 (t0) cc_final: 0.8377 (t0) REVERT: E 275 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8646 (pmtt) REVERT: F 1 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.6242 (pmt) REVERT: F 88 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8481 (pm20) REVERT: F 174 ARG cc_start: 0.8632 (ptm160) cc_final: 0.8188 (tmm-80) REVERT: F 175 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8768 (ptmm) REVERT: F 202 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: F 314 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: G 220 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8719 (m) REVERT: G 247 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8344 (tpt) REVERT: G 260 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8852 (mtp) REVERT: G 539 GLU cc_start: 0.8320 (tp30) cc_final: 0.7872 (tp30) REVERT: G 585 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.7990 (mmm-85) REVERT: H 27 GLU cc_start: 0.7607 (tp30) cc_final: 0.7124 (tp30) REVERT: H 36 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7239 (pm20) REVERT: H 74 TYR cc_start: 0.7336 (t80) cc_final: 0.7133 (t80) REVERT: H 118 GLU cc_start: 0.8157 (pp20) cc_final: 0.7829 (pp20) REVERT: H 149 TYR cc_start: 0.8223 (p90) cc_final: 0.7609 (p90) REVERT: H 154 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8105 (pp20) REVERT: I 153 TYR cc_start: 0.3336 (OUTLIER) cc_final: 0.2675 (t80) REVERT: I 258 LYS cc_start: 0.8442 (mmpt) cc_final: 0.7759 (mtmt) REVERT: I 275 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8333 (tmmm) REVERT: I 276 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.6985 (t0) REVERT: I 286 LYS cc_start: 0.7995 (tppp) cc_final: 0.7762 (tmtt) REVERT: I 308 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8746 (mmp) REVERT: I 310 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: I 313 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: I 322 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8077 (ttmm) REVERT: I 330 MET cc_start: 0.7619 (tmm) cc_final: 0.7091 (tmt) REVERT: I 350 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: I 384 GLU cc_start: 0.8900 (mp0) cc_final: 0.8472 (mp0) REVERT: J 104 GLN cc_start: 0.7945 (mt0) cc_final: 0.7646 (mm-40) REVERT: J 120 PRO cc_start: 0.8386 (Cg_endo) cc_final: 0.8031 (Cg_exo) REVERT: J 281 LYS cc_start: 0.5930 (OUTLIER) cc_final: 0.5454 (mtmm) REVERT: J 308 MET cc_start: 0.7641 (tmm) cc_final: 0.6953 (mmp) REVERT: J 379 CYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7660 (m) outliers start: 159 outliers final: 109 residues processed: 387 average time/residue: 0.5134 time to fit residues: 241.9969 Evaluate side-chains 385 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 254 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 438 LYS Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 153 TYR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 268 PHE Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain I residue 313 GLU Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 332 GLU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 334 CYS Chi-restraints excluded: chain I residue 350 GLN Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain J residue 230 TRP Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 281 LYS Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 379 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 30.0000 chunk 266 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 67 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.111916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.078440 restraints weight = 61990.116| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.59 r_work: 0.3060 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30261 Z= 0.126 Angle : 0.571 11.286 41551 Z= 0.297 Chirality : 0.040 0.175 4572 Planarity : 0.004 0.097 5000 Dihedral : 15.053 98.221 5116 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.33 % Allowed : 34.12 % Favored : 60.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3407 helix: 1.26 (0.16), residues: 1130 sheet: 0.19 (0.24), residues: 503 loop : -0.95 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 110 TYR 0.015 0.001 TYR A 63 PHE 0.015 0.001 PHE H 162 TRP 0.053 0.001 TRP I 206 HIS 0.007 0.001 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (30261) covalent geometry : angle 0.57110 / 0.30 (41551) hydrogen bonds : bond 0.03586 / 3.49 ( 972) hydrogen bonds : angle 4.37199 / 5.77 ( 2594) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6814 Ramachandran restraints generated. 3407 Oldfield, 0 Emsley, 3407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 260 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7734 (p0) REVERT: A 236 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: A 325 MET cc_start: 0.8571 (tpp) cc_final: 0.8323 (tpt) REVERT: C 342 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8873 (mt) REVERT: C 344 GLN cc_start: 0.8491 (pt0) cc_final: 0.7726 (pp30) REVERT: D 99 LYS cc_start: 0.8563 (ptmm) cc_final: 0.8157 (ttmt) REVERT: D 310 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8324 (pp30) REVERT: E 247 ASP cc_start: 0.8606 (t0) cc_final: 0.8390 (t0) REVERT: E 275 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8637 (pmtt) REVERT: F 1 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.6234 (pmt) REVERT: F 88 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8460 (pm20) REVERT: F 174 ARG cc_start: 0.8627 (ptm160) cc_final: 0.8194 (tmm-80) REVERT: F 175 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8755 (ptmm) REVERT: F 202 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8483 (pm20) REVERT: F 314 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: G 247 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8313 (tpt) REVERT: G 264 LEU cc_start: 0.8530 (mm) cc_final: 0.8160 (mt) REVERT: G 539 GLU cc_start: 0.8328 (tp30) cc_final: 0.7871 (tp30) REVERT: G 585 ARG cc_start: 0.8424 (mmm-85) cc_final: 0.7997 (mmm-85) REVERT: H 27 GLU cc_start: 0.7580 (tp30) cc_final: 0.7141 (tp30) REVERT: H 36 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7256 (pm20) REVERT: H 118 GLU cc_start: 0.8127 (pp20) cc_final: 0.7799 (pp20) REVERT: H 149 TYR cc_start: 0.8252 (p90) cc_final: 0.7683 (p90) REVERT: H 154 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8049 (pp20) REVERT: I 153 TYR cc_start: 0.3412 (OUTLIER) cc_final: 0.2756 (t80) REVERT: I 206 TRP cc_start: 0.6670 (t60) cc_final: 0.6463 (t60) REVERT: I 258 LYS cc_start: 0.8436 (mmpt) cc_final: 0.7739 (mtmt) REVERT: I 275 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8335 (tmmm) REVERT: I 276 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.6969 (t0) REVERT: I 286 LYS cc_start: 0.7982 (tppp) cc_final: 0.7760 (tmtt) REVERT: I 308 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8744 (mmp) REVERT: I 310 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: I 313 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: I 322 LYS cc_start: 0.8575 (ttpp) cc_final: 0.8067 (ttmm) REVERT: I 330 MET cc_start: 0.7663 (tmm) cc_final: 0.7133 (tmt) REVERT: I 384 GLU cc_start: 0.8875 (mp0) cc_final: 0.8353 (mp0) REVERT: J 104 GLN cc_start: 0.7921 (mt0) cc_final: 0.7530 (mm-40) REVERT: J 120 PRO cc_start: 0.8401 (Cg_endo) cc_final: 0.8052 (Cg_exo) REVERT: J 281 LYS cc_start: 0.5948 (OUTLIER) cc_final: 0.5473 (mtmm) REVERT: J 308 MET cc_start: 0.7749 (tmm) cc_final: 0.7061 (mmp) outliers start: 150 outliers final: 108 residues processed: 384 average time/residue: 0.5404 time to fit residues: 254.2041 Evaluate side-chains 378 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 253 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 PHE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain G residue 438 LYS Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 598 THR Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 153 TYR Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 268 PHE Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 291 SER Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain I residue 313 GLU Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 332 GLU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 334 CYS Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain J residue 230 TRP Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 281 LYS Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 379 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 57 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 277 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 220 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 67 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** 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 = 0.3749 r_free = 0.3749 target = 0.112445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.078864 restraints weight = 62372.636| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.61 r_work: 0.3070 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30261 Z= 0.118 Angle : 0.569 11.168 41551 Z= 0.297 Chirality : 0.040 0.168 4572 Planarity : 0.004 0.097 5000 Dihedral : 15.031 99.162 5116 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 5.08 % Allowed : 34.26 % Favored : 60.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3407 helix: 1.28 (0.16), residues: 1124 sheet: 0.27 (0.24), residues: 498 loop : -0.94 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 110 TYR 0.016 0.001 TYR A 63 PHE 0.024 0.001 PHE I 245 TRP 0.046 0.001 TRP I 206 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (30261) covalent geometry : angle 0.56940 / 0.30 (41551) hydrogen bonds : bond 0.03539 / 3.43 ( 972) hydrogen bonds : angle 4.35440 / 5.74 ( 2594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9975.98 seconds wall clock time: 171 minutes 13.85 seconds (10273.85 seconds total)