Starting phenix.real_space_refine on Fri Mar 6 10:04:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vtr_65340/03_2026/9vtr_65340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vtr_65340/03_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_65340/03_2026/9vtr_65340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vtr_65340/03_2026/9vtr_65340.map" model { file = "/net/cci-nas-00/data/ceres_data/9vtr_65340/03_2026/9vtr_65340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vtr_65340/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.84, per 1000 atoms: 0.20 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: 2.41 Conformation dependent library (CDL) restraints added in 1.4 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: 3.50 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: 5.11 Time building geometry restraints manager: 3.05 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=" C SER I 106 " pdb=" N PRO I 107 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.04e+00 bond pdb=" CB ILE J 312 " pdb=" CG2 ILE J 312 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.94e+00 bond pdb=" CB ASP F 272 " pdb=" CG ASP F 272 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.35e+00 bond pdb=" CB ASN G 55 " pdb=" CG ASN G 55 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.99e+00 bond pdb=" CB GLU H 153 " pdb=" CG GLU H 153 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 ... (remaining 30256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 41257 2.83 - 5.66: 250 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=" CB MET I 330 " pdb=" CG MET I 330 " pdb=" SD MET I 330 " ideal model delta sigma weight residual 112.70 124.97 -12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" N ILE J 96 " pdb=" CA ILE J 96 " pdb=" C ILE J 96 " ideal model delta sigma weight residual 113.42 108.66 4.76 1.17e+00 7.31e-01 1.65e+01 angle pdb=" C MET J 308 " pdb=" CA MET J 308 " pdb=" CB MET J 308 " ideal model delta sigma weight residual 109.72 117.32 -7.60 1.92e+00 2.71e-01 1.57e+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: 4191 0.070 - 0.140: 370 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: 8.660 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.750 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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= 0.122 Angle : 0.608 14.148 41551 Z= 0.314 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 covalent geometry : bond 0.00265 (30261) covalent geometry : angle 0.60823 (41551) hydrogen bonds : bond 0.13757 ( 972) hydrogen bonds : angle 5.67429 ( 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 : 1.136 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: 0.5454 time to fit residues: 244.7137 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 : 1.029 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** 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 = 0.111961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078394 restraints weight = 62368.132| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.61 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: 0.8512 moved from start: 0.0560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30261 Z= 0.119 Angle : 0.530 8.288 41551 Z= 0.274 Chirality : 0.039 0.164 4572 Planarity : 0.004 0.062 5000 Dihedral : 15.397 97.416 5227 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.57 % Allowed : 31.24 % Favored : 62.19 % 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: -0.07 (0.15), residues: 3407 helix: 1.20 (0.16), residues: 1128 sheet: 0.14 (0.24), residues: 507 loop : -0.93 (0.15), residues: 1772 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 0.013 0.001 PHE J 248 TRP 0.028 0.001 TRP J 229 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00265 (30261) covalent geometry : angle 0.53013 (41551) hydrogen bonds : bond 0.03828 ( 972) hydrogen bonds : angle 4.67450 ( 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 474 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 289 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.7814 (p0) REVERT: C 1 MET cc_start: 0.7887 (ttm) cc_final: 0.7510 (ptp) REVERT: C 325 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8663 (ttm) REVERT: D 99 LYS cc_start: 0.8653 (ptmm) cc_final: 0.8225 (ttmt) REVERT: D 310 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8319 (pp30) REVERT: E 247 ASP cc_start: 0.8205 (t0) cc_final: 0.7962 (t0) REVERT: E 314 GLN cc_start: 0.8936 (tp40) cc_final: 0.8652 (tp-100) REVERT: F 88 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: F 174 ARG cc_start: 0.8601 (ptm160) cc_final: 0.8147 (tmm-80) REVERT: G 220 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8794 (m) REVERT: G 539 GLU cc_start: 0.8312 (tp30) cc_final: 0.7891 (tp30) REVERT: H 27 GLU cc_start: 0.7626 (tp30) cc_final: 0.7206 (tp30) REVERT: H 36 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7181 (pm20) REVERT: H 40 ILE cc_start: 0.6323 (OUTLIER) cc_final: 0.5984 (tp) REVERT: H 149 TYR cc_start: 0.7782 (p90) cc_final: 0.7514 (p90) REVERT: I 121 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6967 (ttp-110) REVERT: I 153 TYR cc_start: 0.3268 (OUTLIER) cc_final: 0.2915 (t80) REVERT: I 286 LYS cc_start: 0.8016 (tppp) cc_final: 0.7312 (pttm) REVERT: I 310 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7376 (mt0) REVERT: I 322 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8065 (ttpp) REVERT: I 330 MET cc_start: 0.7612 (tmm) cc_final: 0.7281 (tmt) REVERT: I 384 GLU cc_start: 0.8787 (mp0) cc_final: 0.8447 (mp0) REVERT: J 104 GLN cc_start: 0.8047 (mt0) cc_final: 0.7696 (mm-40) REVERT: J 151 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.6205 (t80) REVERT: J 197 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: J 312 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7736 (pp) outliers start: 185 outliers final: 74 residues processed: 442 average time/residue: 0.5002 time to fit residues: 269.9311 Evaluate side-chains 342 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 256 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 138 ASN 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 8 SER 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 325 MET 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 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 206 LEU 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 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 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 220 SER Chi-restraints excluded: chain G residue 274 HIS 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 40 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 191 SER 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 310 GLN Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 333 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 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 305 LEU Chi-restraints excluded: chain J residue 312 ILE Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 0.7980 chunk 259 optimal weight: 4.9990 chunk 321 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 338 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 266 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 17 ASN H 77 GLN I 350 GLN I 386 GLN ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.112521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.078950 restraints weight = 62441.559| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.61 r_work: 0.3071 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30261 Z= 0.112 Angle : 0.528 11.853 41551 Z= 0.271 Chirality : 0.039 0.182 4572 Planarity : 0.004 0.058 5000 Dihedral : 15.127 98.040 5129 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 7.07 % Allowed : 30.88 % Favored : 62.05 % 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: -0.04 (0.15), residues: 3407 helix: 1.25 (0.16), residues: 1124 sheet: 0.19 (0.24), residues: 506 loop : -0.93 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 110 TYR 0.013 0.001 TYR J 44 PHE 0.011 0.001 PHE B 302 TRP 0.027 0.001 TRP J 229 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00252 (30261) covalent geometry : angle 0.52790 (41551) hydrogen bonds : bond 0.03494 ( 972) hydrogen bonds : angle 4.49743 ( 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 470 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 271 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8349 (p0) REVERT: A 138 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7712 (p0) REVERT: B 236 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: C 1 MET cc_start: 0.7937 (ttm) cc_final: 0.7584 (ptp) REVERT: C 325 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8615 (ttm) REVERT: D 99 LYS cc_start: 0.8635 (ptmm) cc_final: 0.8180 (ttmt) REVERT: D 310 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8323 (pp30) REVERT: E 247 ASP cc_start: 0.8324 (t0) cc_final: 0.8017 (t0) REVERT: E 314 GLN cc_start: 0.8919 (tp40) cc_final: 0.8637 (tp-100) REVERT: F 88 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8451 (pm20) REVERT: F 172 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8487 (m-30) REVERT: F 174 ARG cc_start: 0.8575 (ptm160) cc_final: 0.8136 (tmm-80) REVERT: F 175 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8742 (ptmm) REVERT: G 53 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6057 (mt0) REVERT: G 264 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8157 (mt) REVERT: G 268 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8955 (pm20) REVERT: G 539 GLU cc_start: 0.8299 (tp30) cc_final: 0.7906 (tp30) REVERT: H 27 GLU cc_start: 0.7595 (tp30) cc_final: 0.7084 (tp30) REVERT: H 36 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7185 (pm20) REVERT: H 40 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.5978 (tp) REVERT: H 74 TYR cc_start: 0.7218 (t80) cc_final: 0.6799 (t80) REVERT: H 118 GLU cc_start: 0.8049 (pp20) cc_final: 0.7786 (pp20) REVERT: H 129 ARG cc_start: 0.5709 (OUTLIER) cc_final: 0.5495 (ptt180) REVERT: H 149 TYR cc_start: 0.7905 (p90) cc_final: 0.7481 (p90) REVERT: I 147 HIS cc_start: 0.6442 (OUTLIER) cc_final: 0.6241 (p-80) REVERT: I 153 TYR cc_start: 0.3353 (OUTLIER) cc_final: 0.2969 (t80) REVERT: I 281 LYS cc_start: 0.7091 (pttt) cc_final: 0.6684 (pmtt) REVERT: I 286 LYS cc_start: 0.7957 (tppp) cc_final: 0.7241 (pttm) REVERT: I 308 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8764 (mmp) REVERT: I 310 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: I 322 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8051 (ttmm) REVERT: I 330 MET cc_start: 0.7610 (tmm) cc_final: 0.7248 (tmt) REVERT: I 384 GLU cc_start: 0.8780 (mp0) cc_final: 0.8392 (mp0) REVERT: J 101 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.7762 (t0) REVERT: J 104 GLN cc_start: 0.8058 (mt0) cc_final: 0.7734 (mm-40) REVERT: J 120 PRO cc_start: 0.8391 (Cg_endo) cc_final: 0.8081 (Cg_exo) REVERT: J 197 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: J 281 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5625 (mtmm) outliers start: 199 outliers final: 81 residues processed: 434 average time/residue: 0.5043 time to fit residues: 266.8635 Evaluate side-chains 363 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 262 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 104 SER 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 320 VAL 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 326 ILE Chi-restraints excluded: chain C residue 64 SER 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 325 MET 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 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 206 LEU 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 88 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 207 CYS 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 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 146 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 268 GLU 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 598 THR 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 129 ARG 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 147 HIS 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 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 334 CYS Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 388 ASP 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 269 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 84 optimal weight: 0.0980 chunk 340 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 321 optimal weight: 0.9990 chunk 207 optimal weight: 0.0060 chunk 216 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 77 GLN I 386 GLN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.112081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078475 restraints weight = 62104.269| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.61 r_work: 0.3062 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30261 Z= 0.125 Angle : 0.538 10.322 41551 Z= 0.275 Chirality : 0.040 0.186 4572 Planarity : 0.004 0.069 5000 Dihedral : 15.053 97.582 5116 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 7.46 % Allowed : 31.02 % Favored : 61.51 % 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: -0.02 (0.15), residues: 3407 helix: 1.26 (0.16), residues: 1128 sheet: 0.18 (0.24), residues: 509 loop : -0.92 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 110 TYR 0.029 0.001 TYR I 270 PHE 0.017 0.001 PHE J 248 TRP 0.028 0.001 TRP J 229 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00284 (30261) covalent geometry : angle 0.53810 (41551) hydrogen bonds : bond 0.03442 ( 972) hydrogen bonds : angle 4.41832 ( 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 492 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 282 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7754 (p0) REVERT: A 138 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7735 (p0) REVERT: B 236 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: B 306 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: C 1 MET cc_start: 0.7938 (ttm) cc_final: 0.7605 (ptp) REVERT: C 325 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8604 (ttm) REVERT: D 1 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8044 (tpt) REVERT: D 310 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8336 (pp30) REVERT: E 247 ASP cc_start: 0.8459 (t0) cc_final: 0.8165 (t0) REVERT: E 275 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8663 (pmtt) REVERT: E 314 GLN cc_start: 0.8908 (tp40) cc_final: 0.8666 (tp-100) REVERT: F 1 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.6301 (pmt) REVERT: F 2 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8381 (tptp) REVERT: F 88 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: F 172 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8500 (m-30) REVERT: F 174 ARG cc_start: 0.8610 (ptm160) cc_final: 0.8172 (tmm-80) REVERT: F 175 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8746 (ptmm) REVERT: F 202 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8528 (pm20) REVERT: G 53 GLN cc_start: 0.6828 (OUTLIER) cc_final: 0.6073 (mt0) REVERT: G 220 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8734 (m) REVERT: G 264 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8147 (mt) REVERT: G 539 GLU cc_start: 0.8305 (tp30) cc_final: 0.7921 (tp30) REVERT: G 585 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: H 17 ASN cc_start: 0.7280 (OUTLIER) cc_final: 0.7065 (p0) REVERT: H 27 GLU cc_start: 0.7634 (tp30) cc_final: 0.7136 (tp30) REVERT: H 36 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7213 (pm20) REVERT: H 40 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5968 (tp) REVERT: H 118 GLU cc_start: 0.8121 (pp20) cc_final: 0.7797 (pp20) REVERT: H 129 ARG cc_start: 0.5743 (OUTLIER) cc_final: 0.5530 (ptt180) REVERT: H 149 TYR cc_start: 0.8029 (p90) cc_final: 0.7505 (p90) REVERT: I 103 MET cc_start: 0.4248 (tmt) cc_final: 0.3920 (tmt) REVERT: I 153 TYR cc_start: 0.3338 (OUTLIER) cc_final: 0.2901 (t80) REVERT: I 286 LYS cc_start: 0.7924 (tppp) cc_final: 0.7224 (pttm) REVERT: I 308 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8772 (mmp) REVERT: I 310 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7457 (mt0) REVERT: I 313 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: I 322 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8064 (ttmm) REVERT: I 330 MET cc_start: 0.7647 (tmm) cc_final: 0.7230 (tmt) REVERT: I 384 GLU cc_start: 0.8763 (mp0) cc_final: 0.8396 (mp0) REVERT: J 42 LYS cc_start: 0.9197 (tttt) cc_final: 0.8552 (tptt) REVERT: J 104 GLN cc_start: 0.7980 (mt0) cc_final: 0.7655 (mm-40) REVERT: J 120 PRO cc_start: 0.8406 (Cg_endo) cc_final: 0.8121 (Cg_exo) REVERT: J 281 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5572 (mtmm) outliers start: 210 outliers final: 97 residues processed: 452 average time/residue: 0.5254 time to fit residues: 288.5082 Evaluate side-chains 385 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 263 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 104 SER 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 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 206 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 306 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 64 SER 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 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 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 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 245 ASP Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain F residue 1 MET 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 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 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 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 109 CYS Chi-restraints excluded: chain G residue 146 VAL 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 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 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 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 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 388 ASP 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 377 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 40 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 293 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 344 optimal weight: 30.0000 chunk 17 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 17 ASN H 77 GLN I 386 GLN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.110659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.077082 restraints weight = 62244.213| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.59 r_work: 0.3031 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30261 Z= 0.170 Angle : 0.562 9.386 41551 Z= 0.288 Chirality : 0.041 0.176 4572 Planarity : 0.004 0.073 5000 Dihedral : 15.027 95.406 5116 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 7.43 % Allowed : 31.27 % Favored : 61.30 % 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: -0.03 (0.15), residues: 3407 helix: 1.29 (0.16), residues: 1122 sheet: 0.12 (0.24), residues: 519 loop : -0.93 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG I 341 TYR 0.023 0.001 TYR I 222 PHE 0.014 0.001 PHE C 302 TRP 0.030 0.001 TRP J 229 HIS 0.006 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00391 (30261) covalent geometry : angle 0.56156 (41551) hydrogen bonds : bond 0.03648 ( 972) hydrogen bonds : angle 4.43464 ( 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: 209 poor density : 260 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7844 (p0) REVERT: A 236 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: B 167 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8178 (pp) REVERT: B 236 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7714 (pm20) REVERT: C 325 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8595 (tmm) REVERT: D 1 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8032 (tpt) REVERT: D 99 LYS cc_start: 0.8598 (ptmm) cc_final: 0.8174 (ttmt) REVERT: D 310 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8342 (pp30) REVERT: E 247 ASP cc_start: 0.8559 (t0) cc_final: 0.8306 (t0) REVERT: E 275 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8650 (pmtt) REVERT: E 314 GLN cc_start: 0.8925 (tp40) cc_final: 0.8614 (tp-100) REVERT: F 1 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.6283 (pmt) REVERT: F 2 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8405 (tptp) REVERT: F 88 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: F 174 ARG cc_start: 0.8642 (ptm160) cc_final: 0.8200 (tmm-80) REVERT: F 175 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8810 (ptmm) REVERT: F 202 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8503 (pm20) REVERT: G 247 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8315 (tpt) REVERT: G 539 GLU cc_start: 0.8368 (tp30) cc_final: 0.7906 (tp30) REVERT: G 585 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.8012 (mmm-85) REVERT: H 27 GLU cc_start: 0.7649 (tp30) cc_final: 0.7162 (tp30) REVERT: H 36 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7232 (pm20) REVERT: H 118 GLU cc_start: 0.8171 (pp20) cc_final: 0.7851 (pp20) REVERT: H 129 ARG cc_start: 0.5725 (OUTLIER) cc_final: 0.5513 (ptt180) REVERT: H 149 TYR cc_start: 0.8172 (p90) cc_final: 0.7628 (p90) REVERT: I 100 ARG cc_start: 0.7174 (ttp80) cc_final: 0.6682 (ttm-80) REVERT: I 145 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.6179 (pmm-80) REVERT: I 153 TYR cc_start: 0.3310 (OUTLIER) cc_final: 0.2663 (t80) REVERT: I 281 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6537 (pmtt) REVERT: I 286 LYS cc_start: 0.7974 (tppp) cc_final: 0.7747 (tmtt) REVERT: I 308 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8771 (mmp) REVERT: I 310 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7514 (mt0) REVERT: I 313 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: I 322 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8153 (ttmm) REVERT: I 330 MET cc_start: 0.7716 (tmm) cc_final: 0.7232 (tmt) REVERT: I 350 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: I 384 GLU cc_start: 0.8865 (mp0) cc_final: 0.8407 (mp0) REVERT: J 104 GLN cc_start: 0.8032 (mt0) cc_final: 0.7681 (mm-40) REVERT: J 281 LYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5532 (mtmt) outliers start: 209 outliers final: 114 residues processed: 431 average time/residue: 0.5353 time to fit residues: 279.0393 Evaluate side-chains 399 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 262 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 104 SER 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 342 LEU Chi-restraints excluded: chain B residue 8 SER 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 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 326 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 64 SER 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 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 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 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 275 LYS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET 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 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 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 183 LEU 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 42 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 129 ARG 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 145 ARG 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 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 344 VAL 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 138 GLU 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 377 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 89 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 56 optimal weight: 0.2980 chunk 275 optimal weight: 8.9990 chunk 324 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** 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 = 0.110393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.076839 restraints weight = 61980.465| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.58 r_work: 0.3026 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30261 Z= 0.170 Angle : 0.571 9.732 41551 Z= 0.292 Chirality : 0.041 0.175 4572 Planarity : 0.004 0.071 5000 Dihedral : 15.023 95.113 5116 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 7.14 % Allowed : 31.31 % 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: -0.06 (0.15), residues: 3407 helix: 1.26 (0.16), residues: 1122 sheet: 0.07 (0.23), residues: 520 loop : -0.93 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 341 TYR 0.016 0.001 TYR I 222 PHE 0.014 0.001 PHE C 302 TRP 0.031 0.001 TRP J 229 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00393 (30261) covalent geometry : angle 0.57146 (41551) hydrogen bonds : bond 0.03666 ( 972) hydrogen bonds : angle 4.42261 ( 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 475 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 274 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.7917 (p0) REVERT: A 236 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: B 167 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8230 (pp) REVERT: B 236 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: D 194 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8557 (tppt) REVERT: D 310 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8316 (pp30) REVERT: E 247 ASP cc_start: 0.8624 (t0) cc_final: 0.8419 (t0) REVERT: E 275 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8663 (pmtt) REVERT: E 314 GLN cc_start: 0.8935 (tp40) cc_final: 0.8633 (tp-100) REVERT: F 1 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.6290 (pmt) REVERT: F 2 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8402 (tptp) REVERT: F 88 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8507 (pm20) REVERT: F 174 ARG cc_start: 0.8642 (ptm160) cc_final: 0.8191 (tmm-80) REVERT: F 175 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8795 (ptmm) REVERT: F 314 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: G 55 ASN cc_start: 0.7228 (p0) cc_final: 0.7025 (p0) REVERT: G 247 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8359 (tpt) REVERT: G 539 GLU cc_start: 0.8340 (tp30) cc_final: 0.7913 (tp30) REVERT: G 585 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8008 (mmm-85) REVERT: H 23 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7700 (pttm) REVERT: H 27 GLU cc_start: 0.7621 (tp30) cc_final: 0.7150 (tp30) REVERT: H 36 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7222 (pm20) REVERT: H 118 GLU cc_start: 0.8183 (pp20) cc_final: 0.7851 (pp20) REVERT: H 129 ARG cc_start: 0.5694 (OUTLIER) cc_final: 0.5484 (ptt180) REVERT: H 149 TYR cc_start: 0.8266 (p90) cc_final: 0.7680 (p90) REVERT: I 100 ARG cc_start: 0.7223 (ttp80) cc_final: 0.6771 (ttm-80) REVERT: I 145 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6332 (pmm-80) REVERT: I 153 TYR cc_start: 0.3300 (OUTLIER) cc_final: 0.2644 (t80) REVERT: I 156 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: I 258 LYS cc_start: 0.8500 (mmpt) cc_final: 0.7806 (mtmt) REVERT: I 275 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8279 (ttpp) REVERT: I 286 LYS cc_start: 0.7998 (tppp) cc_final: 0.7785 (tmtt) REVERT: I 308 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8767 (mmp) REVERT: I 310 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: I 322 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8163 (ttmm) REVERT: I 330 MET cc_start: 0.7667 (tmm) cc_final: 0.7163 (tmt) REVERT: I 350 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: I 384 GLU cc_start: 0.8873 (mp0) cc_final: 0.8373 (mp0) REVERT: I 390 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7447 (t80) REVERT: J 104 GLN cc_start: 0.8036 (mt0) cc_final: 0.7703 (mm-40) REVERT: J 120 PRO cc_start: 0.8376 (Cg_endo) cc_final: 0.8037 (Cg_exo) REVERT: J 281 LYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5494 (mtmm) REVERT: J 308 MET cc_start: 0.7735 (tmm) cc_final: 0.7007 (mmp) outliers start: 201 outliers final: 116 residues processed: 432 average time/residue: 0.5278 time to fit residues: 277.4243 Evaluate side-chains 405 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 267 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 342 LEU Chi-restraints excluded: chain B residue 8 SER 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 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 326 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 64 SER 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 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 194 LYS Chi-restraints excluded: chain D residue 226 SER 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 231 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 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 172 ASP Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 211 VAL 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 183 LEU 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 42 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 129 ARG 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 105 PHE Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 145 ARG 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 221 SER Chi-restraints excluded: chain I residue 268 PHE 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 334 CYS Chi-restraints excluded: chain I residue 344 VAL 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 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 138 GLU 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 377 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 158 optimal weight: 0.6980 chunk 235 optimal weight: 30.0000 chunk 305 optimal weight: 9.9990 chunk 276 optimal weight: 6.9990 chunk 314 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 chunk 312 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 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 = 0.3708 r_free = 0.3708 target = 0.109738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.076158 restraints weight = 62482.995| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.58 r_work: 0.3015 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30261 Z= 0.184 Angle : 0.580 10.404 41551 Z= 0.298 Chirality : 0.041 0.191 4572 Planarity : 0.004 0.079 5000 Dihedral : 15.028 94.487 5116 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 6.68 % Allowed : 31.77 % 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: -0.11 (0.15), residues: 3407 helix: 1.23 (0.16), residues: 1123 sheet: 0.05 (0.23), residues: 520 loop : -0.97 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 110 TYR 0.022 0.001 TYR I 222 PHE 0.015 0.001 PHE C 302 TRP 0.034 0.001 TRP J 229 HIS 0.006 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00425 (30261) covalent geometry : angle 0.57977 (41551) hydrogen bonds : bond 0.03755 ( 972) hydrogen bonds : angle 4.45307 ( 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 461 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 273 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.7888 (p0) REVERT: A 236 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: B 167 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8274 (pp) REVERT: B 236 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: D 310 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8321 (pp30) REVERT: E 275 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8654 (pmtt) REVERT: E 314 GLN cc_start: 0.8946 (tp40) cc_final: 0.8639 (tp-100) REVERT: F 1 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.6222 (pmt) REVERT: F 2 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8399 (tptp) REVERT: F 88 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8521 (pm20) REVERT: F 174 ARG cc_start: 0.8668 (ptm160) cc_final: 0.8217 (tmm-80) REVERT: F 175 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8788 (ptmm) REVERT: F 314 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: G 55 ASN cc_start: 0.7505 (p0) cc_final: 0.7292 (p0) REVERT: G 247 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8351 (tpt) REVERT: G 539 GLU cc_start: 0.8310 (tp30) cc_final: 0.7854 (tp30) REVERT: G 585 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8028 (mmm-85) REVERT: H 23 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7788 (pttm) REVERT: H 27 GLU cc_start: 0.7629 (tp30) cc_final: 0.7197 (tp30) REVERT: H 36 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7216 (pm20) REVERT: H 78 MET cc_start: 0.7830 (mmt) cc_final: 0.7501 (mmt) REVERT: H 118 GLU cc_start: 0.8175 (pp20) cc_final: 0.7832 (pp20) REVERT: H 149 TYR cc_start: 0.8316 (p90) cc_final: 0.7738 (p90) REVERT: H 154 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7986 (tm-30) REVERT: I 100 ARG cc_start: 0.7297 (ttp80) cc_final: 0.6784 (ttm-80) REVERT: I 105 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6159 (m-80) REVERT: I 153 TYR cc_start: 0.3330 (OUTLIER) cc_final: 0.2682 (t80) REVERT: I 281 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6592 (pmtt) REVERT: I 286 LYS cc_start: 0.8044 (tppp) cc_final: 0.7811 (tmtt) REVERT: I 308 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8752 (mmp) REVERT: I 310 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: I 313 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: I 322 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8172 (ttmm) REVERT: I 330 MET cc_start: 0.7665 (tmm) cc_final: 0.7159 (tmt) REVERT: I 342 GLU cc_start: 0.8415 (pp20) cc_final: 0.8064 (tm-30) REVERT: I 384 GLU cc_start: 0.8933 (mp0) cc_final: 0.8385 (mp0) REVERT: I 390 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7462 (t80) REVERT: J 42 LYS cc_start: 0.9168 (tttt) cc_final: 0.8966 (tttt) REVERT: J 104 GLN cc_start: 0.8043 (mt0) cc_final: 0.7713 (mm-40) REVERT: J 281 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5453 (mtmm) REVERT: J 286 LYS cc_start: 0.8071 (tptm) cc_final: 0.6590 (mtmt) outliers start: 188 outliers final: 115 residues processed: 430 average time/residue: 0.5385 time to fit residues: 280.1313 Evaluate side-chains 401 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 266 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 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 342 LEU Chi-restraints excluded: chain B residue 8 SER 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 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 326 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 64 SER 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 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 226 SER 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 231 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 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 172 ASP Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 211 VAL 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 183 LEU 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 99 VAL 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 105 PHE 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 159 VAL Chi-restraints excluded: chain I residue 203 ILE 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 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 344 VAL 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 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 138 GLU 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 377 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 344 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 312 optimal weight: 0.2980 chunk 138 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 271 optimal weight: 30.0000 chunk 28 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 316 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN E 67 GLN F 335 ASN H 77 GLN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.111477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077989 restraints weight = 62103.793| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.59 r_work: 0.3049 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1123 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= 0.127 Angle : 0.569 10.733 41551 Z= 0.290 Chirality : 0.040 0.229 4572 Planarity : 0.004 0.083 5000 Dihedral : 14.995 96.648 5115 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.33 % Allowed : 32.34 % Favored : 61.34 % 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: -0.06 (0.15), residues: 3407 helix: 1.26 (0.16), residues: 1123 sheet: 0.14 (0.24), residues: 505 loop : -0.95 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 110 TYR 0.027 0.001 TYR I 222 PHE 0.013 0.001 PHE B 302 TRP 0.037 0.001 TRP I 206 HIS 0.006 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00293 (30261) covalent geometry : angle 0.56935 (41551) hydrogen bonds : bond 0.03446 ( 972) hydrogen bonds : angle 4.37038 ( 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 451 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 273 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8372 (p0) REVERT: A 138 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7790 (p0) REVERT: C 342 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8894 (mt) REVERT: D 102 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8525 (pttt) REVERT: D 310 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8274 (pp30) REVERT: E 275 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8624 (pmtt) REVERT: E 314 GLN cc_start: 0.8920 (tp40) cc_final: 0.8617 (tp-100) REVERT: F 1 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.6188 (pmt) REVERT: F 2 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8394 (tptp) REVERT: F 88 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8458 (pm20) REVERT: F 174 ARG cc_start: 0.8642 (ptm160) cc_final: 0.8181 (tmm-80) REVERT: F 175 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8745 (ptmm) REVERT: F 314 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: G 247 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8345 (tpt) REVERT: G 539 GLU cc_start: 0.8331 (tp30) cc_final: 0.7886 (tp30) REVERT: G 585 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.7983 (mmm-85) REVERT: H 27 GLU cc_start: 0.7662 (tp30) cc_final: 0.7221 (tp30) REVERT: H 36 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7253 (pm20) REVERT: H 118 GLU cc_start: 0.8211 (pp20) cc_final: 0.7829 (pp20) REVERT: H 149 TYR cc_start: 0.8342 (p90) cc_final: 0.7770 (p90) REVERT: I 100 ARG cc_start: 0.7243 (ttp80) cc_final: 0.6757 (ttm-80) REVERT: I 145 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6327 (pmm-80) REVERT: I 153 TYR cc_start: 0.3437 (OUTLIER) cc_final: 0.2791 (t80) REVERT: I 258 LYS cc_start: 0.8443 (mmpt) cc_final: 0.7752 (mtmt) REVERT: I 275 LYS cc_start: 0.8663 (tppt) cc_final: 0.8343 (ttpp) REVERT: I 281 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6655 (pmtt) REVERT: I 286 LYS cc_start: 0.8064 (tppp) cc_final: 0.7828 (tmtt) REVERT: I 308 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8757 (mmp) REVERT: I 310 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7458 (mt0) REVERT: I 322 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8156 (ttmm) REVERT: I 330 MET cc_start: 0.7643 (tmm) cc_final: 0.7187 (tmt) REVERT: I 342 GLU cc_start: 0.8420 (pp20) cc_final: 0.8071 (tm-30) REVERT: I 384 GLU cc_start: 0.8910 (mp0) cc_final: 0.8333 (mp0) REVERT: I 390 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7540 (t80) REVERT: J 104 GLN cc_start: 0.8001 (mt0) cc_final: 0.7592 (mm110) REVERT: J 120 PRO cc_start: 0.8353 (Cg_endo) cc_final: 0.7946 (Cg_exo) REVERT: J 281 LYS cc_start: 0.5977 (OUTLIER) cc_final: 0.5498 (mtmm) REVERT: J 308 MET cc_start: 0.7966 (tmm) cc_final: 0.7403 (mmp) outliers start: 178 outliers final: 107 residues processed: 417 average time/residue: 0.5149 time to fit residues: 260.7583 Evaluate side-chains 390 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 264 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 69 ASN 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 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 8 SER 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 297 THR Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 123 VAL 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 102 LYS 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 231 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 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 175 LYS Chi-restraints excluded: chain F residue 207 CYS 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 99 VAL Chi-restraints excluded: chain H residue 132 ILE 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 145 ARG 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 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 343 GLN 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 I residue 388 ASP Chi-restraints excluded: chain I residue 390 PHE 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 138 GLU 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 377 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 270 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 chunk 180 optimal weight: 0.1980 chunk 236 optimal weight: 30.0000 chunk 214 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN E 67 GLN F 335 ASN H 77 GLN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.112378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.078809 restraints weight = 62311.585| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.61 r_work: 0.3068 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1197 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= 0.116 Angle : 0.577 11.283 41551 Z= 0.294 Chirality : 0.040 0.206 4572 Planarity : 0.004 0.095 5000 Dihedral : 14.968 98.226 5115 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.98 % Allowed : 33.94 % Favored : 61.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3407 helix: 1.27 (0.16), residues: 1122 sheet: 0.19 (0.24), residues: 502 loop : -0.93 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG I 341 TYR 0.018 0.001 TYR A 63 PHE 0.017 0.001 PHE I 245 TRP 0.043 0.001 TRP I 206 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00267 (30261) covalent geometry : angle 0.57710 (41551) hydrogen bonds : bond 0.03358 ( 972) hydrogen bonds : angle 4.33865 ( 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 410 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 270 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.7805 (p0) REVERT: A 138 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7655 (p0) REVERT: A 325 MET cc_start: 0.8573 (tpp) cc_final: 0.8338 (tpt) REVERT: C 1 MET cc_start: 0.7971 (ttm) cc_final: 0.7589 (ptp) REVERT: C 55 GLN cc_start: 0.8459 (pm20) cc_final: 0.8237 (pm20) REVERT: C 342 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8856 (mt) REVERT: C 344 GLN cc_start: 0.8471 (pt0) cc_final: 0.7764 (pp30) REVERT: D 102 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8498 (pttt) REVERT: D 290 TYR cc_start: 0.8789 (t80) cc_final: 0.8422 (t80) REVERT: E 275 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8662 (pmtt) REVERT: E 314 GLN cc_start: 0.8909 (tp40) cc_final: 0.8614 (tp-100) REVERT: F 1 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.6303 (pmt) REVERT: F 2 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8402 (tptp) REVERT: F 88 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8442 (pm20) REVERT: F 174 ARG cc_start: 0.8619 (ptm160) cc_final: 0.8159 (tmm-80) REVERT: F 314 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: G 247 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8387 (tpt) REVERT: G 264 LEU cc_start: 0.8526 (mm) cc_final: 0.8167 (mt) REVERT: G 539 GLU cc_start: 0.8328 (tp30) cc_final: 0.7924 (tp30) REVERT: G 585 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: H 27 GLU cc_start: 0.7676 (tp30) cc_final: 0.7301 (tp30) REVERT: H 36 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7237 (pm20) REVERT: H 118 GLU cc_start: 0.8206 (pp20) cc_final: 0.7855 (pp20) REVERT: H 149 TYR cc_start: 0.8330 (p90) cc_final: 0.7801 (p90) REVERT: I 153 TYR cc_start: 0.3473 (OUTLIER) cc_final: 0.2824 (t80) REVERT: I 258 LYS cc_start: 0.8478 (mmpt) cc_final: 0.7800 (mtmt) REVERT: I 286 LYS cc_start: 0.8049 (tppp) cc_final: 0.7835 (tmtt) REVERT: I 308 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8741 (mmp) REVERT: I 310 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7443 (mt0) REVERT: I 322 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8093 (ttmm) REVERT: I 330 MET cc_start: 0.7703 (tmm) cc_final: 0.7194 (tmt) REVERT: I 384 GLU cc_start: 0.8868 (mp0) cc_final: 0.8000 (mp0) REVERT: J 102 GLN cc_start: 0.7525 (pm20) cc_final: 0.7114 (pm20) REVERT: J 104 GLN cc_start: 0.8036 (mt0) cc_final: 0.7660 (mm-40) REVERT: J 120 PRO cc_start: 0.8382 (Cg_endo) cc_final: 0.7993 (Cg_exo) REVERT: J 281 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5459 (mtmm) REVERT: J 308 MET cc_start: 0.7939 (tmm) cc_final: 0.7387 (mmp) REVERT: J 379 CYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7778 (m) outliers start: 140 outliers final: 95 residues processed: 383 average time/residue: 0.5236 time to fit residues: 243.6073 Evaluate side-chains 372 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 262 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR 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 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 246 VAL Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 123 VAL 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 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 64 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 102 LYS 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 206 LEU 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 275 LYS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET 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 172 ASP Chi-restraints excluded: chain F residue 207 CYS 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 99 VAL Chi-restraints excluded: chain H residue 132 ILE 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 203 ILE Chi-restraints excluded: chain I residue 268 PHE 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 334 CYS 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 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 138 GLU 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 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: 1.9990 chunk 33 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN E 67 GLN F 335 ASN H 77 GLN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.112446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.078944 restraints weight = 61954.470| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.60 r_work: 0.3065 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30261 Z= 0.125 Angle : 0.588 12.694 41551 Z= 0.297 Chirality : 0.040 0.192 4572 Planarity : 0.004 0.085 5000 Dihedral : 14.921 98.268 5113 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.55 % Allowed : 34.61 % 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: -0.03 (0.15), residues: 3407 helix: 1.29 (0.16), residues: 1121 sheet: 0.20 (0.24), residues: 502 loop : -0.94 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 341 TYR 0.020 0.001 TYR A 63 PHE 0.019 0.001 PHE I 248 TRP 0.055 0.002 TRP I 230 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00290 (30261) covalent geometry : angle 0.58815 (41551) hydrogen bonds : bond 0.03386 ( 972) hydrogen bonds : angle 4.33308 ( 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 392 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 264 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8473 (p0) REVERT: A 138 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7647 (p0) REVERT: A 236 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: C 1 MET cc_start: 0.7952 (ttm) cc_final: 0.7559 (ptp) REVERT: C 55 GLN cc_start: 0.8449 (pm20) cc_final: 0.8234 (pm20) REVERT: C 342 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8856 (mt) REVERT: C 344 GLN cc_start: 0.8485 (pt0) cc_final: 0.7751 (pp30) REVERT: D 99 LYS cc_start: 0.8538 (ptmm) cc_final: 0.8149 (ttmt) REVERT: D 290 TYR cc_start: 0.8786 (t80) cc_final: 0.8411 (t80) REVERT: E 275 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8652 (pmtt) REVERT: E 314 GLN cc_start: 0.8904 (tp40) cc_final: 0.8615 (tp-100) REVERT: F 1 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.6270 (pmt) REVERT: F 2 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8398 (tptp) REVERT: F 88 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: F 174 ARG cc_start: 0.8629 (ptm160) cc_final: 0.8172 (tmm-80) REVERT: F 314 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: G 247 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8411 (tpt) REVERT: G 264 LEU cc_start: 0.8500 (mm) cc_final: 0.8140 (mt) REVERT: G 539 GLU cc_start: 0.8323 (tp30) cc_final: 0.7915 (tp30) REVERT: G 585 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7944 (mmm-85) REVERT: H 26 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8128 (ttpt) REVERT: H 27 GLU cc_start: 0.7709 (tp30) cc_final: 0.7287 (tp30) REVERT: H 36 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7248 (pm20) REVERT: H 149 TYR cc_start: 0.8320 (p90) cc_final: 0.7757 (p90) REVERT: I 145 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6325 (pmm-80) REVERT: I 153 TYR cc_start: 0.3427 (OUTLIER) cc_final: 0.2828 (t80) REVERT: I 258 LYS cc_start: 0.8479 (mmpt) cc_final: 0.7813 (mtmt) REVERT: I 275 LYS cc_start: 0.8624 (tppt) cc_final: 0.8309 (tptp) REVERT: I 286 LYS cc_start: 0.8086 (tppp) cc_final: 0.7845 (tmtt) REVERT: I 308 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8750 (mmp) REVERT: I 310 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7439 (mt0) REVERT: I 322 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8131 (ttmm) REVERT: I 330 MET cc_start: 0.7651 (tmm) cc_final: 0.7140 (tmt) REVERT: I 342 GLU cc_start: 0.8459 (pp20) cc_final: 0.8152 (tm-30) REVERT: I 384 GLU cc_start: 0.8888 (mp0) cc_final: 0.8013 (mp0) REVERT: J 102 GLN cc_start: 0.7496 (pm20) cc_final: 0.7182 (pm20) REVERT: J 104 GLN cc_start: 0.8039 (mt0) cc_final: 0.7689 (mm-40) REVERT: J 120 PRO cc_start: 0.8365 (Cg_endo) cc_final: 0.7983 (Cg_exo) REVERT: J 126 LYS cc_start: 0.8863 (pmtt) cc_final: 0.7847 (ptmt) REVERT: J 281 LYS cc_start: 0.5953 (OUTLIER) cc_final: 0.5421 (mtmm) REVERT: J 308 MET cc_start: 0.7995 (tmm) cc_final: 0.7441 (mmp) REVERT: J 379 CYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7751 (m) REVERT: J 386 GLN cc_start: 0.6520 (tp40) cc_final: 0.6270 (tp-100) outliers start: 128 outliers final: 94 residues processed: 366 average time/residue: 0.5321 time to fit residues: 236.1634 Evaluate side-chains 369 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 259 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR 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 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 246 VAL Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 123 VAL 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 226 SER Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 320 VAL 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 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 206 LEU 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 275 LYS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET 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 172 ASP Chi-restraints excluded: chain F residue 207 CYS 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 606 LEU 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 124 LEU Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 145 ARG 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 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 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 138 GLU Chi-restraints excluded: chain J residue 143 SER 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 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: 1.9990 chunk 47 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 166 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 220 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN E 67 GLN F 335 ASN H 77 GLN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.111701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.078080 restraints weight = 62383.163| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.61 r_work: 0.3053 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30261 Z= 0.141 Angle : 0.590 11.067 41551 Z= 0.300 Chirality : 0.040 0.219 4572 Planarity : 0.004 0.086 5000 Dihedral : 14.899 97.424 5113 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.69 % Allowed : 34.33 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3407 helix: 1.31 (0.16), residues: 1116 sheet: 0.17 (0.24), residues: 517 loop : -0.93 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG I 341 TYR 0.020 0.001 TYR A 63 PHE 0.019 0.001 PHE I 248 TRP 0.058 0.002 TRP I 206 HIS 0.005 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00327 (30261) covalent geometry : angle 0.59023 (41551) hydrogen bonds : bond 0.03435 ( 972) hydrogen bonds : angle 4.33489 ( 2594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9349.66 seconds wall clock time: 160 minutes 23.59 seconds (9623.59 seconds total)