Starting phenix.real_space_refine on Fri Mar 6 11:47:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vtq_65339/03_2026/9vtq_65339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vtq_65339/03_2026/9vtq_65339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vtq_65339/03_2026/9vtq_65339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vtq_65339/03_2026/9vtq_65339.map" model { file = "/net/cci-nas-00/data/ceres_data/9vtq_65339/03_2026/9vtq_65339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vtq_65339/03_2026/9vtq_65339.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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 98 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 18727 2.51 5 N 5169 2.21 5 O 5791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29928 Number of models: 1 Model: "" Number of chains: 14 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': 18, 'rna2p_pyr': 6, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 23, 'rna3p': 33} Chain breaks: 1 Chain: "2" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 737 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} 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: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2387 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 277} 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: 4790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4790 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 29, 'TRANS': 566} Chain breaks: 2 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: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2876 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 5, 'GLU:plan': 5, 'ASN:plan1': 5, 'HIS:plan': 3, 'TRP:plan': 1, 'PHE:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 148 Chain: "J" Number of atoms: 2636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2636 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 16, 'TRANS': 328} 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: 6.82, per 1000 atoms: 0.23 Number of scatterers: 29928 At special positions: 0 Unit cell: (121.824, 181.232, 192.512, 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 142 16.00 P 98 15.00 Mg 1 11.99 O 5791 8.00 N 5169 7.00 C 18727 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS I 132 " - pdb=" SG CYS I 135 " distance=2.03 Simple disulfide: pdb=" SG CYS I 165 " - pdb=" SG CYS I 185 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6654 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 48 sheets defined 38.5% alpha, 15.9% beta 35 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.063A pdb=" N ALA A 49 " --> pdb=" O GLY A 45 " (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 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.650A 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: 6.404A pdb=" N ARG B 144 " --> pdb=" O TRP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.550A 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: 3.863A 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 63 through 67 removed outlier: 3.534A pdb=" N GLN C 67 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 179 through 185 removed outlier: 3.535A pdb=" N PHE C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) 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: 3.548A pdb=" N LEU C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 317 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 144 through 148 removed outlier: 3.967A pdb=" N CYS D 148 " --> pdb=" O ASN D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 removed outlier: 3.545A pdb=" N TYR D 177 " --> pdb=" O ILE D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 3.572A 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 removed outlier: 3.590A pdb=" N LEU D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 317 Processing helix chain 'D' and resid 322 through 339 Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.925A pdb=" N GLN E 55 " --> pdb=" O TYR E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.600A pdb=" N ALA E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 123 Processing helix chain 'E' and resid 125 through 138 Processing helix chain 'E' and resid 144 through 148 removed outlier: 3.749A pdb=" N CYS E 148 " --> pdb=" O ASN E 145 " (cutoff:3.500A) 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: 3.527A 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 Processing helix chain 'F' and resid 125 through 138 Processing helix chain 'F' and resid 139 through 147 removed outlier: 6.642A pdb=" N ARG F 144 " --> pdb=" O TRP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 255 through 264 Processing helix chain 'F' and resid 294 through 298 Processing helix chain 'F' and resid 300 through 306 removed outlier: 3.561A pdb=" N LEU F 304 " --> pdb=" O ASP F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.534A pdb=" N GLN F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) 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: 4.172A pdb=" N ALA G 39 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 67 Processing helix chain 'G' and resid 69 through 77 Processing helix chain 'G' and resid 78 through 82 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 134 removed outlier: 3.525A pdb=" N CYS G 134 " --> pdb=" O MET G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 158 through 167 removed outlier: 3.755A pdb=" N ASN G 162 " --> pdb=" O HIS G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 184 removed outlier: 3.533A pdb=" N ILE G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 230 Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 243 through 248 removed outlier: 3.689A pdb=" N MET G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 254 removed outlier: 3.871A pdb=" N CYS G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 270 removed outlier: 3.546A pdb=" N LYS G 269 " --> pdb=" O PRO G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 296 removed outlier: 4.609A pdb=" N SER G 296 " --> pdb=" O TYR G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 325 Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 353 through 357 removed outlier: 3.749A pdb=" N ALA G 357 " --> pdb=" O ASN G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 375 removed outlier: 3.517A pdb=" N HIS G 375 " --> pdb=" O GLY G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 432 removed outlier: 3.504A pdb=" N THR G 432 " --> pdb=" O ARG G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 502 Processing helix chain 'G' and resid 516 through 520 Processing helix chain 'G' and resid 528 through 535 Processing helix chain 'G' and resid 554 through 563 removed outlier: 3.511A 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 'G' and resid 613 through 617 removed outlier: 3.517A pdb=" N TYR G 617 " --> pdb=" O PRO G 614 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 35 removed outlier: 3.926A pdb=" N ILE H 20 " --> pdb=" O ASN H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 71 removed outlier: 3.510A pdb=" N LEU H 66 " --> pdb=" O ASN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 104 through 111 removed outlier: 3.794A pdb=" N ASP H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR H 111 " --> pdb=" O ILE H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 134 through 139 removed outlier: 3.909A pdb=" N ALA H 137 " --> pdb=" O ASP H 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 30 Processing helix chain 'I' and resid 33 through 47 removed outlier: 3.949A pdb=" N ASP I 47 " --> pdb=" O ARG I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 53 removed outlier: 6.711A pdb=" N ARG I 51 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 85 removed outlier: 3.764A pdb=" N ARG I 75 " --> pdb=" O HIS I 71 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU I 85 " --> pdb=" O HIS I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 138 Processing helix chain 'I' and resid 143 through 148 removed outlier: 3.770A pdb=" N PHE I 148 " --> pdb=" O ARG I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 177 Processing helix chain 'I' and resid 201 through 208 Processing helix chain 'I' and resid 219 through 234 removed outlier: 3.517A pdb=" N ARG I 223 " --> pdb=" O PRO I 219 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP I 224 " --> pdb=" O LEU I 220 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY I 225 " --> pdb=" O SER I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 251 removed outlier: 3.737A pdb=" N PHE I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 270 Processing helix chain 'I' and resid 284 through 289 Processing helix chain 'I' and resid 302 through 315 Processing helix chain 'I' and resid 321 through 325 removed outlier: 3.997A pdb=" N ASN I 325 " --> pdb=" O LYS I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 337 Processing helix chain 'I' and resid 340 through 351 removed outlier: 3.766A pdb=" N GLY I 351 " --> pdb=" O MET I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 384 Processing helix chain 'J' and resid 22 through 29 Processing helix chain 'J' and resid 33 through 49 removed outlier: 3.536A pdb=" N PHE J 37 " --> pdb=" O ASP J 33 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE J 48 " --> pdb=" O TYR J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 removed outlier: 3.548A pdb=" N ILE J 63 " --> pdb=" O ILE J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 83 removed outlier: 3.536A pdb=" N ARG J 75 " --> pdb=" O HIS J 71 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER J 83 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 139 removed outlier: 3.655A pdb=" N GLU J 138 " --> pdb=" O CYS J 134 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS J 139 " --> pdb=" O CYS J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 148 Processing helix chain 'J' and resid 172 through 177 Processing helix chain 'J' and resid 197 through 207 Processing helix chain 'J' and resid 219 through 233 removed outlier: 3.858A pdb=" N MET J 227 " --> pdb=" O ARG J 223 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS J 228 " --> pdb=" O TRP J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 243 No H-bonds generated for 'chain 'J' and resid 241 through 243' Processing helix chain 'J' and resid 244 through 249 Processing helix chain 'J' and resid 251 through 271 removed outlier: 3.900A pdb=" N PHE J 256 " --> pdb=" O TRP J 252 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N HIS J 257 " --> pdb=" O PRO J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 289 removed outlier: 3.747A pdb=" N PHE J 289 " --> pdb=" O GLY J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 310 Processing helix chain 'J' and resid 342 through 350 Processing helix chain 'J' and resid 376 through 385 removed outlier: 3.942A pdb=" N LEU J 380 " --> pdb=" O ASP J 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 395 removed outlier: 3.718A pdb=" N PHE J 394 " --> pdb=" O ASN J 391 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 103 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 18 through 23 current: chain 'A' and resid 151 through 158 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 94 current: chain 'A' and resid 243 through 246 Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 41 Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.666A pdb=" N TYR A 290 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AA8, first strand: chain 'B' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 24 current: chain 'B' and resid 151 through 158 Processing sheet with id=AA9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.863A pdb=" N ARG B 28 " --> pdb=" O TRP B 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 94 current: chain 'B' and resid 243 through 246 Processing sheet with id=AB1, first strand: chain 'B' and resid 34 through 42 Processing sheet with id=AB2, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.653A pdb=" N TYR B 290 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 23 current: chain 'C' and resid 151 through 158 Processing sheet with id=AB5, first strand: chain 'C' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 94 current: chain 'C' and resid 243 through 246 Processing sheet with id=AB6, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 283 through 285 removed outlier: 3.661A pdb=" N TYR C 290 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 102 through 103 removed outlier: 3.578A pdb=" N LYS D 102 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 23 current: chain 'D' and resid 151 through 158 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 84 through 94 current: chain 'D' and resid 243 through 246 Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 42 Processing sheet with id=AC3, first strand: chain 'D' and resid 265 through 267 Processing sheet with id=AC4, first strand: chain 'D' and resid 283 through 285 Processing sheet with id=AC5, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AC6, first strand: chain 'E' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 23 current: chain 'E' and resid 151 through 158 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 94 current: chain 'E' and resid 243 through 246 Processing sheet with id=AC8, first strand: chain 'E' and resid 35 through 42 Processing sheet with id=AC9, first strand: chain 'E' and resid 265 through 267 Processing sheet with id=AD1, first strand: chain 'E' and resid 284 through 285 removed outlier: 3.738A pdb=" N TYR E 290 " --> pdb=" O HIS E 285 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 8 through 9 Processing sheet with id=AD3, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.552A pdb=" N GLU F 14 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.552A pdb=" N GLU F 14 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER F 151 " --> pdb=" O ARG F 216 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AD6, first strand: chain 'F' and resid 74 through 75 Processing sheet with id=AD7, first strand: chain 'F' and resid 283 through 285 Processing sheet with id=AD8, first strand: chain 'G' and resid 85 through 86 removed outlier: 4.071A pdb=" N VAL G 217 " --> pdb=" O ASN G 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 97 through 99 Processing sheet with id=AE1, first strand: chain 'G' and resid 139 through 142 Processing sheet with id=AE2, first strand: chain 'G' and resid 201 through 204 removed outlier: 9.036A pdb=" N ALA G 594 " --> pdb=" O TYR G 210 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER G 212 " --> pdb=" O ALA G 594 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL G 596 " --> pdb=" O SER G 212 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N SER G 214 " --> pdb=" O VAL G 596 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR G 598 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL G 444 " --> pdb=" O LEU G 544 " (cutoff:3.500A) removed outlier: 10.077A pdb=" N LEU G 546 " --> pdb=" O PHE G 442 " (cutoff:3.500A) removed outlier: 14.557A pdb=" N PHE G 442 " --> pdb=" O LEU G 546 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER G 441 " --> pdb=" O ARG G 488 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA G 482 " --> pdb=" O HIS G 447 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE G 449 " --> pdb=" O ASP G 480 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP G 480 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL G 451 " --> pdb=" O GLN G 478 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN G 478 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N CYS G 479 " --> pdb=" O GLY G 401 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY G 401 " --> pdb=" O CYS G 479 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU G 485 " --> pdb=" O PRO G 395 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU G 487 " --> pdb=" O LEU G 393 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU G 393 " --> pdb=" O LEU G 487 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 201 through 204 removed outlier: 9.036A pdb=" N ALA G 594 " --> pdb=" O TYR G 210 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER G 212 " --> pdb=" O ALA G 594 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL G 596 " --> pdb=" O SER G 212 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N SER G 214 " --> pdb=" O VAL G 596 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR G 598 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE G 595 " --> pdb=" O ARG G 577 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG G 577 " --> pdb=" O PHE G 595 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU G 597 " --> pdb=" O TYR G 575 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR G 575 " --> pdb=" O GLU G 597 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE G 599 " --> pdb=" O ILE G 573 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 236 through 239 Processing sheet with id=AE5, first strand: chain 'G' and resid 461 through 462 Processing sheet with id=AE6, first strand: chain 'G' and resid 619 through 624 Processing sheet with id=AE7, first strand: chain 'H' and resid 55 through 58 removed outlier: 3.685A pdb=" N THR H 9 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AE9, first strand: chain 'H' and resid 150 through 155 Processing sheet with id=AF1, first strand: chain 'I' and resid 99 through 105 removed outlier: 5.892A pdb=" N ASN I 101 " --> pdb=" O ILE I 113 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE I 113 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N MET I 103 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA I 111 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR I 109 " --> pdb=" O PHE I 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 98 through 101 removed outlier: 4.430A pdb=" N ALA J 111 " --> pdb=" O ASN J 101 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 181 through 182 1071 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 6.29 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5442 1.32 - 1.45: 8586 1.45 - 1.57: 16470 1.57 - 1.69: 193 1.69 - 1.81: 187 Bond restraints: 30878 Sorted by residual: bond pdb=" C GLY I 351 " pdb=" N LEU I 352 " ideal model delta sigma weight residual 1.332 1.304 0.028 1.40e-02 5.10e+03 3.99e+00 bond pdb=" CA TRP B 125 " pdb=" C TRP B 125 " ideal model delta sigma weight residual 1.522 1.495 0.026 1.72e-02 3.38e+03 2.32e+00 bond pdb=" CG1 ILE J 73 " pdb=" CD1 ILE J 73 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.81e+00 bond pdb=" CB GLU I 342 " pdb=" CG GLU I 342 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CG1 ILE C 13 " pdb=" CD1 ILE C 13 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.45e+00 ... (remaining 30873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 41902 2.52 - 5.05: 395 5.05 - 7.57: 32 7.57 - 10.10: 14 10.10 - 12.62: 3 Bond angle restraints: 42346 Sorted by residual: angle pdb=" C ASN G 564 " pdb=" N ASN G 565 " pdb=" CA ASN G 565 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" CA MET G 319 " pdb=" CB MET G 319 " pdb=" CG MET G 319 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CB MET J 308 " pdb=" CG MET J 308 " pdb=" SD MET J 308 " ideal model delta sigma weight residual 112.70 123.67 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA LEU J 79 " pdb=" CB LEU J 79 " pdb=" CG LEU J 79 " ideal model delta sigma weight residual 116.30 128.92 -12.62 3.50e+00 8.16e-02 1.30e+01 angle pdb=" CB ARG H 30 " pdb=" CG ARG H 30 " pdb=" CD ARG H 30 " ideal model delta sigma weight residual 111.30 119.39 -8.09 2.30e+00 1.89e-01 1.24e+01 ... (remaining 42341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 15261 17.76 - 35.52: 2082 35.52 - 53.27: 680 53.27 - 71.03: 211 71.03 - 88.79: 57 Dihedral angle restraints: 18291 sinusoidal: 7980 harmonic: 10311 Sorted by residual: 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 -55.32 -72.68 1 1.70e+01 3.46e-03 2.33e+01 dihedral pdb=" CA LEU G 394 " pdb=" C LEU G 394 " pdb=" N PRO G 395 " pdb=" CA PRO G 395 " ideal model delta harmonic sigma weight residual -180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" O4' C 1 18 " pdb=" C1' C 1 18 " pdb=" N1 C 1 18 " pdb=" C2 C 1 18 " ideal model delta sinusoidal sigma weight residual -160.00 -106.03 -53.97 1 1.50e+01 4.44e-03 1.76e+01 ... (remaining 18288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4181 0.074 - 0.147: 448 0.147 - 0.221: 5 0.221 - 0.295: 1 0.295 - 0.368: 1 Chirality restraints: 4636 Sorted by residual: chirality pdb=" CG LEU J 79 " pdb=" CB LEU J 79 " pdb=" CD1 LEU J 79 " pdb=" CD2 LEU J 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CG LEU J 38 " pdb=" CB LEU J 38 " pdb=" CD1 LEU J 38 " pdb=" CD2 LEU J 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO G 395 " pdb=" N PRO G 395 " pdb=" C PRO G 395 " pdb=" CB PRO G 395 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 4633 not shown) Planarity restraints: 5083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 49 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO J 50 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO J 50 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO J 50 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 6 " -0.031 2.00e-02 2.50e+03 1.42e-02 5.56e+00 pdb=" N9 A 1 6 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A 1 6 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 1 6 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 1 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 1 6 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A 1 6 " -0.008 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 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A 1 6 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 30 " 0.169 9.50e-02 1.11e+02 7.66e-02 4.87e+00 pdb=" NE ARG H 30 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG H 30 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG H 30 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG H 30 " -0.000 2.00e-02 2.50e+03 ... (remaining 5080 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4744 2.76 - 3.29: 28797 3.29 - 3.83: 51309 3.83 - 4.36: 61510 4.36 - 4.90: 102031 Nonbonded interactions: 248391 Sorted by model distance: nonbonded pdb=" OP2 A 1 6 " pdb="MG MG 1 101 " model vdw 2.219 2.170 nonbonded pdb=" O ASP D 247 " pdb=" OD1 ASP D 247 " model vdw 2.416 3.040 nonbonded pdb=" O ASN G 564 " pdb=" OD1 ASN G 565 " model vdw 2.458 3.040 nonbonded pdb=" N GLU I 342 " pdb=" OE1 GLU I 342 " model vdw 2.470 3.120 nonbonded pdb=" O2 U 1 2 " pdb=" O ILE G 508 " model vdw 2.484 3.040 ... (remaining 248386 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 177 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 177 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 177 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 177 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 177 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 233 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 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 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 188 or (resid 189 through 201 and (name N or name CA or \ name C or name O or name CB )) or resid 202 through 230 or (resid 231 through 2 \ 42 and (name N or name CA or name C or name O or name CB )) or resid 243 or (res \ id 244 and (name N or name CA or name C or name O or name CB )) or resid 245 thr \ ough 395)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.740 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: 0.680 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.420 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.006 0.053 30880 Z= 0.273 Angle : 0.631 12.619 42350 Z= 0.326 Chirality : 0.044 0.368 4636 Planarity : 0.004 0.077 5083 Dihedral : 18.908 88.790 11631 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.95 % Allowed : 31.02 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3476 helix: 1.15 (0.15), residues: 1184 sheet: 0.18 (0.22), residues: 543 loop : -0.91 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG H 30 TYR 0.020 0.001 TYR C 52 PHE 0.020 0.002 PHE C 302 TRP 0.032 0.001 TRP G 280 HIS 0.005 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00622 (30878) covalent geometry : angle 0.63134 (42346) SS BOND : bond 0.00178 ( 2) SS BOND : angle 0.38489 ( 4) hydrogen bonds : bond 0.13948 ( 1126) hydrogen bonds : angle 5.80092 ( 3082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 168 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: C 180 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8652 (m) REVERT: E 10 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8807 (tpp) REVERT: F 220 ASN cc_start: 0.8615 (m-40) cc_final: 0.8063 (p0) REVERT: F 230 LYS cc_start: 0.7597 (pptt) cc_final: 0.7115 (pmtt) REVERT: F 239 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7119 (ttt180) REVERT: F 311 TYR cc_start: 0.8448 (m-10) cc_final: 0.8247 (m-80) REVERT: G 147 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8460 (m90) REVERT: G 252 MET cc_start: 0.9218 (tmm) cc_final: 0.8920 (tmm) REVERT: G 271 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7861 (tp40) REVERT: G 498 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7958 (tmm-80) REVERT: H 35 TYR cc_start: 0.7962 (m-80) cc_final: 0.7473 (m-80) REVERT: H 70 ILE cc_start: 0.8539 (mm) cc_final: 0.8052 (mt) REVERT: H 77 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: I 83 SER cc_start: 0.6631 (OUTLIER) cc_final: 0.6277 (p) REVERT: I 146 TRP cc_start: 0.8490 (m-10) cc_final: 0.7773 (m-10) REVERT: J 184 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5949 (pm20) outliers start: 87 outliers final: 64 residues processed: 245 average time/residue: 0.5434 time to fit residues: 163.7914 Evaluate side-chains 224 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 150 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 441 SER Chi-restraints excluded: chain G residue 498 ARG 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 570 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 83 SER Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 199 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 522 HIS H 144 HIS I 77 HIS I 386 GLN J 228 HIS J 310 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.083115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.052827 restraints weight = 78571.123| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.61 r_work: 0.2686 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30880 Z= 0.140 Angle : 0.535 11.240 42350 Z= 0.277 Chirality : 0.041 0.297 4636 Planarity : 0.004 0.052 5083 Dihedral : 15.073 107.333 5243 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.45 % Allowed : 28.51 % Favored : 66.03 % 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: 0.18 (0.15), residues: 3476 helix: 1.37 (0.15), residues: 1206 sheet: 0.39 (0.22), residues: 522 loop : -0.86 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 30 TYR 0.011 0.001 TYR G 420 PHE 0.014 0.001 PHE A 302 TRP 0.016 0.001 TRP J 249 HIS 0.003 0.001 HIS D 71 Details of bonding type rmsd covalent geometry : bond 0.00312 (30878) covalent geometry : angle 0.53480 (42346) SS BOND : bond 0.00225 ( 2) SS BOND : angle 0.48844 ( 4) hydrogen bonds : bond 0.03685 ( 1126) hydrogen bonds : angle 4.70536 ( 3082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 162 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8510 (mttm) REVERT: B 306 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: B 323 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8295 (t70) REVERT: C 187 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8843 (ptmm) REVERT: F 1 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.6477 (pmt) REVERT: F 220 ASN cc_start: 0.8344 (m-40) cc_final: 0.7972 (p0) REVERT: F 230 LYS cc_start: 0.7478 (pptt) cc_final: 0.6939 (pmtt) REVERT: F 321 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7884 (mt) REVERT: F 335 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8851 (m-40) REVERT: G 147 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8450 (m90) REVERT: G 252 MET cc_start: 0.9030 (tmm) cc_final: 0.8686 (tmm) REVERT: G 293 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8483 (p) REVERT: H 32 ASN cc_start: 0.8088 (m110) cc_final: 0.7831 (t0) REVERT: H 35 TYR cc_start: 0.8136 (m-80) cc_final: 0.7333 (m-80) REVERT: H 77 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8451 (mp10) REVERT: H 108 ASP cc_start: 0.9032 (t0) cc_final: 0.8801 (OUTLIER) REVERT: I 109 THR cc_start: 0.8507 (p) cc_final: 0.8250 (p) REVERT: I 146 TRP cc_start: 0.8504 (m-10) cc_final: 0.7706 (m-10) REVERT: I 310 GLN cc_start: 0.8550 (tt0) cc_final: 0.8304 (tp40) REVERT: J 184 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6228 (pm20) REVERT: J 293 GLN cc_start: 0.8085 (pp30) cc_final: 0.7743 (pp30) REVERT: J 308 MET cc_start: 0.9457 (tpp) cc_final: 0.9036 (tmm) REVERT: J 386 GLN cc_start: 0.8131 (tp40) cc_final: 0.7672 (tp40) outliers start: 161 outliers final: 56 residues processed: 305 average time/residue: 0.4937 time to fit residues: 187.5864 Evaluate side-chains 213 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 147 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 123 VAL 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 246 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 155 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 228 HIS Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 40 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 334 optimal weight: 7.9990 chunk 330 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 331 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 55 GLN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.082549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.052104 restraints weight = 78953.135| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.62 r_work: 0.2666 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30880 Z= 0.171 Angle : 0.539 9.260 42350 Z= 0.280 Chirality : 0.042 0.293 4636 Planarity : 0.004 0.057 5083 Dihedral : 14.783 88.548 5176 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.11 % Allowed : 28.68 % Favored : 66.20 % 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: 0.20 (0.14), residues: 3476 helix: 1.45 (0.15), residues: 1207 sheet: 0.35 (0.23), residues: 494 loop : -0.86 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 30 TYR 0.016 0.001 TYR C 52 PHE 0.015 0.001 PHE C 302 TRP 0.018 0.001 TRP J 249 HIS 0.004 0.001 HIS J 228 Details of bonding type rmsd covalent geometry : bond 0.00390 (30878) covalent geometry : angle 0.53950 (42346) SS BOND : bond 0.00185 ( 2) SS BOND : angle 0.42555 ( 4) hydrogen bonds : bond 0.03692 ( 1126) hydrogen bonds : angle 4.57943 ( 3082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 159 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8541 (mttm) REVERT: B 306 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: B 323 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8342 (t70) REVERT: C 187 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8842 (ptmm) REVERT: D 325 MET cc_start: 0.8601 (ttm) cc_final: 0.8151 (tmm) REVERT: F 1 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.6470 (pmt) REVERT: F 121 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8925 (mp0) REVERT: F 220 ASN cc_start: 0.8359 (m-40) cc_final: 0.7961 (p0) REVERT: F 230 LYS cc_start: 0.7467 (pptt) cc_final: 0.6963 (pmtt) REVERT: F 239 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.6814 (ttt180) REVERT: F 286 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7105 (mtp85) REVERT: F 321 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7900 (mt) REVERT: F 335 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8876 (m-40) REVERT: G 147 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8457 (m90) REVERT: G 218 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8695 (p) REVERT: G 223 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8449 (tp30) REVERT: G 252 MET cc_start: 0.9077 (tmm) cc_final: 0.8796 (tmm) REVERT: G 293 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8563 (p) REVERT: H 32 ASN cc_start: 0.8136 (m110) cc_final: 0.7926 (t0) REVERT: H 35 TYR cc_start: 0.8131 (m-80) cc_final: 0.7384 (m-80) REVERT: H 77 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8428 (mp10) REVERT: H 108 ASP cc_start: 0.9089 (t0) cc_final: 0.8882 (OUTLIER) REVERT: H 155 ASP cc_start: 0.8763 (p0) cc_final: 0.8378 (t0) REVERT: H 158 SER cc_start: 0.9260 (OUTLIER) cc_final: 0.9034 (p) REVERT: I 146 TRP cc_start: 0.8488 (m-10) cc_final: 0.7700 (m-10) REVERT: I 310 GLN cc_start: 0.8547 (tt0) cc_final: 0.8306 (tp40) REVERT: J 36 TRP cc_start: 0.8673 (m100) cc_final: 0.8458 (m100) REVERT: J 293 GLN cc_start: 0.7975 (pp30) cc_final: 0.7629 (pp30) REVERT: J 386 GLN cc_start: 0.8093 (tp40) cc_final: 0.7586 (tp40) outliers start: 151 outliers final: 73 residues processed: 295 average time/residue: 0.5179 time to fit residues: 189.6220 Evaluate side-chains 233 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 145 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 123 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 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 552 LEU Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 155 HIS Chi-restraints excluded: chain J residue 337 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 281 optimal weight: 9.9990 chunk 88 optimal weight: 0.1980 chunk 255 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN F 242 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN I 77 HIS J 147 HIS J 343 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.083222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.053006 restraints weight = 78176.932| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.61 r_work: 0.2691 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30880 Z= 0.135 Angle : 0.525 10.038 42350 Z= 0.270 Chirality : 0.041 0.307 4636 Planarity : 0.004 0.059 5083 Dihedral : 14.760 89.803 5170 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.01 % Allowed : 28.82 % Favored : 66.17 % 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: 0.28 (0.15), residues: 3476 helix: 1.54 (0.15), residues: 1209 sheet: 0.40 (0.23), residues: 500 loop : -0.84 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 357 TYR 0.010 0.001 TYR H 74 PHE 0.013 0.001 PHE A 302 TRP 0.020 0.001 TRP J 249 HIS 0.003 0.000 HIS J 228 Details of bonding type rmsd covalent geometry : bond 0.00305 (30878) covalent geometry : angle 0.52485 (42346) SS BOND : bond 0.00155 ( 2) SS BOND : angle 0.48769 ( 4) hydrogen bonds : bond 0.03409 ( 1126) hydrogen bonds : angle 4.45054 ( 3082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 167 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8538 (ptp) cc_final: 0.8169 (ptp) REVERT: A 67 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8482 (mt0) REVERT: B 306 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: C 187 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8808 (ptmm) REVERT: E 123 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7275 (p) REVERT: F 1 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.6341 (pmt) REVERT: F 194 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8676 (tttp) REVERT: F 220 ASN cc_start: 0.8344 (m-40) cc_final: 0.7955 (p0) REVERT: F 230 LYS cc_start: 0.7498 (pptt) cc_final: 0.6983 (pmtt) REVERT: F 242 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8645 (mt0) REVERT: F 286 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6987 (mtp85) REVERT: F 321 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7850 (mt) REVERT: G 147 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8486 (m90) REVERT: G 218 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8673 (p) REVERT: G 252 MET cc_start: 0.9060 (tmm) cc_final: 0.8778 (tmm) REVERT: G 293 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8540 (p) REVERT: H 32 ASN cc_start: 0.8170 (m110) cc_final: 0.7966 (t0) REVERT: H 35 TYR cc_start: 0.8162 (m-80) cc_final: 0.7452 (m-10) REVERT: H 77 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8452 (mp10) REVERT: H 155 ASP cc_start: 0.8712 (p0) cc_final: 0.8332 (t0) REVERT: H 158 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.9038 (p) REVERT: I 146 TRP cc_start: 0.8472 (m-10) cc_final: 0.7669 (m-10) REVERT: I 252 TRP cc_start: 0.6711 (t-100) cc_final: 0.6488 (t-100) REVERT: J 36 TRP cc_start: 0.8668 (m100) cc_final: 0.8448 (m100) REVERT: J 184 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: J 293 GLN cc_start: 0.8051 (pp30) cc_final: 0.7700 (pp30) REVERT: J 386 GLN cc_start: 0.8073 (tp40) cc_final: 0.7616 (tp40) outliers start: 148 outliers final: 76 residues processed: 300 average time/residue: 0.5065 time to fit residues: 186.8986 Evaluate side-chains 237 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 146 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 123 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 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 286 ARG 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 113 SER Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 155 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 336 optimal weight: 7.9990 chunk 324 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 292 optimal weight: 20.0000 chunk 257 optimal weight: 0.9980 chunk 338 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 353 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 55 GLN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS I 77 HIS I 310 GLN I 391 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.051644 restraints weight = 78732.307| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.60 r_work: 0.2654 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30880 Z= 0.213 Angle : 0.566 10.478 42350 Z= 0.291 Chirality : 0.043 0.341 4636 Planarity : 0.004 0.061 5083 Dihedral : 14.729 86.753 5168 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.66 % Allowed : 28.34 % Favored : 66.00 % 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: 0.20 (0.14), residues: 3476 helix: 1.48 (0.15), residues: 1211 sheet: 0.33 (0.23), residues: 500 loop : -0.88 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 300 TYR 0.016 0.001 TYR C 52 PHE 0.017 0.001 PHE C 302 TRP 0.022 0.001 TRP J 249 HIS 0.003 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00491 (30878) covalent geometry : angle 0.56616 (42346) SS BOND : bond 0.00333 ( 2) SS BOND : angle 0.47529 ( 4) hydrogen bonds : bond 0.03718 ( 1126) hydrogen bonds : angle 4.53214 ( 3082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 155 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8560 (mttm) REVERT: A 67 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8382 (mt0) REVERT: A 323 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8441 (t0) REVERT: B 306 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: C 187 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8855 (ptmm) REVERT: D 247 ASP cc_start: 0.8503 (t0) cc_final: 0.8285 (t0) REVERT: F 1 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.6500 (pmt) REVERT: F 121 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8917 (mp0) REVERT: F 194 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8570 (ttpt) REVERT: F 220 ASN cc_start: 0.8355 (m-40) cc_final: 0.7966 (p0) REVERT: F 230 LYS cc_start: 0.7478 (pptt) cc_final: 0.6971 (pmtt) REVERT: F 239 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.6542 (ttt180) REVERT: F 242 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8618 (mt0) REVERT: F 286 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7111 (mtp85) REVERT: F 309 ASP cc_start: 0.9324 (OUTLIER) cc_final: 0.8856 (OUTLIER) REVERT: F 321 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7855 (mt) REVERT: G 147 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8445 (m90) REVERT: G 218 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8685 (p) REVERT: G 223 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8493 (tp30) REVERT: G 252 MET cc_start: 0.9098 (tmm) cc_final: 0.8816 (tmm) REVERT: G 271 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7642 (tp40) REVERT: G 293 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8572 (p) REVERT: H 35 TYR cc_start: 0.8084 (m-80) cc_final: 0.7338 (m-80) REVERT: H 77 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: H 155 ASP cc_start: 0.8722 (p0) cc_final: 0.8470 (t0) REVERT: H 158 SER cc_start: 0.9274 (OUTLIER) cc_final: 0.9042 (p) REVERT: I 104 GLN cc_start: 0.7726 (tp-100) cc_final: 0.7446 (tp40) REVERT: I 146 TRP cc_start: 0.8466 (m-10) cc_final: 0.7694 (m-10) REVERT: I 310 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8287 (tp40) REVERT: J 36 TRP cc_start: 0.8680 (m100) cc_final: 0.8455 (m100) REVERT: J 293 GLN cc_start: 0.8123 (pp30) cc_final: 0.7755 (pp30) REVERT: J 386 GLN cc_start: 0.8109 (tp40) cc_final: 0.7702 (tp40) outliers start: 167 outliers final: 92 residues processed: 304 average time/residue: 0.5124 time to fit residues: 192.7141 Evaluate side-chains 256 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 144 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 180 THR 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 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 309 ASP 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 113 SER Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 522 HIS Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 155 HIS Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 217 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 322 optimal weight: 6.9990 chunk 294 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN D 114 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS J 228 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.082999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.052766 restraints weight = 78454.555| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.62 r_work: 0.2685 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30880 Z= 0.138 Angle : 0.543 11.356 42350 Z= 0.277 Chirality : 0.041 0.351 4636 Planarity : 0.004 0.064 5083 Dihedral : 14.745 88.783 5168 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.88 % Allowed : 29.22 % Favored : 65.90 % 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: 0.28 (0.15), residues: 3476 helix: 1.52 (0.15), residues: 1209 sheet: 0.42 (0.23), residues: 493 loop : -0.83 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 300 TYR 0.016 0.001 TYR C 52 PHE 0.016 0.001 PHE J 248 TRP 0.022 0.001 TRP J 249 HIS 0.003 0.000 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00314 (30878) covalent geometry : angle 0.54302 (42346) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.43865 ( 4) hydrogen bonds : bond 0.03382 ( 1126) hydrogen bonds : angle 4.44684 ( 3082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 157 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8488 (mt0) REVERT: A 343 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8536 (pt0) REVERT: B 28 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7523 (mtp-110) REVERT: B 306 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: C 187 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8809 (ptmm) REVERT: D 247 ASP cc_start: 0.8553 (t0) cc_final: 0.8337 (t0) REVERT: F 1 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.6372 (pmt) REVERT: F 14 GLU cc_start: 0.8783 (pt0) cc_final: 0.8495 (pt0) REVERT: F 194 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8695 (tttp) REVERT: F 220 ASN cc_start: 0.8323 (m-40) cc_final: 0.7974 (p0) REVERT: F 230 LYS cc_start: 0.7467 (pptt) cc_final: 0.6986 (pmtt) REVERT: F 239 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.6507 (ttt180) REVERT: F 286 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7007 (mtp85) REVERT: F 309 ASP cc_start: 0.9330 (OUTLIER) cc_final: 0.8853 (OUTLIER) REVERT: F 321 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7825 (mt) REVERT: G 147 HIS cc_start: 0.8960 (OUTLIER) cc_final: 0.8470 (m90) REVERT: G 218 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8660 (p) REVERT: G 223 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8496 (tp30) REVERT: G 252 MET cc_start: 0.9078 (tmm) cc_final: 0.8801 (tmm) REVERT: G 271 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7579 (tp40) REVERT: G 293 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8564 (p) REVERT: H 77 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8468 (mp10) REVERT: H 155 ASP cc_start: 0.8742 (p0) cc_final: 0.8432 (t0) REVERT: H 158 SER cc_start: 0.9278 (OUTLIER) cc_final: 0.9048 (p) REVERT: I 146 TRP cc_start: 0.8459 (m-10) cc_final: 0.7680 (m-10) REVERT: J 36 TRP cc_start: 0.8672 (m100) cc_final: 0.8398 (m100) REVERT: J 184 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6325 (pm20) REVERT: J 293 GLN cc_start: 0.8088 (pp30) cc_final: 0.7739 (pp30) REVERT: J 386 GLN cc_start: 0.7976 (tp40) cc_final: 0.7643 (tp40) outliers start: 144 outliers final: 85 residues processed: 284 average time/residue: 0.5412 time to fit residues: 188.2327 Evaluate side-chains 251 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 148 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 180 THR 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 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP 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 113 SER Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 330 MET Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 228 HIS Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 39 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 55 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.082393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.052116 restraints weight = 78301.270| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.60 r_work: 0.2666 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30880 Z= 0.184 Angle : 0.562 11.751 42350 Z= 0.287 Chirality : 0.042 0.364 4636 Planarity : 0.004 0.067 5083 Dihedral : 14.706 87.848 5166 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.15 % Allowed : 29.06 % Favored : 65.80 % 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: 0.25 (0.15), residues: 3476 helix: 1.52 (0.15), residues: 1208 sheet: 0.36 (0.23), residues: 499 loop : -0.86 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG H 30 TYR 0.016 0.001 TYR C 52 PHE 0.015 0.001 PHE C 302 TRP 0.027 0.001 TRP J 381 HIS 0.003 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00422 (30878) covalent geometry : angle 0.56186 (42346) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.42918 ( 4) hydrogen bonds : bond 0.03539 ( 1126) hydrogen bonds : angle 4.47830 ( 3082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 157 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8536 (mttm) REVERT: A 67 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8385 (mt0) REVERT: A 175 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9175 (ptmm) REVERT: B 306 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: C 187 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8821 (ptmm) REVERT: F 1 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.6399 (pmt) REVERT: F 14 GLU cc_start: 0.8814 (pt0) cc_final: 0.8577 (pt0) REVERT: F 121 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8925 (mp0) REVERT: F 194 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8577 (ttpt) REVERT: F 220 ASN cc_start: 0.8335 (m-40) cc_final: 0.7982 (p0) REVERT: F 230 LYS cc_start: 0.7489 (pptt) cc_final: 0.7007 (pmtt) REVERT: F 239 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.6535 (ttt180) REVERT: F 286 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7026 (mtp85) REVERT: F 309 ASP cc_start: 0.9327 (OUTLIER) cc_final: 0.8860 (OUTLIER) REVERT: F 321 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7863 (mt) REVERT: G 147 HIS cc_start: 0.8956 (OUTLIER) cc_final: 0.8424 (m90) REVERT: G 218 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8701 (p) REVERT: G 223 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8488 (tp30) REVERT: G 252 MET cc_start: 0.9095 (tmm) cc_final: 0.8816 (tmm) REVERT: G 271 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7624 (tp40) REVERT: G 293 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8547 (p) REVERT: H 77 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8461 (mp10) REVERT: H 155 ASP cc_start: 0.8749 (p0) cc_final: 0.8402 (t0) REVERT: H 158 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.9046 (p) REVERT: I 146 TRP cc_start: 0.8461 (m-10) cc_final: 0.7688 (m-10) REVERT: J 36 TRP cc_start: 0.8679 (m100) cc_final: 0.8399 (m100) REVERT: J 145 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8475 (mpt-90) REVERT: J 184 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6329 (pm20) REVERT: J 293 GLN cc_start: 0.8079 (pp30) cc_final: 0.7709 (pp30) REVERT: J 386 GLN cc_start: 0.7953 (tp40) cc_final: 0.7615 (tp40) outliers start: 152 outliers final: 96 residues processed: 292 average time/residue: 0.5189 time to fit residues: 187.1106 Evaluate side-chains 262 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 146 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 180 THR 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 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP 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 113 SER Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 522 HIS Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 145 ARG Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 155 HIS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 347 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.083885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.053818 restraints weight = 78565.976| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.62 r_work: 0.2713 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30880 Z= 0.114 Angle : 0.539 12.282 42350 Z= 0.275 Chirality : 0.040 0.346 4636 Planarity : 0.004 0.071 5083 Dihedral : 14.699 91.535 5166 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.17 % Allowed : 30.24 % Favored : 65.59 % 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: 0.34 (0.15), residues: 3476 helix: 1.59 (0.15), residues: 1214 sheet: 0.46 (0.23), residues: 493 loop : -0.82 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 30 TYR 0.016 0.001 TYR C 52 PHE 0.012 0.001 PHE A 302 TRP 0.033 0.001 TRP J 381 HIS 0.003 0.000 HIS H 105 Details of bonding type rmsd covalent geometry : bond 0.00256 (30878) covalent geometry : angle 0.53864 (42346) SS BOND : bond 0.00225 ( 2) SS BOND : angle 0.45086 ( 4) hydrogen bonds : bond 0.03161 ( 1126) hydrogen bonds : angle 4.35546 ( 3082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 161 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8486 (mttm) REVERT: A 67 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8368 (mt0) REVERT: B 306 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: C 187 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8773 (ptmm) REVERT: F 1 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.6322 (pmt) REVERT: F 14 GLU cc_start: 0.8751 (pt0) cc_final: 0.8545 (pt0) REVERT: F 194 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8554 (ttpt) REVERT: F 220 ASN cc_start: 0.8296 (m-40) cc_final: 0.7971 (p0) REVERT: F 230 LYS cc_start: 0.7469 (pptt) cc_final: 0.6996 (pmtt) REVERT: F 239 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.6476 (ttt180) REVERT: F 286 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6887 (mtp85) REVERT: F 309 ASP cc_start: 0.9321 (OUTLIER) cc_final: 0.8826 (OUTLIER) REVERT: F 321 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7802 (mt) REVERT: G 147 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.8466 (m90) REVERT: G 252 MET cc_start: 0.9046 (tmm) cc_final: 0.8771 (tmm) REVERT: G 271 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7542 (tp40) REVERT: G 293 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8586 (p) REVERT: H 77 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8845 (mp10) REVERT: H 155 ASP cc_start: 0.8742 (p0) cc_final: 0.8380 (t0) REVERT: H 158 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.9066 (p) REVERT: I 146 TRP cc_start: 0.8486 (m-10) cc_final: 0.7680 (m-10) REVERT: J 36 TRP cc_start: 0.8682 (m100) cc_final: 0.8405 (m100) REVERT: J 145 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8462 (mpt-90) REVERT: J 184 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6251 (pm20) REVERT: J 227 MET cc_start: 0.9299 (mpm) cc_final: 0.8938 (mtm) REVERT: J 293 GLN cc_start: 0.8073 (pp30) cc_final: 0.7701 (pp30) REVERT: J 386 GLN cc_start: 0.7891 (tp40) cc_final: 0.7513 (tp40) outliers start: 123 outliers final: 76 residues processed: 271 average time/residue: 0.5384 time to fit residues: 179.4340 Evaluate side-chains 239 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 147 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 180 THR 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 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP 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 113 SER Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 145 ARG Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 122 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 105 optimal weight: 0.0010 chunk 199 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 311 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.084221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.054211 restraints weight = 78363.875| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.62 r_work: 0.2723 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30880 Z= 0.110 Angle : 0.547 12.549 42350 Z= 0.278 Chirality : 0.041 0.369 4636 Planarity : 0.004 0.073 5083 Dihedral : 14.661 92.999 5164 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.56 % Allowed : 31.02 % Favored : 65.42 % 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: 0.40 (0.15), residues: 3476 helix: 1.62 (0.15), residues: 1214 sheet: 0.58 (0.23), residues: 523 loop : -0.82 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 300 TYR 0.013 0.001 TYR H 74 PHE 0.011 0.001 PHE A 302 TRP 0.039 0.001 TRP J 381 HIS 0.003 0.000 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00246 (30878) covalent geometry : angle 0.54656 (42346) SS BOND : bond 0.00222 ( 2) SS BOND : angle 0.43007 ( 4) hydrogen bonds : bond 0.03121 ( 1126) hydrogen bonds : angle 4.32833 ( 3082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 154 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8461 (mttm) REVERT: A 67 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: B 306 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: C 187 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8749 (ptmm) REVERT: F 1 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.6283 (pmt) REVERT: F 194 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8536 (ttpt) REVERT: F 220 ASN cc_start: 0.8281 (m-40) cc_final: 0.7957 (p0) REVERT: F 230 LYS cc_start: 0.7545 (pptt) cc_final: 0.7073 (pmtt) REVERT: F 239 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.6491 (ttt180) REVERT: F 286 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6810 (mtp85) REVERT: F 309 ASP cc_start: 0.9323 (OUTLIER) cc_final: 0.8814 (OUTLIER) REVERT: F 321 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7802 (mt) REVERT: G 147 HIS cc_start: 0.8923 (OUTLIER) cc_final: 0.8469 (m90) REVERT: G 218 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8666 (p) REVERT: G 252 MET cc_start: 0.9030 (tmm) cc_final: 0.8708 (tmm) REVERT: G 271 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7538 (tp40) REVERT: H 77 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8868 (mp10) REVERT: H 155 ASP cc_start: 0.8728 (p0) cc_final: 0.8361 (t0) REVERT: H 158 SER cc_start: 0.9270 (OUTLIER) cc_final: 0.9050 (p) REVERT: I 146 TRP cc_start: 0.8490 (m-10) cc_final: 0.7725 (m-10) REVERT: J 36 TRP cc_start: 0.8682 (m100) cc_final: 0.8400 (m100) REVERT: J 145 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8442 (mpt-90) REVERT: J 184 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6281 (pm20) REVERT: J 227 MET cc_start: 0.9300 (mpm) cc_final: 0.8934 (mtm) REVERT: J 293 GLN cc_start: 0.8093 (pp30) cc_final: 0.7731 (pp30) REVERT: J 386 GLN cc_start: 0.7863 (tp40) cc_final: 0.7420 (tp40) outliers start: 105 outliers final: 76 residues processed: 246 average time/residue: 0.5260 time to fit residues: 161.1608 Evaluate side-chains 236 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 144 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP 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 113 SER Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 145 ARG Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 249 TRP Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 151 optimal weight: 0.9990 chunk 329 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 289 optimal weight: 0.0040 chunk 17 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 312 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 275 optimal weight: 9.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 314 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS J 228 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.084461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.054487 restraints weight = 78370.117| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.62 r_work: 0.2729 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30880 Z= 0.110 Angle : 0.542 12.886 42350 Z= 0.275 Chirality : 0.040 0.367 4636 Planarity : 0.004 0.073 5083 Dihedral : 14.599 93.742 5161 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.59 % Allowed : 30.95 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 3476 helix: 1.66 (0.16), residues: 1211 sheet: 0.60 (0.22), residues: 523 loop : -0.82 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 300 TYR 0.015 0.001 TYR C 52 PHE 0.013 0.001 PHE J 22 TRP 0.039 0.001 TRP J 381 HIS 0.003 0.000 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00246 (30878) covalent geometry : angle 0.54172 (42346) SS BOND : bond 0.00212 ( 2) SS BOND : angle 0.42546 ( 4) hydrogen bonds : bond 0.03079 ( 1126) hydrogen bonds : angle 4.30968 ( 3082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6952 Ramachandran restraints generated. 3476 Oldfield, 0 Emsley, 3476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 154 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8463 (mttm) REVERT: A 67 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: B 306 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: C 187 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8739 (ptmm) REVERT: E 123 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7311 (p) REVERT: F 194 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8532 (ttpt) REVERT: F 220 ASN cc_start: 0.8272 (m-40) cc_final: 0.7964 (p0) REVERT: F 230 LYS cc_start: 0.7551 (pptt) cc_final: 0.7101 (pmtt) REVERT: F 239 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.6406 (ttt180) REVERT: F 286 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6793 (mtp85) REVERT: F 321 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7764 (mt) REVERT: G 147 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.8502 (m170) REVERT: G 218 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8658 (p) REVERT: G 252 MET cc_start: 0.9001 (tmm) cc_final: 0.8630 (tmm) REVERT: G 271 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7563 (tp40) REVERT: H 77 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8874 (mp10) REVERT: H 155 ASP cc_start: 0.8712 (p0) cc_final: 0.8349 (t0) REVERT: H 158 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.9084 (p) REVERT: I 146 TRP cc_start: 0.8486 (m-10) cc_final: 0.7725 (m-10) REVERT: J 36 TRP cc_start: 0.8683 (m100) cc_final: 0.8401 (m100) REVERT: J 145 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8428 (mpt-90) REVERT: J 184 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6277 (pm20) REVERT: J 227 MET cc_start: 0.9308 (mpm) cc_final: 0.8935 (mtm) REVERT: J 293 GLN cc_start: 0.8113 (pp30) cc_final: 0.7755 (pp30) REVERT: J 386 GLN cc_start: 0.7887 (tp40) cc_final: 0.7437 (tp40) outliers start: 106 outliers final: 77 residues processed: 249 average time/residue: 0.5456 time to fit residues: 167.1273 Evaluate side-chains 242 residues out of total 3127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 149 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 180 THR 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 247 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 309 ASP 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 113 SER Chi-restraints excluded: chain G residue 147 HIS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 526 CYS Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 387 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 145 ARG Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 329 optimal weight: 3.9990 chunk 334 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 336 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 319 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.082698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.052348 restraints weight = 78900.277| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.62 r_work: 0.2673 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30880 Z= 0.194 Angle : 0.579 12.466 42350 Z= 0.295 Chirality : 0.042 0.367 4636 Planarity : 0.004 0.086 5083 Dihedral : 14.591 89.262 5161 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.52 % Allowed : 31.12 % Favored : 65.36 % 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: 0.32 (0.15), residues: 3476 helix: 1.57 (0.15), residues: 1215 sheet: 0.43 (0.22), residues: 537 loop : -0.86 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG H 30 TYR 0.014 0.001 TYR H 74 PHE 0.016 0.001 PHE C 302 TRP 0.041 0.001 TRP J 381 HIS 0.003 0.001 HIS J 251 Details of bonding type rmsd covalent geometry : bond 0.00446 (30878) covalent geometry : angle 0.57878 (42346) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.38556 ( 4) hydrogen bonds : bond 0.03493 ( 1126) hydrogen bonds : angle 4.43155 ( 3082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12034.43 seconds wall clock time: 205 minutes 29.96 seconds (12329.96 seconds total)