Starting phenix.real_space_refine on Sun Jul 5 02:04:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hei_52077/07_2026/9hei_52077.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hei_52077/07_2026/9hei_52077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hei_52077/07_2026/9hei_52077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hei_52077/07_2026/9hei_52077.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hei_52077/07_2026/9hei_52077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hei_52077/07_2026/9hei_52077.map" } resolution = 2.92 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= 0.002 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: 10 Type Number sf(0) Gaussians Ca 1 9.91 5 Mn 4 7.51 5 Fe 2 7.16 5 P 4 5.49 5 Mg 35 5.21 5 S 72 5.16 5 Cl 2 4.86 5 C 16769 2.51 5 N 3656 2.21 5 O 4152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24697 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2491 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 1 Chain: "B" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3755 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 25, 'TRANS': 454} Chain: "V" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 224 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "C" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3498 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 25, 'TRANS': 423} Chain: "D" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2771 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 14, 'TRANS': 333} Chain: "E" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "F" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "H" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 501 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "I" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 275 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "J" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 262 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "K" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "L" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 290 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "M" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "O" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1808 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 10, 'TRANS': 229} Chain: "P" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1444 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1192 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "T" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 247 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "X" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 220 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "Z" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 458 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "U" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 176 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "W" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 344 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "A" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 339 Ad-hoc single atom residues: {'FE2': 1, ' CL': 2} Unusual residues: {'BCR': 1, 'CLA': 3, 'OEX': 1, 'PHO': 1, 'SQD': 1} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1191 Unusual residues: {'BCR': 2, 'CLA': 15, 'LHG': 2, 'LMG': 2} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1155 Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 3, 'LMG': 1, 'LMU': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 473 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 2, 'LMG': 1, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'CLA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.19 Number of scatterers: 24697 At special positions: 0 Unit cell: (136.08, 126, 125.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Fe 2 26.01 Mn 4 24.99 Ca 1 19.99 Cl 2 17.00 S 72 16.00 P 4 15.00 Mg 35 11.99 O 4152 8.00 N 3656 7.00 C 16769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=38, symmetry=0 Number of additional bonds: simple=38, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 761.6 milliseconds 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4926 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 15 sheets defined 59.7% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 31 through 55 removed outlier: 3.765A pdb=" N ILE A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 109 through 138 removed outlier: 4.120A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.678A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 224 Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 267 through 294 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 316 through 332 Processing helix chain 'B' and resid 4 through 13 removed outlier: 3.581A pdb=" N VAL B 8 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N HIS B 9 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 44 removed outlier: 3.715A pdb=" N SER B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 4.169A pdb=" N PHE B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 195 through 219 removed outlier: 4.121A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 233 through 259 removed outlier: 3.672A pdb=" N VAL B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.819A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 295 Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.743A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'V' and resid 3 through 29 removed outlier: 4.169A pdb=" N GLY V 19 " --> pdb=" O VAL V 15 " (cutoff:3.500A) Proline residue: V 20 - end of helix Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 22 through 31 removed outlier: 6.092A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 62 Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 75 through 83 removed outlier: 3.913A pdb=" N HIS C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.637A pdb=" N GLU C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 120 removed outlier: 3.501A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 169 Processing helix chain 'C' and resid 193 through 203 removed outlier: 3.923A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.540A pdb=" N SER C 214 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 241 Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 255 through 281 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 293 through 313 Processing helix chain 'C' and resid 341 through 347 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 409 through 442 Processing helix chain 'C' and resid 452 through 457 removed outlier: 3.745A pdb=" N SER C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 33 through 55 Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 108 through 137 removed outlier: 4.071A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 146 Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 175 through 190 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 194 through 221 Processing helix chain 'D' and resid 245 through 257 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 275 - end of helix removed outlier: 3.523A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 328 Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'E' and resid 9 through 14 Processing helix chain 'E' and resid 16 through 40 removed outlier: 4.176A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 41 through 47 Processing helix chain 'E' and resid 71 through 80 Processing helix chain 'F' and resid 16 through 40 removed outlier: 3.527A pdb=" N ILE F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL F 27 " --> pdb=" O HIS F 23 " (cutoff:3.500A) Proline residue: F 28 - end of helix Processing helix chain 'H' and resid 24 through 36 Proline residue: H 32 - end of helix removed outlier: 3.992A pdb=" N GLU H 36 " --> pdb=" O PRO H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 69 Processing helix chain 'H' and resid 80 through 85 Processing helix chain 'I' and resid 2 through 25 Processing helix chain 'I' and resid 26 through 31 removed outlier: 3.647A pdb=" N ASN I 31 " --> pdb=" O PRO I 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 35 Processing helix chain 'K' and resid 15 through 17 No H-bonds generated for 'chain 'K' and resid 15 through 17' Processing helix chain 'K' and resid 18 through 25 Processing helix chain 'K' and resid 27 through 44 removed outlier: 3.765A pdb=" N PHE K 31 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 38 removed outlier: 4.557A pdb=" N SER L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 15 Processing helix chain 'M' and resid 16 through 31 Processing helix chain 'O' and resid 53 through 60 Processing helix chain 'O' and resid 61 through 66 Processing helix chain 'O' and resid 69 through 73 Processing helix chain 'O' and resid 226 through 231 Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 133 through 141 Processing helix chain 'P' and resid 142 through 145 Processing helix chain 'P' and resid 196 through 199 Processing helix chain 'P' and resid 224 through 228 Processing helix chain 'P' and resid 230 through 242 removed outlier: 3.853A pdb=" N GLU P 234 " --> pdb=" O GLY P 230 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 66 removed outlier: 4.236A pdb=" N ARG Q 64 " --> pdb=" O ASP Q 60 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 80 through 86 Processing helix chain 'Q' and resid 86 through 93 Processing helix chain 'Q' and resid 93 through 109 Processing helix chain 'Q' and resid 112 through 119 Processing helix chain 'Q' and resid 120 through 128 Processing helix chain 'Q' and resid 129 through 133 Processing helix chain 'Q' and resid 134 through 146 removed outlier: 3.593A pdb=" N LYS Q 146 " --> pdb=" O LEU Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 174 Processing helix chain 'Q' and resid 176 through 199 Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'X' and resid 66 through 96 Processing helix chain 'Z' and resid 2 through 29 Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 36 through 60 Processing helix chain 'U' and resid 93 through 102 Proline residue: U 100 - end of helix Processing helix chain 'W' and resid 72 through 76 Processing helix chain 'W' and resid 78 through 100 removed outlier: 3.521A pdb=" N GLY W 82 " --> pdb=" O ASP W 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA2, first strand: chain 'A' and resid 297 through 298 Processing sheet with id=AA3, first strand: chain 'B' and resid 73 through 74 removed outlier: 3.548A pdb=" N TRP B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.596A pdb=" N ILE B 166 " --> pdb=" O GLN B 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.413A pdb=" N GLU B 431 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.153A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 409 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AA8, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA9, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'O' and resid 117 through 120 removed outlier: 3.923A pdb=" N ASN O 96 " --> pdb=" O MET O 135 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N MET O 135 " --> pdb=" O ASN O 96 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS O 98 " --> pdb=" O ASP O 133 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP O 133 " --> pdb=" O CYS O 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 117 through 120 removed outlier: 5.545A pdb=" N LEU O 94 " --> pdb=" O LYS O 291 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS O 291 " --> pdb=" O LEU O 94 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASN O 96 " --> pdb=" O GLN O 289 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN O 289 " --> pdb=" O ASN O 96 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR O 283 " --> pdb=" O THR O 102 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE O 104 " --> pdb=" O LYS O 281 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS O 281 " --> pdb=" O PHE O 104 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL O 106 " --> pdb=" O ASP O 279 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASP O 279 " --> pdb=" O VAL O 106 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL O 261 " --> pdb=" O VAL O 248 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL O 248 " --> pdb=" O VAL O 261 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLU O 263 " --> pdb=" O PHE O 246 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N PHE O 246 " --> pdb=" O GLU O 263 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE O 265 " --> pdb=" O ALA O 244 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA O 244 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLY O 242 " --> pdb=" O PRO O 267 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE O 246 " --> pdb=" O ILE O 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 123 through 124 Processing sheet with id=AB4, first strand: chain 'P' and resid 75 through 79 Processing sheet with id=AB5, first strand: chain 'P' and resid 92 through 93 removed outlier: 5.568A pdb=" N VAL P 102 " --> pdb=" O ALA P 120 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA P 120 " --> pdb=" O VAL P 102 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS P 214 " --> pdb=" O GLY P 210 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL P 209 " --> pdb=" O THR P 183 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR P 183 " --> pdb=" O VAL P 209 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU P 190 " --> pdb=" O LEU P 170 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU P 170 " --> pdb=" O LEU P 190 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG P 192 " --> pdb=" O ALA P 168 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ALA P 168 " --> pdb=" O ARG P 192 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP Q 56 " --> pdb=" O SER P 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 147 through 148 1250 hydrogen bonds defined for protein. 3546 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.68: 25312 1.68 - 2.16: 244 2.16 - 2.64: 37 2.64 - 3.12: 2 3.12 - 3.60: 4 Bond restraints: 25599 Sorted by residual: bond pdb=" C25 BCR C 516 " pdb=" C26 BCR C 516 " ideal model delta sigma weight residual 1.347 1.612 -0.265 2.00e-02 2.50e+03 1.75e+02 bond pdb=" C25 BCR C 514 " pdb=" C26 BCR C 514 " ideal model delta sigma weight residual 1.347 1.609 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C25 BCR B 517 " pdb=" C26 BCR B 517 " ideal model delta sigma weight residual 1.347 1.609 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C25 BCR C 515 " pdb=" C26 BCR C 515 " ideal model delta sigma weight residual 1.347 1.608 -0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C25 BCR K 101 " pdb=" C26 BCR K 101 " ideal model delta sigma weight residual 1.347 1.605 -0.258 2.00e-02 2.50e+03 1.66e+02 ... (remaining 25594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.36: 34802 6.36 - 12.72: 372 12.72 - 19.08: 36 19.08 - 25.45: 2 25.45 - 31.81: 1 Bond angle restraints: 35213 Sorted by residual: angle pdb="MN3 OEX A 401 " pdb=" O5 OEX A 401 " pdb="MN4 OEX A 401 " ideal model delta sigma weight residual 73.50 105.31 -31.81 2.00e+00 2.50e-01 2.53e+02 angle pdb="CA1 OEX A 401 " pdb=" O5 OEX A 401 " pdb="MN4 OEX A 401 " ideal model delta sigma weight residual 92.50 115.46 -22.96 2.00e+00 2.50e-01 1.32e+02 angle pdb=" O1 OEX A 401 " pdb="MN1 OEX A 401 " pdb=" O5 OEX A 401 " ideal model delta sigma weight residual 93.00 71.60 21.40 2.00e+00 2.50e-01 1.15e+02 angle pdb="MN2 OEX A 401 " pdb=" O3 OEX A 401 " pdb="MN3 OEX A 401 " ideal model delta sigma weight residual 89.00 105.00 -16.00 2.00e+00 2.50e-01 6.40e+01 angle pdb="MN1 OEX A 401 " pdb=" O3 OEX A 401 " pdb="MN2 OEX A 401 " ideal model delta sigma weight residual 88.00 102.71 -14.71 2.00e+00 2.50e-01 5.41e+01 ... (remaining 35208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 13406 31.94 - 63.89: 477 63.89 - 95.83: 57 95.83 - 127.77: 65 127.77 - 159.72: 2 Dihedral angle restraints: 14007 sinusoidal: 6285 harmonic: 7722 Sorted by residual: dihedral pdb=" C2B HEM F 101 " pdb=" C3B HEM F 101 " pdb=" CAB HEM F 101 " pdb=" CBB HEM F 101 " ideal model delta sinusoidal sigma weight residual 0.00 59.08 -59.08 2 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" C3A DGD C 517 " pdb=" C1A DGD C 517 " pdb=" C2A DGD C 517 " pdb=" O1A DGD C 517 " ideal model delta sinusoidal sigma weight residual 335.78 176.06 159.72 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C4D PHO D 402 " pdb=" CBD PHO D 402 " pdb=" CHA PHO D 402 " pdb=" CGD PHO D 402 " ideal model delta sinusoidal sigma weight residual 243.52 115.25 128.27 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 14004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 2955 0.147 - 0.293: 552 0.293 - 0.439: 0 0.439 - 0.586: 0 0.586 - 0.732: 35 Chirality restraints: 3542 Sorted by residual: chirality pdb=" C3A CLA B 514 " pdb=" C2A CLA B 514 " pdb=" C4A CLA B 514 " pdb=" CMA CLA B 514 " both_signs ideal model delta sigma weight residual False -2.76 -2.03 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C3A CLA B 504 " pdb=" C2A CLA B 504 " pdb=" C4A CLA B 504 " pdb=" CMA CLA B 504 " both_signs ideal model delta sigma weight residual False -2.76 -2.06 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" C3A CLA C 506 " pdb=" C2A CLA C 506 " pdb=" C4A CLA C 506 " pdb=" CMA CLA C 506 " both_signs ideal model delta sigma weight residual False -2.76 -2.06 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 3539 not shown) Planarity restraints: 4409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO D 402 " -0.065 2.00e-02 2.50e+03 1.07e-01 9.15e+02 pdb=" ND PHO D 402 " -0.072 2.00e-02 2.50e+03 pdb=" C1A PHO D 402 " -0.017 2.00e-02 2.50e+03 pdb=" C1B PHO D 402 " -0.033 2.00e-02 2.50e+03 pdb=" C1C PHO D 402 " -0.096 2.00e-02 2.50e+03 pdb=" C1D PHO D 402 " -0.087 2.00e-02 2.50e+03 pdb=" C2A PHO D 402 " -0.033 2.00e-02 2.50e+03 pdb=" C2B PHO D 402 " 0.031 2.00e-02 2.50e+03 pdb=" C2C PHO D 402 " 0.004 2.00e-02 2.50e+03 pdb=" C2D PHO D 402 " -0.039 2.00e-02 2.50e+03 pdb=" C3A PHO D 402 " 0.127 2.00e-02 2.50e+03 pdb=" C3B PHO D 402 " 0.038 2.00e-02 2.50e+03 pdb=" C3C PHO D 402 " 0.108 2.00e-02 2.50e+03 pdb=" C3D PHO D 402 " 0.005 2.00e-02 2.50e+03 pdb=" C4A PHO D 402 " -0.010 2.00e-02 2.50e+03 pdb=" C4B PHO D 402 " -0.023 2.00e-02 2.50e+03 pdb=" C4C PHO D 402 " -0.107 2.00e-02 2.50e+03 pdb=" C4D PHO D 402 " -0.017 2.00e-02 2.50e+03 pdb=" CAB PHO D 402 " 0.098 2.00e-02 2.50e+03 pdb=" CAC PHO D 402 " 0.383 2.00e-02 2.50e+03 pdb=" CAD PHO D 402 " 0.065 2.00e-02 2.50e+03 pdb=" CBD PHO D 402 " 0.160 2.00e-02 2.50e+03 pdb=" CHA PHO D 402 " 0.028 2.00e-02 2.50e+03 pdb=" CHB PHO D 402 " -0.058 2.00e-02 2.50e+03 pdb=" CHC PHO D 402 " -0.039 2.00e-02 2.50e+03 pdb=" CHD PHO D 402 " -0.136 2.00e-02 2.50e+03 pdb=" CMB PHO D 402 " 0.083 2.00e-02 2.50e+03 pdb=" CMC PHO D 402 " 0.003 2.00e-02 2.50e+03 pdb=" CMD PHO D 402 " -0.037 2.00e-02 2.50e+03 pdb=" NA PHO D 402 " -0.067 2.00e-02 2.50e+03 pdb=" NC PHO D 402 " -0.258 2.00e-02 2.50e+03 pdb=" OBD PHO D 402 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO A 407 " 0.015 2.00e-02 2.50e+03 1.05e-01 8.85e+02 pdb=" ND PHO A 407 " -0.006 2.00e-02 2.50e+03 pdb=" C1A PHO A 407 " -0.031 2.00e-02 2.50e+03 pdb=" C1B PHO A 407 " 0.000 2.00e-02 2.50e+03 pdb=" C1C PHO A 407 " 0.062 2.00e-02 2.50e+03 pdb=" C1D PHO A 407 " 0.012 2.00e-02 2.50e+03 pdb=" C2A PHO A 407 " -0.134 2.00e-02 2.50e+03 pdb=" C2B PHO A 407 " 0.046 2.00e-02 2.50e+03 pdb=" C2C PHO A 407 " -0.037 2.00e-02 2.50e+03 pdb=" C2D PHO A 407 " 0.051 2.00e-02 2.50e+03 pdb=" C3A PHO A 407 " -0.312 2.00e-02 2.50e+03 pdb=" C3B PHO A 407 " 0.083 2.00e-02 2.50e+03 pdb=" C3C PHO A 407 " -0.133 2.00e-02 2.50e+03 pdb=" C3D PHO A 407 " 0.053 2.00e-02 2.50e+03 pdb=" C4A PHO A 407 " -0.103 2.00e-02 2.50e+03 pdb=" C4B PHO A 407 " 0.067 2.00e-02 2.50e+03 pdb=" C4C PHO A 407 " -0.003 2.00e-02 2.50e+03 pdb=" C4D PHO A 407 " 0.020 2.00e-02 2.50e+03 pdb=" CAB PHO A 407 " 0.142 2.00e-02 2.50e+03 pdb=" CAC PHO A 407 " -0.326 2.00e-02 2.50e+03 pdb=" CAD PHO A 407 " 0.080 2.00e-02 2.50e+03 pdb=" CBD PHO A 407 " 0.068 2.00e-02 2.50e+03 pdb=" CHA PHO A 407 " 0.017 2.00e-02 2.50e+03 pdb=" CHB PHO A 407 " -0.050 2.00e-02 2.50e+03 pdb=" CHC PHO A 407 " 0.092 2.00e-02 2.50e+03 pdb=" CHD PHO A 407 " -0.006 2.00e-02 2.50e+03 pdb=" CMB PHO A 407 " 0.045 2.00e-02 2.50e+03 pdb=" CMC PHO A 407 " -0.039 2.00e-02 2.50e+03 pdb=" CMD PHO A 407 " 0.080 2.00e-02 2.50e+03 pdb=" NA PHO A 407 " 0.022 2.00e-02 2.50e+03 pdb=" NC PHO A 407 " 0.118 2.00e-02 2.50e+03 pdb=" OBD PHO A 407 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PL9 D 407 " -0.053 2.00e-02 2.50e+03 1.19e-01 3.87e+02 pdb=" C2 PL9 D 407 " -0.088 2.00e-02 2.50e+03 pdb=" C3 PL9 D 407 " 0.026 2.00e-02 2.50e+03 pdb=" C4 PL9 D 407 " -0.070 2.00e-02 2.50e+03 pdb=" C5 PL9 D 407 " 0.010 2.00e-02 2.50e+03 pdb=" C52 PL9 D 407 " 0.064 2.00e-02 2.50e+03 pdb=" C53 PL9 D 407 " 0.133 2.00e-02 2.50e+03 pdb=" C6 PL9 D 407 " 0.030 2.00e-02 2.50e+03 pdb=" C7 PL9 D 407 " 0.251 2.00e-02 2.50e+03 pdb=" O1 PL9 D 407 " -0.211 2.00e-02 2.50e+03 pdb=" O2 PL9 D 407 " -0.093 2.00e-02 2.50e+03 ... (remaining 4406 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 5 2.15 - 2.84: 8244 2.84 - 3.53: 40761 3.53 - 4.21: 68714 4.21 - 4.90: 115327 Nonbonded interactions: 233051 Sorted by model distance: nonbonded pdb="FE FE2 A 402 " pdb=" O2 BCT D 403 " model vdw 1.467 3.000 nonbonded pdb="FE FE2 A 402 " pdb=" C BCT D 403 " model vdw 2.014 3.230 nonbonded pdb=" NE2 HIS D 214 " pdb="FE FE2 A 402 " model vdw 2.025 3.080 nonbonded pdb=" OE2 GLU C 342 " pdb="MN3 OEX A 401 " model vdw 2.117 3.060 nonbonded pdb=" NE2 HIS F 23 " pdb="FE HEM F 101 " model vdw 2.145 3.080 ... (remaining 233046 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.900 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.026 0.849 25637 Z= 1.636 Angle : 1.851 31.807 35213 Z= 1.143 Chirality : 0.119 0.732 3542 Planarity : 0.007 0.119 4409 Dihedral : 17.880 159.718 9081 Min Nonbonded Distance : 1.467 Molprobity Statistics. All-atom Clashscore : 32.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.01 % Favored : 95.73 % Rotamer: Outliers : 3.38 % Allowed : 6.22 % Favored : 90.40 % 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: -0.77 (0.15), residues: 2692 helix: 0.04 (0.12), residues: 1453 sheet: -0.78 (0.39), residues: 167 loop : -1.11 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 249 TYR 0.009 0.001 TYR D 315 PHE 0.012 0.001 PHE C 425 TRP 0.011 0.001 TRP Q 121 HIS 0.004 0.001 HIS D 268 Details of bonding type rmsd/Z covalent geometry : bond 0.02325 / 1.29 (25599) covalent geometry : angle 1.85143 / 1.14 (35213) hydrogen bonds : bond 0.17401 / 11.84 ( 1246) hydrogen bonds : angle 7.48722 / 5.51 ( 3546) Misc. bond : bond 0.31178 / 18.98 ( 38) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 452 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 362 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.8178 (t80) REVERT: L 8 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7023 (tptt) REVERT: T 25 ASP cc_start: 0.7558 (t0) cc_final: 0.7342 (t0) outliers start: 75 outliers final: 6 residues processed: 497 average time/residue: 0.5918 time to fit residues: 338.7381 Evaluate side-chains 223 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain Q residue 148 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 ASN A 108 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 267 ASN A 315 ASN ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 285 GLN B 343 HIS C 56 ASN C 143 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN C 366 ASN C 373 GLN C 376 GLN D 83 ASN D 236 ASN E 71 ASN E 75 GLN L 5 ASN L 7 ASN L 38 ASN O 64 GLN O 72 ASN O 266 GLN P 64 ASN P 203 GLN P 213 ASN Z 58 ASN W 66 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.061915 restraints weight = 63747.621| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.15 r_work: 0.2831 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.393 25637 Z= 0.198 Angle : 0.716 10.690 35213 Z= 0.337 Chirality : 0.045 0.316 3542 Planarity : 0.005 0.045 4409 Dihedral : 18.429 172.859 4435 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.70 % Allowed : 12.80 % Favored : 83.50 % 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: 1.17 (0.16), residues: 2692 helix: 1.67 (0.13), residues: 1483 sheet: -0.17 (0.36), residues: 176 loop : -0.31 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 8 TYR 0.019 0.002 TYR P 78 PHE 0.028 0.002 PHE B 246 TRP 0.019 0.002 TRP Z 33 HIS 0.009 0.002 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (25599) covalent geometry : angle 0.71564 / 0.34 (35213) hydrogen bonds : bond 0.05021 / 3.41 ( 1246) hydrogen bonds : angle 5.13245 / 3.80 ( 3546) Misc. bond : bond 0.07078 / 4.06 ( 38) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 233 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 MET cc_start: 0.9110 (tpt) cc_final: 0.8901 (tpp) REVERT: C 217 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7380 (p0) REVERT: C 365 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8787 (tp) REVERT: C 451 ASP cc_start: 0.8355 (m-30) cc_final: 0.7947 (p0) REVERT: D 8 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.8045 (t80) REVERT: D 323 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8572 (mt-10) REVERT: E 12 ASP cc_start: 0.6728 (t0) cc_final: 0.6434 (t0) REVERT: E 62 GLU cc_start: 0.8514 (pm20) cc_final: 0.8303 (pm20) REVERT: L 8 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.7946 (tptt) REVERT: L 9 GLN cc_start: 0.8482 (mm-40) cc_final: 0.7849 (mp10) REVERT: M 21 PHE cc_start: 0.7582 (t80) cc_final: 0.7372 (t80) REVERT: O 58 GLN cc_start: 0.8853 (mm110) cc_final: 0.8518 (mp10) REVERT: O 79 SER cc_start: 0.8090 (t) cc_final: 0.7876 (t) REVERT: O 88 LYS cc_start: 0.8036 (tmmm) cc_final: 0.7802 (tmmm) REVERT: O 140 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8209 (tmtt) REVERT: P 107 GLU cc_start: 0.8915 (pt0) cc_final: 0.8686 (tt0) REVERT: P 203 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8864 (mp10) REVERT: Q 177 GLN cc_start: 0.8990 (tt0) cc_final: 0.8561 (tt0) REVERT: U 97 LYS cc_start: 0.8410 (tmtt) cc_final: 0.8133 (tttt) REVERT: U 105 SER cc_start: 0.9135 (t) cc_final: 0.8801 (p) REVERT: W 96 TRP cc_start: 0.8783 (OUTLIER) cc_final: 0.7861 (t-100) outliers start: 82 outliers final: 25 residues processed: 288 average time/residue: 0.5649 time to fit residues: 190.2735 Evaluate side-chains 231 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 140 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 203 GLN Chi-restraints excluded: chain Q residue 148 LYS Chi-restraints excluded: chain X residue 90 ILE Chi-restraints excluded: chain W residue 96 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 166 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN A 252 HIS D 61 HIS L 38 ASN P 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.068362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.055546 restraints weight = 65597.591| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.20 r_work: 0.2676 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.346 25637 Z= 0.245 Angle : 0.679 9.317 35213 Z= 0.323 Chirality : 0.044 0.243 3542 Planarity : 0.005 0.053 4409 Dihedral : 17.183 163.716 4432 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.83 % Allowed : 13.17 % Favored : 83.00 % 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: 1.31 (0.16), residues: 2692 helix: 1.80 (0.13), residues: 1479 sheet: -0.25 (0.35), residues: 191 loop : -0.22 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 357 TYR 0.016 0.002 TYR A 246 PHE 0.021 0.002 PHE B 246 TRP 0.016 0.001 TRP C 238 HIS 0.009 0.002 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (25599) covalent geometry : angle 0.67887 / 0.32 (35213) hydrogen bonds : bond 0.05447 / 3.73 ( 1246) hydrogen bonds : angle 4.91766 / 3.64 ( 3546) Misc. bond : bond 0.07854 / 4.26 ( 38) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 210 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASN cc_start: 0.9417 (t0) cc_final: 0.9115 (OUTLIER) REVERT: B 25 MET cc_start: 0.9067 (tpt) cc_final: 0.8851 (tpp) REVERT: B 246 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8804 (p90) REVERT: B 334 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7966 (p0) REVERT: B 409 LEU cc_start: 0.8944 (mm) cc_final: 0.8743 (mt) REVERT: C 71 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8892 (mt-10) REVERT: C 365 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8780 (tp) REVERT: C 451 ASP cc_start: 0.8497 (m-30) cc_final: 0.7981 (p0) REVERT: D 8 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8022 (t80) REVERT: D 11 LYS cc_start: 0.8127 (tppt) cc_final: 0.7779 (tppt) REVERT: D 323 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: E 12 ASP cc_start: 0.7024 (t0) cc_final: 0.6627 (t0) REVERT: E 62 GLU cc_start: 0.8777 (pm20) cc_final: 0.8532 (pm20) REVERT: F 43 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8490 (mm-40) REVERT: H 79 MET cc_start: 0.8784 (mmm) cc_final: 0.8506 (tpp) REVERT: I 34 LYS cc_start: 0.8150 (tptt) cc_final: 0.7879 (tptt) REVERT: L 8 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8155 (tptt) REVERT: L 9 GLN cc_start: 0.8535 (mm-40) cc_final: 0.7708 (mp10) REVERT: O 58 GLN cc_start: 0.9056 (mm110) cc_final: 0.8725 (mp10) REVERT: O 92 TYR cc_start: 0.8342 (m-80) cc_final: 0.8105 (m-80) REVERT: O 263 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8149 (tm-30) REVERT: P 107 GLU cc_start: 0.8874 (pt0) cc_final: 0.8613 (tt0) REVERT: P 176 THR cc_start: 0.8863 (t) cc_final: 0.8529 (p) REVERT: X 96 PHE cc_start: 0.6019 (t80) cc_final: 0.5289 (t80) REVERT: U 105 SER cc_start: 0.9023 (t) cc_final: 0.8700 (p) outliers start: 85 outliers final: 30 residues processed: 272 average time/residue: 0.6068 time to fit residues: 192.9532 Evaluate side-chains 225 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 148 LYS Chi-restraints excluded: chain W residue 96 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 123 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 ASN D 9 GLN L 38 ASN Q 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.056861 restraints weight = 64106.541| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.18 r_work: 0.2726 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.226 25637 Z= 0.143 Angle : 0.580 7.806 35213 Z= 0.277 Chirality : 0.041 0.256 3542 Planarity : 0.004 0.054 4409 Dihedral : 16.096 155.293 4432 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.29 % Allowed : 14.02 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.16), residues: 2692 helix: 1.93 (0.13), residues: 1483 sheet: -0.00 (0.36), residues: 181 loop : -0.19 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 458 TYR 0.013 0.001 TYR A 246 PHE 0.020 0.001 PHE B 246 TRP 0.016 0.001 TRP A 131 HIS 0.004 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (25599) covalent geometry : angle 0.57954 / 0.28 (35213) hydrogen bonds : bond 0.04345 / 2.96 ( 1246) hydrogen bonds : angle 4.60321 / 3.40 ( 3546) Misc. bond : bond 0.04792 / 2.57 ( 38) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 212 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8323 (mt) REVERT: B 14 ASN cc_start: 0.9397 (t0) cc_final: 0.9096 (OUTLIER) REVERT: B 246 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8894 (p90) REVERT: C 158 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8147 (mm) REVERT: C 365 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8840 (tp) REVERT: C 451 ASP cc_start: 0.8491 (m-30) cc_final: 0.8023 (p0) REVERT: D 8 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8262 (m-10) REVERT: E 12 ASP cc_start: 0.7123 (t0) cc_final: 0.6697 (t0) REVERT: E 62 GLU cc_start: 0.8828 (pm20) cc_final: 0.8590 (pm20) REVERT: H 39 LYS cc_start: 0.8741 (mtmm) cc_final: 0.8522 (mtmm) REVERT: H 79 MET cc_start: 0.8809 (mmm) cc_final: 0.8569 (tpp) REVERT: I 34 LYS cc_start: 0.8188 (tptt) cc_final: 0.7930 (tptt) REVERT: L 7 ASN cc_start: 0.8816 (m110) cc_final: 0.8421 (m-40) REVERT: L 8 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8182 (tptt) REVERT: L 9 GLN cc_start: 0.8599 (mm-40) cc_final: 0.7865 (mp10) REVERT: O 58 GLN cc_start: 0.8937 (mm110) cc_final: 0.8629 (mp10) REVERT: O 230 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8692 (tm) REVERT: P 107 GLU cc_start: 0.8921 (pt0) cc_final: 0.8655 (tt0) REVERT: P 176 THR cc_start: 0.8946 (t) cc_final: 0.8595 (p) REVERT: Q 118 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8619 (mptt) REVERT: U 97 LYS cc_start: 0.8566 (tmtt) cc_final: 0.8210 (tptt) REVERT: U 110 ARG cc_start: 0.8838 (tpp80) cc_final: 0.8617 (tpp80) REVERT: U 113 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6708 (pp) REVERT: W 86 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7838 (tm) REVERT: W 96 TRP cc_start: 0.8919 (OUTLIER) cc_final: 0.8698 (t-100) outliers start: 73 outliers final: 31 residues processed: 262 average time/residue: 0.6203 time to fit residues: 190.3381 Evaluate side-chains 228 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain Q residue 148 LYS Chi-restraints excluded: chain X residue 90 ILE Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 96 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 211 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 100 optimal weight: 0.1980 chunk 138 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 ASN Q 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.056816 restraints weight = 64104.659| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.20 r_work: 0.2723 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.228 25637 Z= 0.134 Angle : 0.563 7.778 35213 Z= 0.269 Chirality : 0.040 0.200 3542 Planarity : 0.004 0.054 4409 Dihedral : 15.378 143.818 4432 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.34 % Allowed : 14.65 % Favored : 82.01 % 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: 1.54 (0.16), residues: 2692 helix: 1.98 (0.13), residues: 1483 sheet: 0.10 (0.36), residues: 181 loop : -0.16 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 225 TYR 0.013 0.001 TYR A 246 PHE 0.019 0.001 PHE B 246 TRP 0.015 0.001 TRP A 131 HIS 0.004 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (25599) covalent geometry : angle 0.56260 / 0.27 (35213) hydrogen bonds : bond 0.04214 / 2.87 ( 1246) hydrogen bonds : angle 4.49518 / 3.32 ( 3546) Misc. bond : bond 0.04461 / 2.35 ( 38) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 195 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8379 (mt) REVERT: B 14 ASN cc_start: 0.9409 (t0) cc_final: 0.9076 (OUTLIER) REVERT: B 246 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8808 (p90) REVERT: C 71 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8936 (mt-10) REVERT: C 158 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8183 (mm) REVERT: C 365 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8814 (tp) REVERT: C 451 ASP cc_start: 0.8500 (m-30) cc_final: 0.8102 (p0) REVERT: D 8 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8296 (m-10) REVERT: E 12 ASP cc_start: 0.7176 (t0) cc_final: 0.6735 (t0) REVERT: E 77 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8295 (tmtt) REVERT: H 79 MET cc_start: 0.8853 (mmm) cc_final: 0.8490 (tpp) REVERT: I 34 LYS cc_start: 0.8196 (tptt) cc_final: 0.7952 (tptt) REVERT: L 8 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8408 (tptt) REVERT: L 9 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8339 (mm-40) REVERT: O 58 GLN cc_start: 0.8894 (mm110) cc_final: 0.8585 (mp10) REVERT: O 230 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8732 (tm) REVERT: P 107 GLU cc_start: 0.8964 (pt0) cc_final: 0.8690 (tt0) REVERT: P 176 THR cc_start: 0.8994 (t) cc_final: 0.8668 (p) REVERT: U 97 LYS cc_start: 0.8622 (tmtt) cc_final: 0.8244 (tptt) REVERT: U 113 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6927 (pp) REVERT: W 86 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7715 (tm) outliers start: 74 outliers final: 29 residues processed: 247 average time/residue: 0.6228 time to fit residues: 180.2294 Evaluate side-chains 222 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 110 ARG Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 36 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 156 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN L 38 ASN P 203 GLN Q 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.057510 restraints weight = 63959.023| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.19 r_work: 0.2742 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.204 25637 Z= 0.119 Angle : 0.550 9.710 35213 Z= 0.263 Chirality : 0.039 0.186 3542 Planarity : 0.004 0.053 4409 Dihedral : 14.815 130.445 4428 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.84 % Allowed : 15.83 % Favored : 81.33 % 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: 1.64 (0.16), residues: 2692 helix: 2.05 (0.13), residues: 1482 sheet: 0.23 (0.36), residues: 181 loop : -0.14 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 127 TYR 0.013 0.001 TYR A 246 PHE 0.018 0.001 PHE B 246 TRP 0.015 0.001 TRP A 131 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (25599) covalent geometry : angle 0.55009 / 0.26 (35213) hydrogen bonds : bond 0.03956 / 2.69 ( 1246) hydrogen bonds : angle 4.40684 / 3.26 ( 3546) Misc. bond : bond 0.04484 / 2.42 ( 38) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 200 time to evaluate : 0.683 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 42 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8379 (mt) REVERT: B 246 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8773 (p90) REVERT: C 71 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8941 (mt-10) REVERT: C 451 ASP cc_start: 0.8477 (m-30) cc_final: 0.8254 (p0) REVERT: D 8 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8294 (m-10) REVERT: E 12 ASP cc_start: 0.7181 (t0) cc_final: 0.6713 (t0) REVERT: E 59 ASP cc_start: 0.9426 (t0) cc_final: 0.9221 (t0) REVERT: E 62 GLU cc_start: 0.8681 (pm20) cc_final: 0.8480 (pm20) REVERT: H 79 MET cc_start: 0.8837 (mmm) cc_final: 0.8492 (tpp) REVERT: I 34 LYS cc_start: 0.8221 (tptt) cc_final: 0.7986 (tptt) REVERT: L 8 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8295 (tptt) REVERT: L 9 GLN cc_start: 0.8671 (mm-40) cc_final: 0.7637 (mp10) REVERT: O 58 GLN cc_start: 0.8852 (mm110) cc_final: 0.8560 (mp10) REVERT: O 86 GLU cc_start: 0.7407 (mp0) cc_final: 0.7190 (pm20) REVERT: P 107 GLU cc_start: 0.8975 (pt0) cc_final: 0.8700 (tt0) REVERT: P 176 THR cc_start: 0.9000 (t) cc_final: 0.8630 (p) REVERT: Q 118 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8583 (mptt) REVERT: Q 177 GLN cc_start: 0.9038 (tt0) cc_final: 0.8830 (tm-30) REVERT: T 24 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7805 (ptt180) REVERT: U 113 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6978 (pp) outliers start: 63 outliers final: 29 residues processed: 245 average time/residue: 0.5298 time to fit residues: 153.1380 Evaluate side-chains 223 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain W residue 65 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 102 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 210 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 258 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.065874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.052930 restraints weight = 65630.087| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.23 r_work: 0.2624 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.334 25637 Z= 0.284 Angle : 0.693 8.982 35213 Z= 0.330 Chirality : 0.045 0.250 3542 Planarity : 0.005 0.056 4409 Dihedral : 15.238 122.837 4428 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.80 % Allowed : 16.55 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.16), residues: 2692 helix: 1.74 (0.13), residues: 1477 sheet: 0.11 (0.36), residues: 193 loop : -0.21 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 127 TYR 0.015 0.002 TYR A 246 PHE 0.022 0.002 PHE P 228 TRP 0.016 0.002 TRP A 131 HIS 0.009 0.002 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.28 (25599) covalent geometry : angle 0.69316 / 0.33 (35213) hydrogen bonds : bond 0.05267 / 3.62 ( 1246) hydrogen bonds : angle 4.74117 / 3.50 ( 3546) Misc. bond : bond 0.07174 / 3.86 ( 38) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8422 (mp) REVERT: B 73 GLN cc_start: 0.8259 (mt0) cc_final: 0.7780 (mt0) REVERT: B 246 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8954 (p90) REVERT: B 442 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8414 (p) REVERT: C 451 ASP cc_start: 0.8762 (m-30) cc_final: 0.8234 (p0) REVERT: D 8 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8048 (t80) REVERT: D 323 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: E 12 ASP cc_start: 0.7216 (t0) cc_final: 0.6783 (t0) REVERT: E 62 GLU cc_start: 0.8850 (pm20) cc_final: 0.8584 (pm20) REVERT: I 34 LYS cc_start: 0.8213 (tptt) cc_final: 0.8010 (tptt) REVERT: L 8 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8558 (tptt) REVERT: L 9 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8329 (mm-40) REVERT: O 58 GLN cc_start: 0.9170 (mm110) cc_final: 0.8849 (mp10) REVERT: O 86 GLU cc_start: 0.7199 (mp0) cc_final: 0.6960 (pm20) REVERT: P 176 THR cc_start: 0.8889 (t) cc_final: 0.8568 (p) REVERT: Q 118 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8634 (mptt) REVERT: T 24 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8362 (ptt180) REVERT: W 65 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7999 (ttm) REVERT: W 96 TRP cc_start: 0.8793 (OUTLIER) cc_final: 0.8460 (t-100) outliers start: 62 outliers final: 30 residues processed: 239 average time/residue: 0.6189 time to fit residues: 172.9306 Evaluate side-chains 216 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 214 TYR Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 96 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 56 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 403 ASN D 9 GLN L 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.067789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.054943 restraints weight = 64452.822| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.18 r_work: 0.2677 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.244 25637 Z= 0.155 Angle : 0.598 9.056 35213 Z= 0.287 Chirality : 0.041 0.213 3542 Planarity : 0.004 0.056 4409 Dihedral : 14.792 120.584 4428 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.30 % Allowed : 17.13 % Favored : 80.57 % 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: 1.45 (0.16), residues: 2692 helix: 1.87 (0.13), residues: 1480 sheet: 0.21 (0.37), residues: 183 loop : -0.17 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 110 TYR 0.012 0.001 TYR A 246 PHE 0.020 0.001 PHE D 54 TRP 0.016 0.001 TRP A 131 HIS 0.004 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (25599) covalent geometry : angle 0.59806 / 0.29 (35213) hydrogen bonds : bond 0.04471 / 3.06 ( 1246) hydrogen bonds : angle 4.54773 / 3.36 ( 3546) Misc. bond : bond 0.04975 / 2.65 ( 38) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 73 GLN cc_start: 0.8289 (mt0) cc_final: 0.7764 (mt0) REVERT: B 246 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8937 (p90) REVERT: C 71 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8883 (mt-10) REVERT: C 451 ASP cc_start: 0.8700 (m-30) cc_final: 0.8244 (p0) REVERT: D 8 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.8327 (m-10) REVERT: D 323 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: E 12 ASP cc_start: 0.7255 (t0) cc_final: 0.6790 (t0) REVERT: E 62 GLU cc_start: 0.8858 (pm20) cc_final: 0.8594 (pm20) REVERT: I 34 LYS cc_start: 0.8223 (tptt) cc_final: 0.8022 (tptt) REVERT: L 8 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8586 (tptt) REVERT: L 9 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8325 (mm-40) REVERT: M 20 SER cc_start: 0.8466 (t) cc_final: 0.8153 (m) REVERT: O 58 GLN cc_start: 0.9104 (mm110) cc_final: 0.8798 (mp10) REVERT: O 86 GLU cc_start: 0.7252 (mp0) cc_final: 0.7025 (pm20) REVERT: P 107 GLU cc_start: 0.8883 (pt0) cc_final: 0.8595 (tt0) REVERT: P 176 THR cc_start: 0.8896 (t) cc_final: 0.8600 (p) REVERT: Q 118 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8634 (mptt) REVERT: Q 174 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8108 (mt-10) REVERT: T 24 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8289 (ptt180) REVERT: W 86 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7894 (tm) outliers start: 51 outliers final: 32 residues processed: 229 average time/residue: 0.6248 time to fit residues: 166.8473 Evaluate side-chains 225 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 214 TYR Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 86 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 56 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 403 ASN L 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.053543 restraints weight = 65512.797| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.23 r_work: 0.2639 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.276 25637 Z= 0.228 Angle : 0.645 10.441 35213 Z= 0.308 Chirality : 0.043 0.234 3542 Planarity : 0.005 0.057 4409 Dihedral : 14.746 121.141 4428 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.12 % Allowed : 17.40 % Favored : 80.48 % 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: 1.35 (0.16), residues: 2692 helix: 1.75 (0.13), residues: 1485 sheet: 0.22 (0.37), residues: 183 loop : -0.18 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 127 TYR 0.012 0.001 TYR A 246 PHE 0.021 0.002 PHE B 246 TRP 0.016 0.001 TRP A 131 HIS 0.007 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (25599) covalent geometry : angle 0.64453 / 0.31 (35213) hydrogen bonds : bond 0.04804 / 3.30 ( 1246) hydrogen bonds : angle 4.61393 / 3.41 ( 3546) Misc. bond : bond 0.05675 / 3.03 ( 38) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8391 (mp) REVERT: B 73 GLN cc_start: 0.8270 (mt0) cc_final: 0.7781 (mt0) REVERT: B 246 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8907 (p90) REVERT: C 451 ASP cc_start: 0.8728 (m-30) cc_final: 0.8262 (p0) REVERT: D 8 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.8049 (t80) REVERT: D 323 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8538 (mt-10) REVERT: E 12 ASP cc_start: 0.7304 (t0) cc_final: 0.6865 (t0) REVERT: E 62 GLU cc_start: 0.8869 (pm20) cc_final: 0.8630 (pm20) REVERT: L 8 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8562 (tptt) REVERT: L 9 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8339 (mm-40) REVERT: O 58 GLN cc_start: 0.9167 (mm110) cc_final: 0.8851 (mp10) REVERT: O 86 GLU cc_start: 0.7199 (mp0) cc_final: 0.6951 (pm20) REVERT: P 107 GLU cc_start: 0.8942 (pt0) cc_final: 0.8658 (tt0) REVERT: P 176 THR cc_start: 0.8871 (t) cc_final: 0.8565 (p) REVERT: T 24 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8348 (ptt180) REVERT: X 96 PHE cc_start: 0.4891 (OUTLIER) cc_final: 0.3812 (t80) REVERT: W 65 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8034 (ttm) REVERT: W 86 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7879 (tm) outliers start: 47 outliers final: 28 residues processed: 219 average time/residue: 0.6281 time to fit residues: 160.9017 Evaluate side-chains 217 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 214 TYR Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 166 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 250 optimal weight: 30.0000 chunk 184 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 9 GLN L 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.067411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.054421 restraints weight = 65006.188| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.22 r_work: 0.2665 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.235 25637 Z= 0.175 Angle : 0.608 9.751 35213 Z= 0.292 Chirality : 0.041 0.212 3542 Planarity : 0.004 0.057 4409 Dihedral : 14.554 120.574 4428 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.71 % Allowed : 17.99 % Favored : 80.30 % 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: 1.43 (0.16), residues: 2692 helix: 1.84 (0.13), residues: 1485 sheet: 0.12 (0.37), residues: 176 loop : -0.16 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 127 TYR 0.014 0.001 TYR A 254 PHE 0.020 0.001 PHE B 246 TRP 0.017 0.001 TRP A 131 HIS 0.005 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (25599) covalent geometry : angle 0.60850 / 0.29 (35213) hydrogen bonds : bond 0.04472 / 3.06 ( 1246) hydrogen bonds : angle 4.53358 / 3.35 ( 3546) Misc. bond : bond 0.04694 / 2.49 ( 38) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8387 (mt) REVERT: B 73 GLN cc_start: 0.8267 (mt0) cc_final: 0.7707 (mt0) REVERT: B 246 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8897 (p90) REVERT: C 451 ASP cc_start: 0.8644 (m-30) cc_final: 0.8196 (p0) REVERT: D 8 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.8350 (m-10) REVERT: D 323 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8506 (mt-10) REVERT: E 12 ASP cc_start: 0.7343 (t0) cc_final: 0.6882 (t0) REVERT: E 62 GLU cc_start: 0.8860 (pm20) cc_final: 0.8624 (pm20) REVERT: L 8 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8609 (tptt) REVERT: L 9 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8384 (mm-40) REVERT: O 58 GLN cc_start: 0.9124 (mm110) cc_final: 0.8812 (mp10) REVERT: O 86 GLU cc_start: 0.7273 (mp0) cc_final: 0.7027 (pm20) REVERT: P 107 GLU cc_start: 0.8884 (pt0) cc_final: 0.8592 (tt0) REVERT: P 157 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: P 176 THR cc_start: 0.8828 (t) cc_final: 0.8538 (p) REVERT: T 24 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8336 (ptt180) REVERT: X 96 PHE cc_start: 0.4839 (OUTLIER) cc_final: 0.3722 (t80) REVERT: W 86 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7849 (tm) outliers start: 38 outliers final: 29 residues processed: 216 average time/residue: 0.6396 time to fit residues: 161.2970 Evaluate side-chains 220 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain P residue 157 GLU Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 229 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 239 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 9 GLN L 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.069044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.056112 restraints weight = 64213.594| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.23 r_work: 0.2707 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.190 25637 Z= 0.125 Angle : 0.572 11.322 35213 Z= 0.275 Chirality : 0.040 0.192 3542 Planarity : 0.004 0.057 4409 Dihedral : 14.201 119.439 4428 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.89 % Allowed : 17.81 % Favored : 80.30 % 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: 1.58 (0.16), residues: 2692 helix: 1.98 (0.13), residues: 1483 sheet: 0.45 (0.37), residues: 177 loop : -0.18 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 127 TYR 0.015 0.001 TYR D 315 PHE 0.018 0.001 PHE B 246 TRP 0.019 0.001 TRP A 131 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (25599) covalent geometry : angle 0.57164 / 0.27 (35213) hydrogen bonds : bond 0.03987 / 2.72 ( 1246) hydrogen bonds : angle 4.38950 / 3.25 ( 3546) Misc. bond : bond 0.03546 / 1.85 ( 38) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7072.43 seconds wall clock time: 121 minutes 54.36 seconds (7314.36 seconds total)