Starting phenix.real_space_refine on Sun Sep 13 20:41:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s3e_54531/09_2026/9s3e_54531.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s3e_54531/09_2026/9s3e_54531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s3e_54531/09_2026/9s3e_54531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s3e_54531/09_2026/9s3e_54531.map" model { file = "/net/cci-nas-00/data/ceres_data/9s3e_54531/09_2026/9s3e_54531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s3e_54531/09_2026/9s3e_54531.cif" } resolution = 2.1 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= 0.005 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 6 5.49 5 Mg 35 5.21 5 S 63 5.16 5 Cl 2 4.86 5 C 16607 2.51 5 N 3566 2.21 5 O 4874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25160 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2616 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain: "B" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3771 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 26, 'TRANS': 454} Chain: "C" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3490 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 424} Chain: "D" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2704 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain: "E" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 612 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain: "F" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 241 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "H" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 452 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "I" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 267 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 2, 'TRANS': 30} Chain: "J" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 256 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "K" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 306 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "L" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 295 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "M" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 217 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "O" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1870 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 232} Chain: "P" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1434 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain: "Q" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1157 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 136} Chain: "T" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 245 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 3, 'TRANS': 26} Chain: "W" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 368 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "X" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 249 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "U" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 4, 'TRANS': 23} Chain: "A" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 358 Ad-hoc single atom residues: {'FE2': 1} Unusual residues: {' CL': 2, 'BCR': 1, 'BCT': 1, 'CLA': 3, 'OEX': 1, 'PHO': 1, 'PL9': 1, 'SQD': 1} Classifications: {'undetermined': 11} Link IDs: {None: 9} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 1379 Unusual residues: {'BCR': 3, 'CLA': 16, 'DGD': 1, 'LHG': 2, 'LMG': 2} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 1081 Unusual residues: {'BCR': 1, 'CLA': 13, 'DGD': 3, 'LMG': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 492 Unusual residues: {'BCR': 1, 'CLA': 3, 'LHG': 2, 'LMG': 1, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "E" 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'BCR': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'LHG': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "B" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 176 Classifications: {'water': 176} Link IDs: {None: 175} Chain: "C" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 159 Classifications: {'water': 159} Link IDs: {None: 158} Chain: "D" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "Q" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "W" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.20, per 1000 atoms: 0.21 Number of scatterers: 25160 At special positions: 0 Unit cell: (128.656, 146.931, 109.65, 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 63 16.00 P 6 15.00 Mg 35 11.99 O 4874 8.00 N 3566 7.00 C 16607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS O 29 " - pdb=" SG CYS O 52 " distance=2.03 Simple disulfide: pdb=" SG CYS U 88 " - pdb=" SG CYS U 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=38, symmetry=0 Number of additional bonds: simple=38, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 903.0 milliseconds 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4776 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 18 sheets defined 59.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 30 through 55 removed outlier: 3.745A pdb=" N LEU A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 108 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.931A pdb=" N GLU A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.913A 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 221 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 247 through 259 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 6 through 13 removed outlier: 5.691A pdb=" N HIS B 9 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 45 Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.783A pdb=" N GLY B 59 " --> pdb=" O TRP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 69 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: 3.928A 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: 4.142A pdb=" N VAL B 237 " --> pdb=" O ASN 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: 3.894A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 293 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 314 through 322 Proline residue: B 319 - end of helix removed outlier: 4.092A pdb=" N GLY B 322 " --> pdb=" O PRO B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.681A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.659A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 479 Processing helix chain 'C' and resid 34 through 43 removed outlier: 5.675A pdb=" N ASN C 39 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 75 Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 87 through 95 removed outlier: 4.084A pdb=" N HIS C 91 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.551A pdb=" N GLU C 104 " --> pdb=" O PRO C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 135 Processing helix chain 'C' and resid 153 through 181 Processing helix chain 'C' and resid 205 through 214 removed outlier: 3.725A pdb=" N LEU C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 254 Processing helix chain 'C' and resid 257 through 264 Processing helix chain 'C' and resid 267 through 293 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 305 through 324 Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 376 through 383 Processing helix chain 'C' and resid 385 through 398 Processing helix chain 'C' and resid 421 through 454 Processing helix chain 'C' and resid 460 through 469 removed outlier: 3.947A pdb=" N GLU C 464 " --> pdb=" O ARG C 461 " (cutoff:3.500A) Proline residue: C 465 - end of helix Processing helix chain 'D' and resid 15 through 24 Processing helix chain 'D' and resid 31 through 56 removed outlier: 3.911A pdb=" N LEU D 36 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU D 37 " --> pdb=" O TRP D 33 " (cutoff:3.500A) Proline residue: D 40 - end of helix Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 101 through 109 Processing helix chain 'D' and resid 109 through 137 removed outlier: 3.891A pdb=" N THR D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 147 Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 159 through 165 Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.516A pdb=" N PHE D 236 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 258 Processing helix chain 'D' and resid 264 through 292 Proline residue: D 276 - end of helix removed outlier: 3.774A pdb=" N LEU D 292 " --> pdb=" O VAL D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 314 through 335 removed outlier: 4.933A pdb=" N THR D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN D 333 " --> pdb=" O TRP D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 339 Processing helix chain 'D' and resid 343 through 347 Processing helix chain 'E' and resid 9 through 15 Processing helix chain 'E' and resid 16 through 40 removed outlier: 4.305A pdb=" N ILE E 25 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 27 " --> pdb=" O HIS E 23 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 41 through 48 Processing helix chain 'E' and resid 71 through 82 Processing helix chain 'F' and resid 11 through 35 Proline residue: F 23 - end of helix Processing helix chain 'H' and resid 17 through 24 Processing helix chain 'H' and resid 25 through 28 Processing helix chain 'H' and resid 39 through 62 Processing helix chain 'I' and resid 2 through 25 Processing helix chain 'J' and resid 9 through 33 Processing helix chain 'K' and resid 27 through 32 removed outlier: 4.718A pdb=" N PHE K 32 " --> pdb=" O ALA K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 40 Processing helix chain 'K' and resid 42 through 58 removed outlier: 3.733A pdb=" N PHE K 52 " --> pdb=" O PHE K 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 38 removed outlier: 4.439A pdb=" N ASN L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 31 Proline residue: M 18 - end of helix Processing helix chain 'O' and resid 8 through 15 Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 24 through 28 Processing helix chain 'O' and resid 175 through 184 removed outlier: 5.985A pdb=" N GLY O 180 " --> pdb=" O GLY O 177 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU O 183 " --> pdb=" O GLY O 180 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU O 184 " --> pdb=" O ASP O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 190 Processing helix chain 'P' and resid 70 through 75 Processing helix chain 'P' and resid 76 through 84 Processing helix chain 'P' and resid 85 through 88 Processing helix chain 'P' and resid 138 through 141 Processing helix chain 'P' and resid 165 through 169 Processing helix chain 'P' and resid 171 through 183 removed outlier: 4.046A pdb=" N PHE P 175 " --> pdb=" O GLY P 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 28 Processing helix chain 'Q' and resid 43 through 61 Processing helix chain 'Q' and resid 61 through 68 Processing helix chain 'Q' and resid 69 through 76 Processing helix chain 'Q' and resid 77 through 78 No H-bonds generated for 'chain 'Q' and resid 77 through 78' Processing helix chain 'Q' and resid 79 through 82 Processing helix chain 'Q' and resid 83 through 95 Processing helix chain 'Q' and resid 96 through 123 removed outlier: 3.890A pdb=" N GLN Q 101 " --> pdb=" O LYS Q 97 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER Q 102 " --> pdb=" O ASP Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 148 Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'W' and resid 13 through 17 Processing helix chain 'W' and resid 19 through 43 removed outlier: 3.758A pdb=" N GLY W 23 " --> pdb=" O ASN W 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 79 Processing helix chain 'U' and resid 77 through 84 Processing helix chain 'U' and resid 84 through 91 Processing helix chain 'U' and resid 94 through 98 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.505A pdb=" N LEU A 174 " --> pdb=" O ILE A 82 " (cutoff:3.500A) 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 3 through 4 removed outlier: 5.989A pdb=" N LEU B 3 " --> pdb=" O GLU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 removed outlier: 3.671A pdb=" N TRP B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AA6, first strand: chain 'B' and resid 336 through 340 removed outlier: 5.684A pdb=" N ALA B 337 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASP B 433 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 339 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.959A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL B 356 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 187 Processing sheet with id=AA9, first strand: chain 'C' and resid 341 through 343 Processing sheet with id=AB1, first strand: chain 'C' and resid 370 through 371 Processing sheet with id=AB2, first strand: chain 'D' and resid 78 through 79 Processing sheet with id=AB3, first strand: chain 'O' and resid 73 through 75 removed outlier: 5.348A pdb=" N ILE O 89 " --> pdb=" O LYS O 50 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N CYS O 52 " --> pdb=" O ASP O 87 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP O 87 " --> pdb=" O CYS O 52 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU O 88 " --> pdb=" O ILE O 109 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE O 109 " --> pdb=" O GLU O 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 73 through 75 removed outlier: 3.595A pdb=" N GLU O 247 " --> pdb=" O ASN O 47 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU O 51 " --> pdb=" O TYR O 243 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR O 243 " --> pdb=" O LEU O 51 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU O 53 " --> pdb=" O VAL O 241 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL O 241 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN O 239 " --> pdb=" O PRO O 55 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER O 57 " --> pdb=" O LYS O 237 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS O 237 " --> pdb=" O SER O 57 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR O 59 " --> pdb=" O ASP O 235 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP O 235 " --> pdb=" O THR O 59 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU O 213 " --> pdb=" O THR O 207 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR O 207 " --> pdb=" O GLU O 213 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE O 215 " --> pdb=" O THR O 205 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS O 138 " --> pdb=" O SER O 141 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU O 145 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU O 88 " --> pdb=" O ILE O 109 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE O 109 " --> pdb=" O GLU O 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'P' and resid 18 through 22 Processing sheet with id=AB7, first strand: chain 'P' and resid 34 through 36 removed outlier: 6.611A pdb=" N VAL P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG P 48 " --> pdb=" O VAL P 59 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL P 59 " --> pdb=" O ARG P 48 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU P 132 " --> pdb=" O ILE P 113 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE P 113 " --> pdb=" O LEU P 132 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG P 134 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA P 111 " --> pdb=" O ARG P 134 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLY Q 8 " --> pdb=" O ALA P 109 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA P 111 " --> pdb=" O GLY Q 8 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 90 through 91 Processing sheet with id=AB9, first strand: chain 'P' and resid 120 through 121 1219 hydrogen bonds defined for protein. 3393 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: 5.10 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.62: 24990 1.62 - 2.04: 222 2.04 - 2.47: 77 2.47 - 2.89: 0 2.89 - 3.31: 4 Bond restraints: 25293 Sorted by residual: bond pdb=" O5 OEX A 401 " pdb="MN1 OEX A 401 " ideal model delta sigma weight residual 2.600 1.907 0.693 5.00e-02 4.00e+02 1.92e+02 bond pdb=" C25 BCR B 518 " pdb=" C26 BCR B 518 " ideal model delta sigma weight residual 1.347 1.611 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C25 BCR C 514 " pdb=" C26 BCR C 514 " ideal model delta sigma weight residual 1.347 1.610 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C25 BCR H 101 " pdb=" C26 BCR H 101 " ideal model delta sigma weight residual 1.347 1.608 -0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C25 BCR B 519 " pdb=" C26 BCR B 519 " ideal model delta sigma weight residual 1.347 1.608 -0.261 2.00e-02 2.50e+03 1.71e+02 ... (remaining 25288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 33992 4.84 - 9.69: 700 9.69 - 14.53: 44 14.53 - 19.38: 14 19.38 - 24.22: 1 Bond angle restraints: 34751 Sorted by residual: angle pdb="MN1 OEX A 401 " pdb=" O3 OEX A 401 " pdb="MN3 OEX A 401 " ideal model delta sigma weight residual 117.00 92.78 24.22 2.00e+00 2.50e-01 1.47e+02 angle pdb="MN1 OEX A 401 " pdb=" O5 OEX A 401 " pdb="MN4 OEX A 401 " ideal model delta sigma weight residual 155.00 168.42 -13.42 2.00e+00 2.50e-01 4.50e+01 angle pdb=" CA GLY B 342 " pdb=" C GLY B 342 " pdb=" O GLY B 342 " ideal model delta sigma weight residual 122.45 118.10 4.35 7.20e-01 1.93e+00 3.65e+01 angle pdb=" CA GLY O 2 " pdb=" C GLY O 2 " pdb=" O GLY O 2 " ideal model delta sigma weight residual 122.52 118.16 4.36 7.90e-01 1.60e+00 3.05e+01 angle pdb=" CA GLY B 89 " pdb=" C GLY B 89 " pdb=" O GLY B 89 " ideal model delta sigma weight residual 122.52 118.26 4.26 7.90e-01 1.60e+00 2.91e+01 ... (remaining 34746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.46: 12831 25.46 - 50.91: 744 50.91 - 76.37: 299 76.37 - 101.83: 30 101.83 - 127.28: 31 Dihedral angle restraints: 13935 sinusoidal: 6432 harmonic: 7503 Sorted by residual: dihedral pdb=" CD ARG C 261 " pdb=" NE ARG C 261 " pdb=" CZ ARG C 261 " pdb=" NH1 ARG C 261 " ideal model delta sinusoidal sigma weight residual 0.00 -89.97 89.97 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CD ARG Q 78 " pdb=" NE ARG Q 78 " pdb=" CZ ARG Q 78 " pdb=" NH1 ARG Q 78 " ideal model delta sinusoidal sigma weight residual 0.00 40.25 -40.25 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CG ARG C 261 " pdb=" CD ARG C 261 " pdb=" NE ARG C 261 " pdb=" CZ ARG C 261 " ideal model delta sinusoidal sigma weight residual -90.00 -3.66 -86.34 2 1.50e+01 4.44e-03 2.12e+01 ... (remaining 13932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 3041 0.144 - 0.288: 356 0.288 - 0.432: 1 0.432 - 0.576: 0 0.576 - 0.721: 35 Chirality restraints: 3433 Sorted by residual: 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 -2.04 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C3A CLA C 511 " pdb=" C2A CLA C 511 " pdb=" C4A CLA C 511 " pdb=" CMA CLA C 511 " both_signs ideal model delta sigma weight residual False -2.76 -2.06 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C3A CLA C 507 " pdb=" C2A CLA C 507 " pdb=" C4A CLA C 507 " pdb=" CMA CLA C 507 " both_signs ideal model delta sigma weight residual False -2.76 -2.07 -0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 3430 not shown) Planarity restraints: 4356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO D 402 " -0.024 2.00e-02 2.50e+03 1.02e-01 8.39e+02 pdb=" ND PHO D 402 " -0.090 2.00e-02 2.50e+03 pdb=" C1A PHO D 402 " -0.046 2.00e-02 2.50e+03 pdb=" C1B PHO D 402 " 0.023 2.00e-02 2.50e+03 pdb=" C1C PHO D 402 " -0.092 2.00e-02 2.50e+03 pdb=" C1D PHO D 402 " -0.086 2.00e-02 2.50e+03 pdb=" C2A PHO D 402 " -0.083 2.00e-02 2.50e+03 pdb=" C2B PHO D 402 " 0.014 2.00e-02 2.50e+03 pdb=" C2C PHO D 402 " 0.072 2.00e-02 2.50e+03 pdb=" C2D PHO D 402 " -0.031 2.00e-02 2.50e+03 pdb=" C3A PHO D 402 " 0.219 2.00e-02 2.50e+03 pdb=" C3B PHO D 402 " -0.034 2.00e-02 2.50e+03 pdb=" C3C PHO D 402 " 0.089 2.00e-02 2.50e+03 pdb=" C3D PHO D 402 " -0.002 2.00e-02 2.50e+03 pdb=" C4A PHO D 402 " 0.062 2.00e-02 2.50e+03 pdb=" C4B PHO D 402 " -0.059 2.00e-02 2.50e+03 pdb=" C4C PHO D 402 " -0.095 2.00e-02 2.50e+03 pdb=" C4D PHO D 402 " -0.041 2.00e-02 2.50e+03 pdb=" CAB PHO D 402 " -0.059 2.00e-02 2.50e+03 pdb=" CAC PHO D 402 " 0.253 2.00e-02 2.50e+03 pdb=" CAD PHO D 402 " 0.050 2.00e-02 2.50e+03 pdb=" CBD PHO D 402 " 0.106 2.00e-02 2.50e+03 pdb=" CHA PHO D 402 " -0.012 2.00e-02 2.50e+03 pdb=" CHB PHO D 402 " 0.070 2.00e-02 2.50e+03 pdb=" CHC PHO D 402 " -0.107 2.00e-02 2.50e+03 pdb=" CHD PHO D 402 " -0.124 2.00e-02 2.50e+03 pdb=" CMB PHO D 402 " 0.057 2.00e-02 2.50e+03 pdb=" CMC PHO D 402 " 0.210 2.00e-02 2.50e+03 pdb=" CMD PHO D 402 " -0.009 2.00e-02 2.50e+03 pdb=" NA PHO D 402 " -0.069 2.00e-02 2.50e+03 pdb=" NC PHO D 402 " -0.226 2.00e-02 2.50e+03 pdb=" OBD PHO D 402 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PL9 D 406 " 0.036 2.00e-02 2.50e+03 1.44e-01 5.72e+02 pdb=" C2 PL9 D 406 " -0.051 2.00e-02 2.50e+03 pdb=" C3 PL9 D 406 " -0.044 2.00e-02 2.50e+03 pdb=" C4 PL9 D 406 " 0.102 2.00e-02 2.50e+03 pdb=" C5 PL9 D 406 " -0.036 2.00e-02 2.50e+03 pdb=" C52 PL9 D 406 " -0.193 2.00e-02 2.50e+03 pdb=" C53 PL9 D 406 " -0.045 2.00e-02 2.50e+03 pdb=" C6 PL9 D 406 " -0.015 2.00e-02 2.50e+03 pdb=" C7 PL9 D 406 " -0.219 2.00e-02 2.50e+03 pdb=" O1 PL9 D 406 " 0.322 2.00e-02 2.50e+03 pdb=" O2 PL9 D 406 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO A 407 " 0.027 2.00e-02 2.50e+03 8.03e-02 5.16e+02 pdb=" ND PHO A 407 " -0.029 2.00e-02 2.50e+03 pdb=" C1A PHO A 407 " -0.057 2.00e-02 2.50e+03 pdb=" C1B PHO A 407 " 0.032 2.00e-02 2.50e+03 pdb=" C1C PHO A 407 " -0.075 2.00e-02 2.50e+03 pdb=" C1D PHO A 407 " -0.002 2.00e-02 2.50e+03 pdb=" C2A PHO A 407 " -0.056 2.00e-02 2.50e+03 pdb=" C2B PHO A 407 " 0.006 2.00e-02 2.50e+03 pdb=" C2C PHO A 407 " -0.020 2.00e-02 2.50e+03 pdb=" C2D PHO A 407 " 0.013 2.00e-02 2.50e+03 pdb=" C3A PHO A 407 " 0.238 2.00e-02 2.50e+03 pdb=" C3B PHO A 407 " -0.006 2.00e-02 2.50e+03 pdb=" C3C PHO A 407 " 0.071 2.00e-02 2.50e+03 pdb=" C3D PHO A 407 " -0.004 2.00e-02 2.50e+03 pdb=" C4A PHO A 407 " 0.055 2.00e-02 2.50e+03 pdb=" C4B PHO A 407 " 0.005 2.00e-02 2.50e+03 pdb=" C4C PHO A 407 " -0.046 2.00e-02 2.50e+03 pdb=" C4D PHO A 407 " -0.030 2.00e-02 2.50e+03 pdb=" CAB PHO A 407 " -0.037 2.00e-02 2.50e+03 pdb=" CAC PHO A 407 " 0.241 2.00e-02 2.50e+03 pdb=" CAD PHO A 407 " -0.007 2.00e-02 2.50e+03 pdb=" CBD PHO A 407 " -0.043 2.00e-02 2.50e+03 pdb=" CHA PHO A 407 " -0.048 2.00e-02 2.50e+03 pdb=" CHB PHO A 407 " 0.056 2.00e-02 2.50e+03 pdb=" CHC PHO A 407 " -0.005 2.00e-02 2.50e+03 pdb=" CHD PHO A 407 " 0.005 2.00e-02 2.50e+03 pdb=" CMB PHO A 407 " 0.003 2.00e-02 2.50e+03 pdb=" CMC PHO A 407 " -0.044 2.00e-02 2.50e+03 pdb=" CMD PHO A 407 " 0.041 2.00e-02 2.50e+03 pdb=" NA PHO A 407 " -0.089 2.00e-02 2.50e+03 pdb=" NC PHO A 407 " -0.210 2.00e-02 2.50e+03 pdb=" OBD PHO A 407 " 0.015 2.00e-02 2.50e+03 ... (remaining 4353 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 471 2.64 - 3.20: 23447 3.20 - 3.77: 47490 3.77 - 4.33: 67173 4.33 - 4.90: 102647 Nonbonded interactions: 241228 Sorted by model distance: nonbonded pdb=" NE2 HIS D 215 " pdb="FE FE2 A 402 " model vdw 2.071 3.080 nonbonded pdb="FE FE2 A 402 " pdb=" O3 BCT A 412 " model vdw 2.112 3.000 nonbonded pdb=" OE2 GLU A 333 " pdb="MN4 OEX A 401 " model vdw 2.161 3.060 nonbonded pdb=" NE2 HIS A 215 " pdb="FE FE2 A 402 " model vdw 2.198 3.080 nonbonded pdb=" NE2 HIS E 23 " pdb="FE HEM E 101 " model vdw 2.206 3.080 ... (remaining 241223 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: 3.820 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.020 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.028 0.693 25333 Z= 1.850 Angle : 1.891 24.220 34755 Z= 1.145 Chirality : 0.112 0.721 3433 Planarity : 0.020 0.482 4356 Dihedral : 18.559 127.281 9153 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.14 % Favored : 97.67 % Rotamer: Outliers : 2.55 % Allowed : 4.08 % Favored : 93.37 % 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: 0.36 (0.15), residues: 2622 helix: 0.79 (0.13), residues: 1352 sheet: 0.29 (0.39), residues: 161 loop : -0.34 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 51 TYR 0.016 0.002 TYR Q 83 PHE 0.024 0.002 PHE B 246 TRP 0.017 0.003 TRP A 105 HIS 0.009 0.002 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.02466 / 1.37 (25293) covalent geometry : angle 1.89063 / 1.15 (34751) SS BOND : bond 0.00337 / 0.17 ( 2) SS BOND : angle 0.66882 / 0.35 ( 4) hydrogen bonds : bond 0.16603 / 11.35 ( 1215) hydrogen bonds : angle 6.95875 / 5.12 ( 3393) Misc. bond : bond 0.34489 / 24.21 ( 38) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 382 time to evaluate : 0.931 Fit side-chains REVERT: A 266 ASN cc_start: 0.6413 (t0) cc_final: 0.6203 (p0) REVERT: A 331 MET cc_start: 0.8767 (mmm) cc_final: 0.8288 (mmm) REVERT: B 125 ASP cc_start: 0.6750 (t0) cc_final: 0.6452 (t70) REVERT: B 304 LYS cc_start: 0.7522 (mttm) cc_final: 0.7143 (mtpp) REVERT: C 28 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6436 (tt0) REVERT: C 104 GLU cc_start: 0.7666 (tt0) cc_final: 0.7326 (mt-10) REVERT: C 152 LYS cc_start: 0.8016 (ptmt) cc_final: 0.7669 (pttp) REVERT: C 255 LYS cc_start: 0.8232 (ptpp) cc_final: 0.7991 (mttt) REVERT: C 356 MET cc_start: 0.8571 (ptp) cc_final: 0.8285 (ptp) REVERT: C 389 GLU cc_start: 0.6760 (mt-10) cc_final: 0.5964 (tt0) REVERT: C 394 GLU cc_start: 0.7440 (tt0) cc_final: 0.7161 (tt0) REVERT: D 15 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6557 (tp) REVERT: D 21 ASP cc_start: 0.6890 (m-30) cc_final: 0.6348 (t70) REVERT: D 138 GLN cc_start: 0.7876 (mt0) cc_final: 0.7571 (mm-40) REVERT: D 298 ASP cc_start: 0.8326 (p0) cc_final: 0.8041 (p0) REVERT: D 305 ARG cc_start: 0.7605 (ttt-90) cc_final: 0.7377 (tpt-90) REVERT: D 311 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7383 (mt-10) REVERT: D 333 GLN cc_start: 0.8216 (mp10) cc_final: 0.7665 (mp10) REVERT: D 344 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6777 (mp0) REVERT: E 10 PHE cc_start: 0.6243 (m-80) cc_final: 0.5859 (m-80) REVERT: E 17 ILE cc_start: 0.6439 (OUTLIER) cc_final: 0.6140 (mp) REVERT: E 74 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6860 (mt-10) REVERT: K 25 LYS cc_start: 0.5501 (ptmm) cc_final: 0.5106 (mptp) REVERT: M 16 LEU cc_start: 0.6994 (mt) cc_final: 0.6667 (mt) REVERT: O 15 LYS cc_start: 0.7267 (mtpm) cc_final: 0.6868 (mttp) REVERT: O 33 ASP cc_start: 0.6660 (m-30) cc_final: 0.6328 (m-30) REVERT: O 42 LYS cc_start: 0.6598 (ptpp) cc_final: 0.6138 (ptmm) REVERT: O 49 LYS cc_start: 0.6716 (pttt) cc_final: 0.6095 (mtmt) REVERT: O 63 GLU cc_start: 0.1512 (OUTLIER) cc_final: 0.0853 (pt0) REVERT: O 197 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7520 (pttp) REVERT: O 199 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7357 (tptm) REVERT: O 206 GLN cc_start: 0.7810 (mt0) cc_final: 0.7571 (mt0) REVERT: P 11 LYS cc_start: 0.5520 (OUTLIER) cc_final: 0.5299 (tppt) REVERT: P 41 GLU cc_start: 0.7282 (pt0) cc_final: 0.6467 (pt0) REVERT: P 85 ASP cc_start: 0.5512 (p0) cc_final: 0.5152 (p0) REVERT: Q 56 LYS cc_start: 0.3696 (mtpt) cc_final: 0.3419 (mttp) outliers start: 55 outliers final: 3 residues processed: 411 average time/residue: 0.6557 time to fit residues: 312.0813 Evaluate side-chains 260 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 251 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 68 ASN Chi-restraints excluded: chain O residue 197 LYS Chi-restraints excluded: chain P residue 11 LYS Chi-restraints excluded: chain U residue 97 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN A 181 ASN A 304 GLN B 332 ASN B 425 GLN C 68 ASN C 311 GLN C 313 GLN C 327 ASN C 373 ASN C 415 ASN C 418 ASN D 62 HIS D 143 ASN D 256 GLN D 339 ASN D 351 ASN E 61 GLN H 62 ASN I 26 ASN K 34 ASN L 5 ASN O 28 GLN O 68 ASN O 74 GLN O 170 ASN P 91 GLN P 162 GLN Q 75 ASN Q 101 GLN Q 141 ASN W 20 ASN U 99 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100660 restraints weight = 23240.739| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 0.83 r_work: 0.2978 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.281 25333 Z= 0.182 Angle : 0.727 14.159 34755 Z= 0.346 Chirality : 0.047 0.249 3433 Planarity : 0.006 0.077 4356 Dihedral : 17.307 125.998 4602 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.45 % Favored : 98.51 % Rotamer: Outliers : 1.95 % Allowed : 6.72 % Favored : 91.33 % 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: 1.42 (0.16), residues: 2622 helix: 1.72 (0.13), residues: 1391 sheet: 0.42 (0.40), residues: 171 loop : 0.07 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 7 TYR 0.029 0.003 TYR E 44 PHE 0.040 0.003 PHE B 246 TRP 0.031 0.002 TRP A 131 HIS 0.010 0.003 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (25293) covalent geometry : angle 0.72662 / 0.35 (34751) SS BOND : bond 0.00663 / 0.32 ( 2) SS BOND : angle 1.39182 / 0.80 ( 4) hydrogen bonds : bond 0.06367 / 4.30 ( 1215) hydrogen bonds : angle 5.33003 / 3.92 ( 3393) Misc. bond : bond 0.06991 / 3.32 ( 38) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 0.889 Fit side-chains REVERT: A 331 MET cc_start: 0.9107 (mmm) cc_final: 0.8798 (mmm) REVERT: B 304 LYS cc_start: 0.8602 (mttm) cc_final: 0.8287 (mtpp) REVERT: B 362 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8694 (m-80) REVERT: C 389 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7866 (tt0) REVERT: C 394 GLU cc_start: 0.7770 (tt0) cc_final: 0.7551 (tt0) REVERT: E 18 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6856 (ttt180) REVERT: E 19 TYR cc_start: 0.7965 (t80) cc_final: 0.7680 (t80) REVERT: E 60 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.6048 (ttm170) REVERT: F 10 PHE cc_start: 0.5274 (OUTLIER) cc_final: 0.4957 (p90) REVERT: M 16 LEU cc_start: 0.6805 (mt) cc_final: 0.6468 (mt) REVERT: O 36 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7931 (m) REVERT: O 42 LYS cc_start: 0.7507 (ptpp) cc_final: 0.7063 (ptmm) REVERT: O 49 LYS cc_start: 0.8206 (pttt) cc_final: 0.7941 (mtmp) REVERT: O 63 GLU cc_start: 0.1955 (OUTLIER) cc_final: 0.1029 (pt0) REVERT: O 199 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8460 (tptm) REVERT: P 11 LYS cc_start: 0.6071 (OUTLIER) cc_final: 0.5836 (tppt) REVERT: P 85 ASP cc_start: 0.7109 (p0) cc_final: 0.6744 (p0) REVERT: P 124 LYS cc_start: 0.6964 (mttp) cc_final: 0.6728 (mtpp) REVERT: Q 56 LYS cc_start: 0.5722 (mtpt) cc_final: 0.5225 (mttp) REVERT: Q 62 LYS cc_start: 0.5185 (OUTLIER) cc_final: 0.4925 (tppp) REVERT: Q 93 SER cc_start: 0.5885 (m) cc_final: 0.5577 (p) REVERT: Q 109 LYS cc_start: 0.5580 (tppt) cc_final: 0.4954 (mmtt) REVERT: Q 123 ILE cc_start: 0.5971 (tp) cc_final: 0.5642 (pp) REVERT: W 19 ASN cc_start: 0.6543 (t0) cc_final: 0.6275 (t0) REVERT: U 74 LYS cc_start: 0.7843 (tttt) cc_final: 0.7538 (tttp) outliers start: 42 outliers final: 9 residues processed: 300 average time/residue: 0.6996 time to fit residues: 242.4811 Evaluate side-chains 248 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain F residue 10 PHE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain P residue 11 LYS Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 62 LYS Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain Q residue 146 LYS Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain U residue 97 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 21 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 143 ASN E 61 GLN I 26 ASN P 64 GLN Q 75 ASN W 20 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.099890 restraints weight = 23330.145| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 0.83 r_work: 0.2961 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 25333 Z= 0.156 Angle : 0.634 14.069 34755 Z= 0.308 Chirality : 0.044 0.224 3433 Planarity : 0.005 0.055 4356 Dihedral : 16.133 125.259 4589 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.56 % Favored : 98.40 % Rotamer: Outliers : 1.62 % Allowed : 8.39 % Favored : 89.99 % 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: 1.49 (0.16), residues: 2622 helix: 1.76 (0.14), residues: 1392 sheet: 0.56 (0.40), residues: 169 loop : 0.11 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 323 TYR 0.018 0.002 TYR E 44 PHE 0.035 0.002 PHE B 246 TRP 0.029 0.002 TRP A 131 HIS 0.006 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (25293) covalent geometry : angle 0.63418 / 0.31 (34751) SS BOND : bond 0.00501 / 0.24 ( 2) SS BOND : angle 1.22159 / 0.70 ( 4) hydrogen bonds : bond 0.06134 / 4.15 ( 1215) hydrogen bonds : angle 5.16002 / 3.80 ( 3393) Misc. bond : bond 0.06501 / 3.48 ( 38) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.916 Fit side-chains REVERT: A 13 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7783 (tp) REVERT: A 331 MET cc_start: 0.9134 (mmm) cc_final: 0.8746 (mmm) REVERT: B 182 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7937 (t0) REVERT: B 304 LYS cc_start: 0.8652 (mttm) cc_final: 0.8326 (mtpp) REVERT: B 362 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.8821 (m-80) REVERT: C 389 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7856 (tt0) REVERT: C 394 GLU cc_start: 0.7760 (tt0) cc_final: 0.7539 (tt0) REVERT: D 102 LEU cc_start: 0.9160 (tp) cc_final: 0.8852 (tm) REVERT: E 18 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6908 (ttt180) REVERT: E 19 TYR cc_start: 0.8097 (t80) cc_final: 0.7676 (t80) REVERT: E 60 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.5923 (ttm170) REVERT: F 10 PHE cc_start: 0.5373 (OUTLIER) cc_final: 0.5051 (p90) REVERT: M 6 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7041 (mm) REVERT: M 16 LEU cc_start: 0.6906 (mt) cc_final: 0.6555 (mt) REVERT: O 42 LYS cc_start: 0.7484 (ptpp) cc_final: 0.7041 (ptmm) REVERT: O 49 LYS cc_start: 0.8323 (pttt) cc_final: 0.7931 (mtmp) REVERT: O 63 GLU cc_start: 0.1750 (OUTLIER) cc_final: 0.0916 (pt0) REVERT: O 199 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8495 (tptt) REVERT: P 85 ASP cc_start: 0.7295 (p0) cc_final: 0.6936 (p0) REVERT: Q 56 LYS cc_start: 0.5783 (mtpt) cc_final: 0.5279 (mttp) REVERT: Q 62 LYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4642 (tptp) REVERT: Q 90 THR cc_start: 0.5995 (m) cc_final: 0.5450 (p) REVERT: Q 109 LYS cc_start: 0.5763 (tppt) cc_final: 0.5070 (mmtt) REVERT: Q 123 ILE cc_start: 0.6039 (tp) cc_final: 0.5657 (pp) REVERT: W 19 ASN cc_start: 0.6442 (t0) cc_final: 0.6134 (t0) REVERT: W 39 ILE cc_start: 0.8186 (mm) cc_final: 0.7950 (mt) REVERT: U 74 LYS cc_start: 0.7867 (tttt) cc_final: 0.7610 (tttp) outliers start: 35 outliers final: 11 residues processed: 257 average time/residue: 0.6987 time to fit residues: 206.8535 Evaluate side-chains 238 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 473 ASN Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain F residue 10 PHE Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 62 LYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain U residue 97 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 130 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN D 143 ASN E 61 GLN I 26 ASN O 28 GLN P 64 GLN Q 75 ASN Q 116 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.096252 restraints weight = 23005.178| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 0.82 r_work: 0.2909 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.263 25333 Z= 0.235 Angle : 0.780 13.541 34755 Z= 0.375 Chirality : 0.051 0.257 3433 Planarity : 0.007 0.068 4356 Dihedral : 16.413 126.996 4585 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.64 % Favored : 98.32 % Rotamer: Outliers : 1.58 % Allowed : 8.53 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 2622 helix: 1.44 (0.13), residues: 1382 sheet: 0.54 (0.38), residues: 177 loop : 0.06 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 152 TYR 0.023 0.003 TYR L 35 PHE 0.039 0.003 PHE B 246 TRP 0.039 0.003 TRP A 131 HIS 0.009 0.003 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (25293) covalent geometry : angle 0.77963 / 0.38 (34751) SS BOND : bond 0.00733 / 0.35 ( 2) SS BOND : angle 1.25405 / 0.73 ( 4) hydrogen bonds : bond 0.07259 / 4.91 ( 1215) hydrogen bonds : angle 5.43916 / 3.99 ( 3393) Misc. bond : bond 0.07213 / 3.87 ( 38) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.965 Fit side-chains REVERT: A 13 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7812 (tp) REVERT: A 257 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5485 (mpt90) REVERT: B 130 LYS cc_start: 0.7861 (mtpm) cc_final: 0.7234 (mttm) REVERT: B 182 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7982 (t0) REVERT: C 394 GLU cc_start: 0.7877 (tt0) cc_final: 0.7663 (tt0) REVERT: E 10 PHE cc_start: 0.7157 (m-80) cc_final: 0.6585 (m-80) REVERT: E 18 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7174 (ttt180) REVERT: E 25 ILE cc_start: 0.6866 (mp) cc_final: 0.6584 (mp) REVERT: E 60 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.5927 (ttm170) REVERT: F 10 PHE cc_start: 0.5581 (OUTLIER) cc_final: 0.5220 (p90) REVERT: M 6 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7165 (mm) REVERT: M 16 LEU cc_start: 0.7108 (mt) cc_final: 0.6767 (mt) REVERT: O 49 LYS cc_start: 0.8429 (pttt) cc_final: 0.7904 (mtmp) REVERT: O 63 GLU cc_start: 0.1965 (OUTLIER) cc_final: 0.1011 (pt0) REVERT: O 199 LYS cc_start: 0.8747 (ttmt) cc_final: 0.8508 (tptt) REVERT: P 145 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: Q 56 LYS cc_start: 0.5779 (mtpt) cc_final: 0.5260 (mttp) REVERT: Q 90 THR cc_start: 0.6059 (m) cc_final: 0.5594 (p) REVERT: Q 104 LYS cc_start: 0.5272 (OUTLIER) cc_final: 0.5006 (ptmm) REVERT: Q 109 LYS cc_start: 0.5874 (tppt) cc_final: 0.5553 (tppt) REVERT: W 19 ASN cc_start: 0.6510 (t0) cc_final: 0.6239 (t0) REVERT: W 39 ILE cc_start: 0.8224 (mm) cc_final: 0.7993 (mt) REVERT: U 74 LYS cc_start: 0.7910 (tttt) cc_final: 0.7580 (tttp) outliers start: 34 outliers final: 15 residues processed: 246 average time/residue: 0.6953 time to fit residues: 198.1898 Evaluate side-chains 238 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain F residue 10 PHE Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 104 LYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain U residue 97 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 3 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN B 343 HIS ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN I 26 ASN P 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098673 restraints weight = 23022.351| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 0.82 r_work: 0.2950 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 25333 Z= 0.153 Angle : 0.628 13.792 34755 Z= 0.306 Chirality : 0.044 0.227 3433 Planarity : 0.005 0.051 4356 Dihedral : 15.734 125.009 4583 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.53 % Favored : 98.44 % Rotamer: Outliers : 1.62 % Allowed : 9.04 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.16), residues: 2622 helix: 1.65 (0.14), residues: 1386 sheet: 0.51 (0.39), residues: 169 loop : 0.17 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 152 TYR 0.017 0.002 TYR B 273 PHE 0.033 0.002 PHE B 246 TRP 0.031 0.002 TRP A 131 HIS 0.008 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (25293) covalent geometry : angle 0.62830 / 0.31 (34751) SS BOND : bond 0.00513 / 0.24 ( 2) SS BOND : angle 1.26275 / 0.73 ( 4) hydrogen bonds : bond 0.06010 / 4.06 ( 1215) hydrogen bonds : angle 5.13798 / 3.77 ( 3393) Misc. bond : bond 0.06306 / 3.28 ( 38) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 0.930 Fit side-chains REVERT: A 13 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7796 (tp) REVERT: B 130 LYS cc_start: 0.7856 (mtpm) cc_final: 0.7264 (mttm) REVERT: B 182 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7943 (t0) REVERT: B 304 LYS cc_start: 0.8687 (mttm) cc_final: 0.8346 (mtpp) REVERT: D 102 LEU cc_start: 0.9170 (tp) cc_final: 0.8886 (tm) REVERT: E 10 PHE cc_start: 0.7157 (m-80) cc_final: 0.6507 (m-80) REVERT: E 18 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6852 (ttt180) REVERT: E 25 ILE cc_start: 0.6841 (mp) cc_final: 0.6518 (mp) REVERT: E 60 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.5927 (ttm170) REVERT: F 10 PHE cc_start: 0.5583 (OUTLIER) cc_final: 0.5222 (p90) REVERT: M 6 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6985 (mm) REVERT: M 16 LEU cc_start: 0.7065 (mt) cc_final: 0.6673 (mt) REVERT: O 49 LYS cc_start: 0.8440 (pttt) cc_final: 0.7974 (mtmp) REVERT: O 63 GLU cc_start: 0.1860 (OUTLIER) cc_final: 0.1045 (pt0) REVERT: O 123 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.9090 (mpt-90) REVERT: P 145 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: Q 56 LYS cc_start: 0.5788 (mtpt) cc_final: 0.5268 (mttp) REVERT: Q 90 THR cc_start: 0.6071 (m) cc_final: 0.5616 (p) REVERT: Q 109 LYS cc_start: 0.5780 (tppt) cc_final: 0.5112 (mmtt) REVERT: W 19 ASN cc_start: 0.6418 (t0) cc_final: 0.6170 (t0) REVERT: W 39 ILE cc_start: 0.8194 (mm) cc_final: 0.7970 (mt) REVERT: U 74 LYS cc_start: 0.7906 (tttt) cc_final: 0.7644 (tttp) outliers start: 35 outliers final: 13 residues processed: 243 average time/residue: 0.7046 time to fit residues: 197.9488 Evaluate side-chains 230 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain F residue 10 PHE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain U residue 97 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 124 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 255 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN I 26 ASN P 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.096078 restraints weight = 23001.226| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 0.82 r_work: 0.2904 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.263 25333 Z= 0.231 Angle : 0.765 12.699 34755 Z= 0.369 Chirality : 0.050 0.256 3433 Planarity : 0.007 0.068 4356 Dihedral : 16.200 126.821 4583 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.64 % Favored : 98.32 % Rotamer: Outliers : 1.39 % Allowed : 9.13 % Favored : 89.48 % 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: 1.18 (0.16), residues: 2622 helix: 1.41 (0.13), residues: 1382 sheet: 0.48 (0.38), residues: 180 loop : 0.12 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 152 TYR 0.022 0.003 TYR L 35 PHE 0.038 0.003 PHE B 246 TRP 0.039 0.003 TRP A 131 HIS 0.009 0.002 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (25293) covalent geometry : angle 0.76448 / 0.37 (34751) SS BOND : bond 0.00729 / 0.35 ( 2) SS BOND : angle 1.39007 / 0.81 ( 4) hydrogen bonds : bond 0.07175 / 4.86 ( 1215) hydrogen bonds : angle 5.40242 / 3.96 ( 3393) Misc. bond : bond 0.07050 / 3.77 ( 38) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.927 Fit side-chains REVERT: A 13 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7815 (tp) REVERT: A 230 ASN cc_start: 0.4619 (OUTLIER) cc_final: 0.4047 (p0) REVERT: A 262 TYR cc_start: 0.3877 (OUTLIER) cc_final: 0.2730 (m-10) REVERT: B 130 LYS cc_start: 0.7837 (mtpm) cc_final: 0.7231 (mttm) REVERT: B 182 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.7981 (t0) REVERT: D 102 LEU cc_start: 0.9192 (tp) cc_final: 0.8897 (tm) REVERT: E 10 PHE cc_start: 0.7202 (m-80) cc_final: 0.6535 (m-80) REVERT: E 18 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6965 (ttt180) REVERT: E 25 ILE cc_start: 0.6871 (mp) cc_final: 0.6578 (mp) REVERT: E 60 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.5868 (ttm170) REVERT: F 10 PHE cc_start: 0.5581 (OUTLIER) cc_final: 0.5216 (p90) REVERT: M 6 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7057 (mm) REVERT: M 16 LEU cc_start: 0.7098 (mt) cc_final: 0.6751 (mt) REVERT: O 63 GLU cc_start: 0.2073 (OUTLIER) cc_final: 0.1149 (pt0) REVERT: O 123 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.9087 (mpt-90) REVERT: P 145 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: Q 90 THR cc_start: 0.6135 (m) cc_final: 0.5653 (p) REVERT: Q 104 LYS cc_start: 0.5386 (OUTLIER) cc_final: 0.5123 (ptmm) REVERT: Q 109 LYS cc_start: 0.5862 (tppt) cc_final: 0.5195 (mmtt) REVERT: Q 118 ASP cc_start: 0.7324 (t0) cc_final: 0.7075 (t70) REVERT: W 19 ASN cc_start: 0.6557 (t0) cc_final: 0.6314 (t0) REVERT: W 39 ILE cc_start: 0.8216 (mm) cc_final: 0.7994 (mt) REVERT: U 74 LYS cc_start: 0.7931 (tttt) cc_final: 0.7631 (tttp) REVERT: U 79 GLU cc_start: 0.7776 (mp0) cc_final: 0.7518 (mp0) outliers start: 30 outliers final: 17 residues processed: 238 average time/residue: 0.6932 time to fit residues: 190.7492 Evaluate side-chains 234 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain F residue 10 PHE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 104 LYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain U residue 97 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 124 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN I 26 ASN P 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.098321 restraints weight = 22961.272| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 0.82 r_work: 0.2945 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 25333 Z= 0.155 Angle : 0.632 13.246 34755 Z= 0.308 Chirality : 0.045 0.228 3433 Planarity : 0.005 0.049 4356 Dihedral : 15.741 125.179 4583 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.37 % Favored : 98.59 % Rotamer: Outliers : 1.39 % Allowed : 9.55 % Favored : 89.06 % 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: 1.40 (0.16), residues: 2622 helix: 1.61 (0.14), residues: 1386 sheet: 0.53 (0.39), residues: 168 loop : 0.20 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 152 TYR 0.018 0.002 TYR B 273 PHE 0.033 0.002 PHE B 246 TRP 0.032 0.002 TRP A 131 HIS 0.008 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (25293) covalent geometry : angle 0.63209 / 0.31 (34751) SS BOND : bond 0.00537 / 0.26 ( 2) SS BOND : angle 1.31755 / 0.76 ( 4) hydrogen bonds : bond 0.06041 / 4.08 ( 1215) hydrogen bonds : angle 5.15126 / 3.78 ( 3393) Misc. bond : bond 0.06377 / 3.32 ( 38) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.912 Fit side-chains REVERT: A 13 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7821 (tp) REVERT: A 230 ASN cc_start: 0.4611 (OUTLIER) cc_final: 0.4048 (p0) REVERT: B 130 LYS cc_start: 0.7838 (mtpm) cc_final: 0.7248 (mttm) REVERT: B 182 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7921 (t0) REVERT: B 304 LYS cc_start: 0.8686 (mttm) cc_final: 0.8289 (mtpp) REVERT: D 102 LEU cc_start: 0.9183 (tp) cc_final: 0.8901 (tm) REVERT: E 10 PHE cc_start: 0.7200 (m-80) cc_final: 0.6525 (m-80) REVERT: E 18 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6854 (ttt180) REVERT: E 25 ILE cc_start: 0.6861 (mp) cc_final: 0.6531 (mp) REVERT: E 60 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.5890 (ttm170) REVERT: F 10 PHE cc_start: 0.5678 (OUTLIER) cc_final: 0.5324 (p90) REVERT: M 6 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6937 (mm) REVERT: M 16 LEU cc_start: 0.7079 (mt) cc_final: 0.6685 (mt) REVERT: O 63 GLU cc_start: 0.1816 (OUTLIER) cc_final: 0.1101 (pt0) REVERT: O 123 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.9092 (mpt-90) REVERT: P 145 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: Q 90 THR cc_start: 0.6029 (m) cc_final: 0.5563 (p) REVERT: Q 104 LYS cc_start: 0.5270 (OUTLIER) cc_final: 0.5002 (ptmm) REVERT: Q 109 LYS cc_start: 0.5799 (tppt) cc_final: 0.5132 (mmtt) REVERT: Q 118 ASP cc_start: 0.7261 (t0) cc_final: 0.7000 (t70) REVERT: W 19 ASN cc_start: 0.6421 (t0) cc_final: 0.6182 (t0) REVERT: W 39 ILE cc_start: 0.8187 (mm) cc_final: 0.7969 (mt) REVERT: U 74 LYS cc_start: 0.7905 (tttt) cc_final: 0.7627 (tttp) REVERT: U 79 GLU cc_start: 0.7712 (mp0) cc_final: 0.7387 (mp0) outliers start: 30 outliers final: 16 residues processed: 241 average time/residue: 0.6854 time to fit residues: 191.4294 Evaluate side-chains 232 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain F residue 10 PHE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 104 LYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain U residue 97 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 198 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 251 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN E 61 GLN I 26 ASN P 64 GLN Q 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.095957 restraints weight = 23021.013| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 0.82 r_work: 0.2906 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.258 25333 Z= 0.230 Angle : 0.761 12.283 34755 Z= 0.367 Chirality : 0.050 0.256 3433 Planarity : 0.006 0.066 4356 Dihedral : 16.283 126.859 4583 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.64 % Favored : 98.32 % Rotamer: Outliers : 1.53 % Allowed : 9.50 % Favored : 88.97 % 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: 1.18 (0.16), residues: 2622 helix: 1.41 (0.13), residues: 1382 sheet: 0.47 (0.38), residues: 179 loop : 0.14 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 152 TYR 0.022 0.003 TYR L 35 PHE 0.038 0.003 PHE B 246 TRP 0.040 0.003 TRP A 131 HIS 0.009 0.002 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (25293) covalent geometry : angle 0.76084 / 0.37 (34751) SS BOND : bond 0.00753 / 0.36 ( 2) SS BOND : angle 1.44966 / 0.84 ( 4) hydrogen bonds : bond 0.07154 / 4.85 ( 1215) hydrogen bonds : angle 5.40492 / 3.96 ( 3393) Misc. bond : bond 0.06970 / 3.74 ( 38) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.763 Fit side-chains REVERT: A 230 ASN cc_start: 0.4747 (OUTLIER) cc_final: 0.4150 (p0) REVERT: B 130 LYS cc_start: 0.7848 (mtpm) cc_final: 0.7224 (mttm) REVERT: B 182 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7962 (t0) REVERT: D 102 LEU cc_start: 0.9189 (tp) cc_final: 0.8900 (tm) REVERT: E 10 PHE cc_start: 0.7185 (m-80) cc_final: 0.6635 (m-80) REVERT: E 18 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6943 (ttt180) REVERT: E 25 ILE cc_start: 0.6870 (mp) cc_final: 0.6599 (mp) REVERT: E 60 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.5836 (ttm170) REVERT: F 10 PHE cc_start: 0.5592 (OUTLIER) cc_final: 0.5239 (p90) REVERT: M 6 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7104 (mm) REVERT: M 16 LEU cc_start: 0.7177 (mt) cc_final: 0.6793 (mt) REVERT: O 63 GLU cc_start: 0.2068 (OUTLIER) cc_final: 0.1167 (pt0) REVERT: O 123 ARG cc_start: 0.9360 (OUTLIER) cc_final: 0.9091 (mpt-90) REVERT: P 145 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: Q 90 THR cc_start: 0.6032 (m) cc_final: 0.5547 (p) REVERT: Q 104 LYS cc_start: 0.5351 (OUTLIER) cc_final: 0.5085 (ptmm) REVERT: Q 109 LYS cc_start: 0.5852 (tppt) cc_final: 0.5165 (mmtt) REVERT: W 19 ASN cc_start: 0.6539 (t0) cc_final: 0.6302 (t0) REVERT: W 39 ILE cc_start: 0.8185 (mm) cc_final: 0.7967 (mt) REVERT: U 74 LYS cc_start: 0.7911 (tttt) cc_final: 0.7602 (tttp) REVERT: U 79 GLU cc_start: 0.7785 (mp0) cc_final: 0.7501 (mp0) outliers start: 33 outliers final: 18 residues processed: 233 average time/residue: 0.6699 time to fit residues: 180.9018 Evaluate side-chains 232 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain F residue 10 PHE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 104 LYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain U residue 97 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 182 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 217 optimal weight: 0.5980 chunk 210 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 166 optimal weight: 0.0370 chunk 253 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN C 332 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN I 26 ASN P 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.099760 restraints weight = 23112.176| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 0.82 r_work: 0.2964 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.226 25333 Z= 0.134 Angle : 0.592 12.474 34755 Z= 0.290 Chirality : 0.043 0.217 3433 Planarity : 0.005 0.044 4356 Dihedral : 15.546 124.416 4583 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.41 % Favored : 98.55 % Rotamer: Outliers : 1.39 % Allowed : 9.96 % Favored : 88.65 % 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: 1.49 (0.16), residues: 2622 helix: 1.70 (0.14), residues: 1386 sheet: 0.51 (0.39), residues: 168 loop : 0.25 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 152 TYR 0.017 0.002 TYR B 273 PHE 0.031 0.002 PHE B 246 TRP 0.032 0.002 TRP A 131 HIS 0.008 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (25293) covalent geometry : angle 0.59187 / 0.29 (34751) SS BOND : bond 0.00473 / 0.23 ( 2) SS BOND : angle 1.25951 / 0.72 ( 4) hydrogen bonds : bond 0.05596 / 3.78 ( 1215) hydrogen bonds : angle 5.04904 / 3.71 ( 3393) Misc. bond : bond 0.05970 / 3.09 ( 38) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 230 ASN cc_start: 0.4588 (OUTLIER) cc_final: 0.3981 (p0) REVERT: B 125 ASP cc_start: 0.7729 (t70) cc_final: 0.7474 (t70) REVERT: B 130 LYS cc_start: 0.7823 (mtpm) cc_final: 0.7238 (mttm) REVERT: B 182 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7937 (t0) REVERT: B 304 LYS cc_start: 0.8693 (mttm) cc_final: 0.8306 (mtpp) REVERT: D 102 LEU cc_start: 0.9182 (tp) cc_final: 0.8923 (tm) REVERT: E 10 PHE cc_start: 0.7271 (m-80) cc_final: 0.6653 (m-80) REVERT: E 25 ILE cc_start: 0.6867 (mp) cc_final: 0.6493 (mp) REVERT: E 60 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.5873 (ttm170) REVERT: F 10 PHE cc_start: 0.5660 (OUTLIER) cc_final: 0.5298 (p90) REVERT: M 6 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6865 (mm) REVERT: M 16 LEU cc_start: 0.7098 (mt) cc_final: 0.6705 (mt) REVERT: O 63 GLU cc_start: 0.1755 (OUTLIER) cc_final: 0.1291 (pt0) REVERT: P 145 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: Q 62 LYS cc_start: 0.5334 (tppt) cc_final: 0.5071 (tppp) REVERT: Q 90 THR cc_start: 0.6125 (m) cc_final: 0.5650 (p) REVERT: Q 104 LYS cc_start: 0.5321 (OUTLIER) cc_final: 0.5007 (ptmm) REVERT: W 19 ASN cc_start: 0.6401 (t0) cc_final: 0.6193 (t0) REVERT: W 39 ILE cc_start: 0.8202 (mm) cc_final: 0.7990 (mt) REVERT: U 74 LYS cc_start: 0.7937 (tttt) cc_final: 0.7661 (tttp) REVERT: U 79 GLU cc_start: 0.7722 (mp0) cc_final: 0.7385 (mp0) outliers start: 30 outliers final: 14 residues processed: 241 average time/residue: 0.6783 time to fit residues: 188.6193 Evaluate side-chains 232 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain F residue 10 PHE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 104 LYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain U residue 97 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 104 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 80 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN E 61 GLN I 26 ASN P 64 GLN Q 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097906 restraints weight = 23034.518| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 0.80 r_work: 0.2925 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.252 25333 Z= 0.175 Angle : 0.666 12.449 34755 Z= 0.324 Chirality : 0.046 0.239 3433 Planarity : 0.006 0.052 4356 Dihedral : 15.770 125.695 4583 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.60 % Favored : 98.36 % Rotamer: Outliers : 1.16 % Allowed : 10.15 % Favored : 88.69 % 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: 1.39 (0.16), residues: 2622 helix: 1.59 (0.14), residues: 1385 sheet: 0.48 (0.38), residues: 178 loop : 0.23 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 152 TYR 0.019 0.002 TYR P 21 PHE 0.034 0.002 PHE B 246 TRP 0.034 0.002 TRP A 131 HIS 0.008 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (25293) covalent geometry : angle 0.66631 / 0.32 (34751) SS BOND : bond 0.00611 / 0.29 ( 2) SS BOND : angle 1.38033 / 0.79 ( 4) hydrogen bonds : bond 0.06372 / 4.31 ( 1215) hydrogen bonds : angle 5.19970 / 3.82 ( 3393) Misc. bond : bond 0.06563 / 3.52 ( 38) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.853 Fit side-chains REVERT: A 230 ASN cc_start: 0.4696 (OUTLIER) cc_final: 0.4032 (p0) REVERT: B 125 ASP cc_start: 0.7760 (t70) cc_final: 0.7507 (t70) REVERT: B 130 LYS cc_start: 0.7843 (mtpm) cc_final: 0.7271 (mttm) REVERT: B 182 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7926 (t0) REVERT: D 102 LEU cc_start: 0.9191 (tp) cc_final: 0.8911 (tm) REVERT: E 10 PHE cc_start: 0.7243 (m-80) cc_final: 0.6542 (m-80) REVERT: E 25 ILE cc_start: 0.6870 (mp) cc_final: 0.6535 (mp) REVERT: E 60 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.5862 (ttm170) REVERT: F 10 PHE cc_start: 0.5642 (OUTLIER) cc_final: 0.5290 (p90) REVERT: M 6 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7019 (mm) REVERT: M 16 LEU cc_start: 0.7130 (mt) cc_final: 0.6751 (mt) REVERT: O 63 GLU cc_start: 0.1576 (OUTLIER) cc_final: 0.1226 (pt0) REVERT: P 145 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7619 (mt0) REVERT: Q 90 THR cc_start: 0.6156 (m) cc_final: 0.5667 (p) REVERT: Q 104 LYS cc_start: 0.5374 (OUTLIER) cc_final: 0.5100 (ptmm) REVERT: Q 109 LYS cc_start: 0.5947 (tppt) cc_final: 0.5227 (mmtt) REVERT: W 19 ASN cc_start: 0.6470 (t0) cc_final: 0.6243 (t0) REVERT: W 39 ILE cc_start: 0.8235 (mm) cc_final: 0.8023 (mt) REVERT: U 74 LYS cc_start: 0.7912 (tttt) cc_final: 0.7636 (tttp) REVERT: U 79 GLU cc_start: 0.7761 (mp0) cc_final: 0.7506 (mp0) outliers start: 25 outliers final: 15 residues processed: 228 average time/residue: 0.6750 time to fit residues: 178.5061 Evaluate side-chains 228 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain F residue 10 PHE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 104 LYS Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain W residue 36 LEU Chi-restraints excluded: chain U residue 97 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 96 optimal weight: 7.9990 chunk 210 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 228 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN I 26 ASN P 64 GLN Q 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.096816 restraints weight = 22955.048| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 0.80 r_work: 0.2916 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.261 25333 Z= 0.207 Angle : 0.726 12.366 34755 Z= 0.352 Chirality : 0.048 0.250 3433 Planarity : 0.006 0.063 4356 Dihedral : 16.052 126.463 4583 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.60 % Favored : 98.36 % Rotamer: Outliers : 1.20 % Allowed : 9.96 % Favored : 88.83 % 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: 1.25 (0.16), residues: 2622 helix: 1.45 (0.13), residues: 1383 sheet: 0.63 (0.38), residues: 175 loop : 0.16 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 152 TYR 0.021 0.003 TYR P 21 PHE 0.037 0.003 PHE B 246 TRP 0.037 0.002 TRP A 131 HIS 0.009 0.002 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (25293) covalent geometry : angle 0.72625 / 0.35 (34751) SS BOND : bond 0.00717 / 0.34 ( 2) SS BOND : angle 1.46977 / 0.85 ( 4) hydrogen bonds : bond 0.06890 / 4.66 ( 1215) hydrogen bonds : angle 5.33648 / 3.91 ( 3393) Misc. bond : bond 0.06919 / 3.70 ( 38) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10903.02 seconds wall clock time: 186 minutes 15.43 seconds (11175.43 seconds total)