Starting phenix.real_space_refine on Fri Feb 6 10:39:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hei_52077/02_2026/9hei_52077.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hei_52077/02_2026/9hei_52077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hei_52077/02_2026/9hei_52077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hei_52077/02_2026/9hei_52077.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hei_52077/02_2026/9hei_52077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hei_52077/02_2026/9hei_52077.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 10 Type Number sf(0) Gaussians Ca 1 9.91 5 Mn 4 7.51 5 Fe 2 7.16 5 P 4 5.49 5 Mg 35 5.21 5 S 72 5.16 5 Cl 2 4.86 5 C 16769 2.51 5 N 3656 2.21 5 O 4152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24697 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2491 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 1 Chain: "B" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3755 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 25, 'TRANS': 454} Chain: "V" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 224 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "C" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3498 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 25, 'TRANS': 423} Chain: "D" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2771 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 14, 'TRANS': 333} Chain: "E" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "F" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "H" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 501 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "I" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 275 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "J" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 262 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "K" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "L" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 290 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "M" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "O" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1808 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 10, 'TRANS': 229} Chain: "P" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1444 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1192 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "T" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 247 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "X" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 220 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "Z" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 458 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "U" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 176 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "W" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 344 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "A" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 342 Unusual residues: {' CL': 2, 'BCR': 1, 'CLA': 3, 'FE2': 1, 'OEX': 1, 'PHO': 1, 'SQD': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1191 Unusual residues: {'BCR': 2, 'CLA': 15, 'LHG': 2, 'LMG': 2} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1155 Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 3, 'LMG': 1, 'LMU': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 473 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 2, 'LMG': 1, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'CLA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.97, per 1000 atoms: 0.24 Number of scatterers: 24697 At special positions: 0 Unit cell: (136.08, 126, 125.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Fe 2 26.01 Mn 4 24.99 Ca 1 19.99 Cl 2 17.00 S 72 16.00 P 4 15.00 Mg 35 11.99 O 4152 8.00 N 3656 7.00 C 16769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=38, symmetry=0 Number of additional bonds: simple=38, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.0 seconds 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4926 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 15 sheets defined 59.7% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 31 through 55 removed outlier: 3.765A pdb=" N ILE A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 109 through 138 removed outlier: 4.120A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.678A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 224 Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 267 through 294 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 316 through 332 Processing helix chain 'B' and resid 4 through 13 removed outlier: 3.581A pdb=" N VAL B 8 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N HIS B 9 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 44 removed outlier: 3.715A pdb=" N SER B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 4.169A pdb=" N PHE B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 195 through 219 removed outlier: 4.121A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 233 through 259 removed outlier: 3.672A pdb=" N VAL B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.819A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 295 Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.743A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'V' and resid 3 through 29 removed outlier: 4.169A pdb=" N GLY V 19 " --> pdb=" O VAL V 15 " (cutoff:3.500A) Proline residue: V 20 - end of helix Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 22 through 31 removed outlier: 6.092A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 62 Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 75 through 83 removed outlier: 3.913A pdb=" N HIS C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.637A pdb=" N GLU C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 120 removed outlier: 3.501A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 169 Processing helix chain 'C' and resid 193 through 203 removed outlier: 3.923A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.540A pdb=" N SER C 214 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 241 Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 255 through 281 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 293 through 313 Processing helix chain 'C' and resid 341 through 347 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 409 through 442 Processing helix chain 'C' and resid 452 through 457 removed outlier: 3.745A pdb=" N SER C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 33 through 55 Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 108 through 137 removed outlier: 4.071A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 146 Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 175 through 190 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 194 through 221 Processing helix chain 'D' and resid 245 through 257 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 275 - end of helix removed outlier: 3.523A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 328 Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'E' and resid 9 through 14 Processing helix chain 'E' and resid 16 through 40 removed outlier: 4.176A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 41 through 47 Processing helix chain 'E' and resid 71 through 80 Processing helix chain 'F' and resid 16 through 40 removed outlier: 3.527A pdb=" N ILE F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL F 27 " --> pdb=" O HIS F 23 " (cutoff:3.500A) Proline residue: F 28 - end of helix Processing helix chain 'H' and resid 24 through 36 Proline residue: H 32 - end of helix removed outlier: 3.992A pdb=" N GLU H 36 " --> pdb=" O PRO H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 69 Processing helix chain 'H' and resid 80 through 85 Processing helix chain 'I' and resid 2 through 25 Processing helix chain 'I' and resid 26 through 31 removed outlier: 3.647A pdb=" N ASN I 31 " --> pdb=" O PRO I 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 35 Processing helix chain 'K' and resid 15 through 17 No H-bonds generated for 'chain 'K' and resid 15 through 17' Processing helix chain 'K' and resid 18 through 25 Processing helix chain 'K' and resid 27 through 44 removed outlier: 3.765A pdb=" N PHE K 31 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 38 removed outlier: 4.557A pdb=" N SER L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 15 Processing helix chain 'M' and resid 16 through 31 Processing helix chain 'O' and resid 53 through 60 Processing helix chain 'O' and resid 61 through 66 Processing helix chain 'O' and resid 69 through 73 Processing helix chain 'O' and resid 226 through 231 Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 133 through 141 Processing helix chain 'P' and resid 142 through 145 Processing helix chain 'P' and resid 196 through 199 Processing helix chain 'P' and resid 224 through 228 Processing helix chain 'P' and resid 230 through 242 removed outlier: 3.853A pdb=" N GLU P 234 " --> pdb=" O GLY P 230 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 66 removed outlier: 4.236A pdb=" N ARG Q 64 " --> pdb=" O ASP Q 60 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 80 through 86 Processing helix chain 'Q' and resid 86 through 93 Processing helix chain 'Q' and resid 93 through 109 Processing helix chain 'Q' and resid 112 through 119 Processing helix chain 'Q' and resid 120 through 128 Processing helix chain 'Q' and resid 129 through 133 Processing helix chain 'Q' and resid 134 through 146 removed outlier: 3.593A pdb=" N LYS Q 146 " --> pdb=" O LEU Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 174 Processing helix chain 'Q' and resid 176 through 199 Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'X' and resid 66 through 96 Processing helix chain 'Z' and resid 2 through 29 Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 36 through 60 Processing helix chain 'U' and resid 93 through 102 Proline residue: U 100 - end of helix Processing helix chain 'W' and resid 72 through 76 Processing helix chain 'W' and resid 78 through 100 removed outlier: 3.521A pdb=" N GLY W 82 " --> pdb=" O ASP W 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA2, first strand: chain 'A' and resid 297 through 298 Processing sheet with id=AA3, first strand: chain 'B' and resid 73 through 74 removed outlier: 3.548A pdb=" N TRP B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.596A pdb=" N ILE B 166 " --> pdb=" O GLN B 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.413A pdb=" N GLU B 431 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.153A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 409 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AA8, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA9, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'O' and resid 117 through 120 removed outlier: 3.923A pdb=" N ASN O 96 " --> pdb=" O MET O 135 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N MET O 135 " --> pdb=" O ASN O 96 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS O 98 " --> pdb=" O ASP O 133 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP O 133 " --> pdb=" O CYS O 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 117 through 120 removed outlier: 5.545A pdb=" N LEU O 94 " --> pdb=" O LYS O 291 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS O 291 " --> pdb=" O LEU O 94 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASN O 96 " --> pdb=" O GLN O 289 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN O 289 " --> pdb=" O ASN O 96 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR O 283 " --> pdb=" O THR O 102 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE O 104 " --> pdb=" O LYS O 281 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS O 281 " --> pdb=" O PHE O 104 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL O 106 " --> pdb=" O ASP O 279 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASP O 279 " --> pdb=" O VAL O 106 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL O 261 " --> pdb=" O VAL O 248 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL O 248 " --> pdb=" O VAL O 261 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLU O 263 " --> pdb=" O PHE O 246 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N PHE O 246 " --> pdb=" O GLU O 263 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE O 265 " --> pdb=" O ALA O 244 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA O 244 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLY O 242 " --> pdb=" O PRO O 267 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE O 246 " --> pdb=" O ILE O 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 123 through 124 Processing sheet with id=AB4, first strand: chain 'P' and resid 75 through 79 Processing sheet with id=AB5, first strand: chain 'P' and resid 92 through 93 removed outlier: 5.568A pdb=" N VAL P 102 " --> pdb=" O ALA P 120 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA P 120 " --> pdb=" O VAL P 102 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS P 214 " --> pdb=" O GLY P 210 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL P 209 " --> pdb=" O THR P 183 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR P 183 " --> pdb=" O VAL P 209 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU P 190 " --> pdb=" O LEU P 170 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU P 170 " --> pdb=" O LEU P 190 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG P 192 " --> pdb=" O ALA P 168 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ALA P 168 " --> pdb=" O ARG P 192 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP Q 56 " --> pdb=" O SER P 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 147 through 148 1250 hydrogen bonds defined for protein. 3546 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.68: 25312 1.68 - 2.16: 244 2.16 - 2.64: 37 2.64 - 3.12: 2 3.12 - 3.60: 4 Bond restraints: 25599 Sorted by residual: bond pdb=" C25 BCR C 516 " pdb=" C26 BCR C 516 " ideal model delta sigma weight residual 1.347 1.612 -0.265 2.00e-02 2.50e+03 1.75e+02 bond pdb=" C25 BCR C 514 " pdb=" C26 BCR C 514 " ideal model delta sigma weight residual 1.347 1.609 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C25 BCR B 517 " pdb=" C26 BCR B 517 " ideal model delta sigma weight residual 1.347 1.609 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C25 BCR C 515 " pdb=" C26 BCR C 515 " ideal model delta sigma weight residual 1.347 1.608 -0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C25 BCR K 101 " pdb=" C26 BCR K 101 " ideal model delta sigma weight residual 1.347 1.605 -0.258 2.00e-02 2.50e+03 1.66e+02 ... (remaining 25594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.36: 34802 6.36 - 12.72: 372 12.72 - 19.08: 36 19.08 - 25.45: 2 25.45 - 31.81: 1 Bond angle restraints: 35213 Sorted by residual: angle pdb="MN3 OEX A 401 " pdb=" O5 OEX A 401 " pdb="MN4 OEX A 401 " ideal model delta sigma weight residual 73.50 105.31 -31.81 2.00e+00 2.50e-01 2.53e+02 angle pdb="CA1 OEX A 401 " pdb=" O5 OEX A 401 " pdb="MN4 OEX A 401 " ideal model delta sigma weight residual 92.50 115.46 -22.96 2.00e+00 2.50e-01 1.32e+02 angle pdb=" O1 OEX A 401 " pdb="MN1 OEX A 401 " pdb=" O5 OEX A 401 " ideal model delta sigma weight residual 93.00 71.60 21.40 2.00e+00 2.50e-01 1.15e+02 angle pdb="MN2 OEX A 401 " pdb=" O3 OEX A 401 " pdb="MN3 OEX A 401 " ideal model delta sigma weight residual 89.00 105.00 -16.00 2.00e+00 2.50e-01 6.40e+01 angle pdb="MN1 OEX A 401 " pdb=" O3 OEX A 401 " pdb="MN2 OEX A 401 " ideal model delta sigma weight residual 88.00 102.71 -14.71 2.00e+00 2.50e-01 5.41e+01 ... (remaining 35208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 13406 31.94 - 63.89: 477 63.89 - 95.83: 57 95.83 - 127.77: 65 127.77 - 159.72: 2 Dihedral angle restraints: 14007 sinusoidal: 6285 harmonic: 7722 Sorted by residual: dihedral pdb=" C2B HEM F 101 " pdb=" C3B HEM F 101 " pdb=" CAB HEM F 101 " pdb=" CBB HEM F 101 " ideal model delta sinusoidal sigma weight residual 0.00 59.08 -59.08 2 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" C3A DGD C 517 " pdb=" C1A DGD C 517 " pdb=" C2A DGD C 517 " pdb=" O1A DGD C 517 " ideal model delta sinusoidal sigma weight residual 335.78 176.06 159.72 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C4D PHO D 402 " pdb=" CBD PHO D 402 " pdb=" CHA PHO D 402 " pdb=" CGD PHO D 402 " ideal model delta sinusoidal sigma weight residual 243.52 115.25 128.27 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 14004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 2955 0.147 - 0.293: 552 0.293 - 0.439: 0 0.439 - 0.586: 0 0.586 - 0.732: 35 Chirality restraints: 3542 Sorted by residual: chirality pdb=" C3A CLA B 514 " pdb=" C2A CLA B 514 " pdb=" C4A CLA B 514 " pdb=" CMA CLA B 514 " both_signs ideal model delta sigma weight residual False -2.76 -2.03 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C3A CLA B 504 " pdb=" C2A CLA B 504 " pdb=" C4A CLA B 504 " pdb=" CMA CLA B 504 " both_signs ideal model delta sigma weight residual False -2.76 -2.06 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" C3A CLA C 506 " pdb=" C2A CLA C 506 " pdb=" C4A CLA C 506 " pdb=" CMA CLA C 506 " both_signs ideal model delta sigma weight residual False -2.76 -2.06 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 3539 not shown) Planarity restraints: 4409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO D 402 " -0.065 2.00e-02 2.50e+03 1.07e-01 9.15e+02 pdb=" ND PHO D 402 " -0.072 2.00e-02 2.50e+03 pdb=" C1A PHO D 402 " -0.017 2.00e-02 2.50e+03 pdb=" C1B PHO D 402 " -0.033 2.00e-02 2.50e+03 pdb=" C1C PHO D 402 " -0.096 2.00e-02 2.50e+03 pdb=" C1D PHO D 402 " -0.087 2.00e-02 2.50e+03 pdb=" C2A PHO D 402 " -0.033 2.00e-02 2.50e+03 pdb=" C2B PHO D 402 " 0.031 2.00e-02 2.50e+03 pdb=" C2C PHO D 402 " 0.004 2.00e-02 2.50e+03 pdb=" C2D PHO D 402 " -0.039 2.00e-02 2.50e+03 pdb=" C3A PHO D 402 " 0.127 2.00e-02 2.50e+03 pdb=" C3B PHO D 402 " 0.038 2.00e-02 2.50e+03 pdb=" C3C PHO D 402 " 0.108 2.00e-02 2.50e+03 pdb=" C3D PHO D 402 " 0.005 2.00e-02 2.50e+03 pdb=" C4A PHO D 402 " -0.010 2.00e-02 2.50e+03 pdb=" C4B PHO D 402 " -0.023 2.00e-02 2.50e+03 pdb=" C4C PHO D 402 " -0.107 2.00e-02 2.50e+03 pdb=" C4D PHO D 402 " -0.017 2.00e-02 2.50e+03 pdb=" CAB PHO D 402 " 0.098 2.00e-02 2.50e+03 pdb=" CAC PHO D 402 " 0.383 2.00e-02 2.50e+03 pdb=" CAD PHO D 402 " 0.065 2.00e-02 2.50e+03 pdb=" CBD PHO D 402 " 0.160 2.00e-02 2.50e+03 pdb=" CHA PHO D 402 " 0.028 2.00e-02 2.50e+03 pdb=" CHB PHO D 402 " -0.058 2.00e-02 2.50e+03 pdb=" CHC PHO D 402 " -0.039 2.00e-02 2.50e+03 pdb=" CHD PHO D 402 " -0.136 2.00e-02 2.50e+03 pdb=" CMB PHO D 402 " 0.083 2.00e-02 2.50e+03 pdb=" CMC PHO D 402 " 0.003 2.00e-02 2.50e+03 pdb=" CMD PHO D 402 " -0.037 2.00e-02 2.50e+03 pdb=" NA PHO D 402 " -0.067 2.00e-02 2.50e+03 pdb=" NC PHO D 402 " -0.258 2.00e-02 2.50e+03 pdb=" OBD PHO D 402 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO A 407 " 0.015 2.00e-02 2.50e+03 1.05e-01 8.85e+02 pdb=" ND PHO A 407 " -0.006 2.00e-02 2.50e+03 pdb=" C1A PHO A 407 " -0.031 2.00e-02 2.50e+03 pdb=" C1B PHO A 407 " 0.000 2.00e-02 2.50e+03 pdb=" C1C PHO A 407 " 0.062 2.00e-02 2.50e+03 pdb=" C1D PHO A 407 " 0.012 2.00e-02 2.50e+03 pdb=" C2A PHO A 407 " -0.134 2.00e-02 2.50e+03 pdb=" C2B PHO A 407 " 0.046 2.00e-02 2.50e+03 pdb=" C2C PHO A 407 " -0.037 2.00e-02 2.50e+03 pdb=" C2D PHO A 407 " 0.051 2.00e-02 2.50e+03 pdb=" C3A PHO A 407 " -0.312 2.00e-02 2.50e+03 pdb=" C3B PHO A 407 " 0.083 2.00e-02 2.50e+03 pdb=" C3C PHO A 407 " -0.133 2.00e-02 2.50e+03 pdb=" C3D PHO A 407 " 0.053 2.00e-02 2.50e+03 pdb=" C4A PHO A 407 " -0.103 2.00e-02 2.50e+03 pdb=" C4B PHO A 407 " 0.067 2.00e-02 2.50e+03 pdb=" C4C PHO A 407 " -0.003 2.00e-02 2.50e+03 pdb=" C4D PHO A 407 " 0.020 2.00e-02 2.50e+03 pdb=" CAB PHO A 407 " 0.142 2.00e-02 2.50e+03 pdb=" CAC PHO A 407 " -0.326 2.00e-02 2.50e+03 pdb=" CAD PHO A 407 " 0.080 2.00e-02 2.50e+03 pdb=" CBD PHO A 407 " 0.068 2.00e-02 2.50e+03 pdb=" CHA PHO A 407 " 0.017 2.00e-02 2.50e+03 pdb=" CHB PHO A 407 " -0.050 2.00e-02 2.50e+03 pdb=" CHC PHO A 407 " 0.092 2.00e-02 2.50e+03 pdb=" CHD PHO A 407 " -0.006 2.00e-02 2.50e+03 pdb=" CMB PHO A 407 " 0.045 2.00e-02 2.50e+03 pdb=" CMC PHO A 407 " -0.039 2.00e-02 2.50e+03 pdb=" CMD PHO A 407 " 0.080 2.00e-02 2.50e+03 pdb=" NA PHO A 407 " 0.022 2.00e-02 2.50e+03 pdb=" NC PHO A 407 " 0.118 2.00e-02 2.50e+03 pdb=" OBD PHO A 407 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PL9 D 407 " -0.053 2.00e-02 2.50e+03 1.19e-01 3.87e+02 pdb=" C2 PL9 D 407 " -0.088 2.00e-02 2.50e+03 pdb=" C3 PL9 D 407 " 0.026 2.00e-02 2.50e+03 pdb=" C4 PL9 D 407 " -0.070 2.00e-02 2.50e+03 pdb=" C5 PL9 D 407 " 0.010 2.00e-02 2.50e+03 pdb=" C52 PL9 D 407 " 0.064 2.00e-02 2.50e+03 pdb=" C53 PL9 D 407 " 0.133 2.00e-02 2.50e+03 pdb=" C6 PL9 D 407 " 0.030 2.00e-02 2.50e+03 pdb=" C7 PL9 D 407 " 0.251 2.00e-02 2.50e+03 pdb=" O1 PL9 D 407 " -0.211 2.00e-02 2.50e+03 pdb=" O2 PL9 D 407 " -0.093 2.00e-02 2.50e+03 ... (remaining 4406 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 5 2.15 - 2.84: 8244 2.84 - 3.53: 40761 3.53 - 4.21: 68714 4.21 - 4.90: 115327 Nonbonded interactions: 233051 Sorted by model distance: nonbonded pdb="FE FE2 A 402 " pdb=" O2 BCT D 403 " model vdw 1.467 3.000 nonbonded pdb="FE FE2 A 402 " pdb=" C BCT D 403 " model vdw 2.014 3.230 nonbonded pdb=" NE2 HIS D 214 " pdb="FE FE2 A 402 " model vdw 2.025 3.080 nonbonded pdb=" OE2 GLU C 342 " pdb="MN3 OEX A 401 " model vdw 2.117 3.060 nonbonded pdb=" NE2 HIS F 23 " pdb="FE HEM F 101 " model vdw 2.145 3.080 ... (remaining 233046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.130 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.026 0.849 25637 Z= 1.636 Angle : 1.851 31.807 35213 Z= 1.143 Chirality : 0.119 0.732 3542 Planarity : 0.007 0.119 4409 Dihedral : 17.880 159.718 9081 Min Nonbonded Distance : 1.467 Molprobity Statistics. All-atom Clashscore : 32.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.01 % Favored : 95.73 % Rotamer: Outliers : 3.38 % Allowed : 6.22 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 2692 helix: 0.04 (0.12), residues: 1453 sheet: -0.78 (0.39), residues: 167 loop : -1.11 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 249 TYR 0.009 0.001 TYR D 315 PHE 0.012 0.001 PHE C 425 TRP 0.011 0.001 TRP Q 121 HIS 0.004 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.02325 (25599) covalent geometry : angle 1.85143 (35213) hydrogen bonds : bond 0.17401 ( 1246) hydrogen bonds : angle 7.48722 ( 3546) Misc. bond : bond 0.31178 ( 38) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 452 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 362 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.8178 (t80) REVERT: L 8 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7023 (tptt) REVERT: T 25 ASP cc_start: 0.7558 (t0) cc_final: 0.7342 (t0) outliers start: 75 outliers final: 6 residues processed: 497 average time/residue: 0.7139 time to fit residues: 405.3283 Evaluate side-chains 223 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain Q residue 148 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 108 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 267 ASN A 315 ASN ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 285 GLN B 343 HIS C 56 ASN C 143 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 315 ASN C 366 ASN C 373 GLN C 376 GLN D 83 ASN D 236 ASN E 75 GLN L 5 ASN L 7 ASN L 38 ASN O 64 GLN O 72 ASN O 266 GLN P 64 ASN P 203 GLN P 213 ASN Z 58 ASN W 66 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.062154 restraints weight = 63693.082| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.15 r_work: 0.2835 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.388 25637 Z= 0.197 Angle : 0.709 10.328 35213 Z= 0.334 Chirality : 0.044 0.319 3542 Planarity : 0.005 0.046 4409 Dihedral : 18.483 172.256 4435 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.47 % Allowed : 13.12 % Favored : 83.41 % 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: 2692 helix: 1.68 (0.13), residues: 1483 sheet: -0.17 (0.36), residues: 176 loop : -0.30 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 233 TYR 0.019 0.002 TYR P 78 PHE 0.028 0.002 PHE B 246 TRP 0.020 0.002 TRP Z 33 HIS 0.009 0.002 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00456 (25599) covalent geometry : angle 0.70895 (35213) hydrogen bonds : bond 0.05060 ( 1246) hydrogen bonds : angle 5.14543 ( 3546) Misc. bond : bond 0.07155 ( 38) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 231 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 MET cc_start: 0.9098 (tpt) cc_final: 0.8887 (tpp) REVERT: B 231 MET cc_start: 0.9478 (mtt) cc_final: 0.9242 (mtm) REVERT: C 71 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8666 (mt-10) REVERT: C 217 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7369 (p0) REVERT: C 365 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8787 (tp) REVERT: D 8 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.8096 (t80) REVERT: D 11 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8094 (tppt) REVERT: D 323 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8564 (mt-10) REVERT: E 12 ASP cc_start: 0.6720 (t0) cc_final: 0.6427 (t0) REVERT: E 62 GLU cc_start: 0.8503 (pm20) cc_final: 0.8300 (pm20) REVERT: E 74 GLU cc_start: 0.8056 (pm20) cc_final: 0.7824 (pm20) REVERT: L 8 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.7894 (tptt) REVERT: L 9 GLN cc_start: 0.8475 (mm-40) cc_final: 0.7663 (mp10) REVERT: M 21 PHE cc_start: 0.7584 (t80) cc_final: 0.7374 (t80) REVERT: O 58 GLN cc_start: 0.8860 (mm110) cc_final: 0.8526 (mp10) REVERT: O 79 SER cc_start: 0.8080 (t) cc_final: 0.7866 (t) REVERT: O 88 LYS cc_start: 0.8009 (tmmm) cc_final: 0.7793 (tmmm) REVERT: O 140 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8204 (tmtt) REVERT: P 107 GLU cc_start: 0.8908 (pt0) cc_final: 0.8678 (tt0) REVERT: P 203 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8867 (mp10) REVERT: Q 148 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8104 (ptpt) REVERT: Q 177 GLN cc_start: 0.8973 (tt0) cc_final: 0.8545 (tt0) REVERT: U 97 LYS cc_start: 0.8392 (tmtt) cc_final: 0.8107 (tttt) REVERT: U 105 SER cc_start: 0.9131 (t) cc_final: 0.8792 (p) REVERT: W 96 TRP cc_start: 0.8797 (OUTLIER) cc_final: 0.7874 (t-100) outliers start: 77 outliers final: 23 residues processed: 283 average time/residue: 0.6293 time to fit residues: 207.2428 Evaluate side-chains 233 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 140 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 203 GLN Chi-restraints excluded: chain Q residue 148 LYS Chi-restraints excluded: chain X residue 90 ILE Chi-restraints excluded: chain W residue 96 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 166 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 252 HIS C 301 GLN E 71 ASN L 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.056542 restraints weight = 64769.061| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.21 r_work: 0.2712 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.307 25637 Z= 0.203 Angle : 0.644 9.069 35213 Z= 0.305 Chirality : 0.043 0.229 3542 Planarity : 0.005 0.052 4409 Dihedral : 17.072 162.963 4432 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.52 % Allowed : 13.44 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.16), residues: 2692 helix: 1.88 (0.13), residues: 1479 sheet: -0.22 (0.35), residues: 191 loop : -0.20 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 357 TYR 0.016 0.002 TYR A 246 PHE 0.020 0.002 PHE B 246 TRP 0.014 0.001 TRP C 238 HIS 0.008 0.002 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00474 (25599) covalent geometry : angle 0.64432 (35213) hydrogen bonds : bond 0.05135 ( 1246) hydrogen bonds : angle 4.85875 ( 3546) Misc. bond : bond 0.07067 ( 38) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 213 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASN cc_start: 0.9416 (t0) cc_final: 0.9100 (OUTLIER) REVERT: B 25 MET cc_start: 0.9077 (tpt) cc_final: 0.8843 (tpp) REVERT: B 246 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8903 (p90) REVERT: B 409 LEU cc_start: 0.8924 (mm) cc_final: 0.8723 (mt) REVERT: C 365 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8786 (tp) REVERT: C 451 ASP cc_start: 0.8439 (m-30) cc_final: 0.7938 (p0) REVERT: D 8 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8073 (t80) REVERT: D 323 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: E 12 ASP cc_start: 0.7007 (t0) cc_final: 0.6618 (t0) REVERT: E 62 GLU cc_start: 0.8750 (pm20) cc_final: 0.8501 (pm20) REVERT: H 79 MET cc_start: 0.8775 (mmm) cc_final: 0.8471 (tpp) REVERT: I 34 LYS cc_start: 0.8117 (tptt) cc_final: 0.7810 (tptt) REVERT: L 8 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8135 (tptt) REVERT: L 9 GLN cc_start: 0.8518 (mm-40) cc_final: 0.7928 (mp10) REVERT: O 58 GLN cc_start: 0.8970 (mm110) cc_final: 0.8643 (mp10) REVERT: O 92 TYR cc_start: 0.8209 (m-80) cc_final: 0.7968 (m-80) REVERT: O 263 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8165 (tm-30) REVERT: P 107 GLU cc_start: 0.8873 (pt0) cc_final: 0.8592 (tt0) REVERT: P 176 THR cc_start: 0.8867 (t) cc_final: 0.8526 (p) REVERT: Q 177 GLN cc_start: 0.9114 (tt0) cc_final: 0.8856 (tt0) REVERT: X 96 PHE cc_start: 0.5978 (t80) cc_final: 0.5268 (t80) REVERT: U 97 LYS cc_start: 0.8509 (tmtt) cc_final: 0.8185 (tmtt) REVERT: U 105 SER cc_start: 0.9005 (t) cc_final: 0.8713 (p) outliers start: 78 outliers final: 29 residues processed: 272 average time/residue: 0.6307 time to fit residues: 199.7295 Evaluate side-chains 221 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain W residue 96 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 123 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 255 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN L 38 ASN P 203 GLN Q 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.056803 restraints weight = 64098.960| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.18 r_work: 0.2720 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 25637 Z= 0.159 Angle : 0.589 7.983 35213 Z= 0.280 Chirality : 0.041 0.257 3542 Planarity : 0.004 0.054 4409 Dihedral : 16.150 156.091 4428 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.38 % Allowed : 13.71 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.16), residues: 2692 helix: 1.89 (0.13), residues: 1480 sheet: -0.02 (0.36), residues: 181 loop : -0.16 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 24 TYR 0.013 0.001 TYR P 143 PHE 0.021 0.001 PHE B 246 TRP 0.016 0.001 TRP A 131 HIS 0.005 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00372 (25599) covalent geometry : angle 0.58887 (35213) hydrogen bonds : bond 0.04462 ( 1246) hydrogen bonds : angle 4.63633 ( 3546) Misc. bond : bond 0.05231 ( 38) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 208 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8354 (mt) REVERT: B 14 ASN cc_start: 0.9394 (t0) cc_final: 0.9109 (OUTLIER) REVERT: B 246 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8896 (p90) REVERT: C 71 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8915 (mt-10) REVERT: C 158 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8183 (mm) REVERT: C 365 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8845 (tp) REVERT: C 451 ASP cc_start: 0.8485 (m-30) cc_final: 0.7993 (p0) REVERT: D 8 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8056 (t80) REVERT: E 12 ASP cc_start: 0.7113 (t0) cc_final: 0.6688 (t0) REVERT: E 62 GLU cc_start: 0.8813 (pm20) cc_final: 0.8580 (pm20) REVERT: H 79 MET cc_start: 0.8827 (mmm) cc_final: 0.8573 (tpp) REVERT: I 34 LYS cc_start: 0.8145 (tptt) cc_final: 0.7869 (tptt) REVERT: L 7 ASN cc_start: 0.8834 (m110) cc_final: 0.8499 (m-40) REVERT: L 8 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8160 (tptt) REVERT: L 9 GLN cc_start: 0.8583 (mm-40) cc_final: 0.7878 (mp10) REVERT: O 58 GLN cc_start: 0.8932 (mm110) cc_final: 0.8634 (mp10) REVERT: O 230 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8660 (tm) REVERT: P 107 GLU cc_start: 0.8929 (pt0) cc_final: 0.8680 (tt0) REVERT: P 176 THR cc_start: 0.8959 (t) cc_final: 0.8598 (p) REVERT: Q 177 GLN cc_start: 0.9110 (tt0) cc_final: 0.8845 (tt0) REVERT: X 96 PHE cc_start: 0.6084 (t80) cc_final: 0.5349 (t80) REVERT: U 97 LYS cc_start: 0.8577 (tmtt) cc_final: 0.8244 (tptt) REVERT: U 105 SER cc_start: 0.8992 (t) cc_final: 0.8781 (p) REVERT: U 107 LYS cc_start: 0.8722 (tptt) cc_final: 0.8471 (mmmt) REVERT: U 110 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8351 (tmm-80) REVERT: U 113 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6652 (pp) REVERT: W 86 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7863 (tm) REVERT: W 96 TRP cc_start: 0.8976 (OUTLIER) cc_final: 0.8449 (t-100) outliers start: 75 outliers final: 36 residues processed: 260 average time/residue: 0.6005 time to fit residues: 181.3779 Evaluate side-chains 237 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain X residue 90 ILE Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 110 ARG Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 96 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 211 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 251 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 ASN P 203 GLN Q 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.068044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.055241 restraints weight = 64636.899| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.18 r_work: 0.2682 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.276 25637 Z= 0.193 Angle : 0.608 9.834 35213 Z= 0.290 Chirality : 0.042 0.221 3542 Planarity : 0.005 0.055 4409 Dihedral : 15.636 146.529 4428 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.65 % Allowed : 14.25 % Favored : 82.10 % 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: 2692 helix: 1.83 (0.13), residues: 1481 sheet: -0.06 (0.35), residues: 191 loop : -0.15 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 223 TYR 0.014 0.001 TYR A 246 PHE 0.020 0.002 PHE B 246 TRP 0.016 0.001 TRP A 131 HIS 0.006 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00451 (25599) covalent geometry : angle 0.60782 (35213) hydrogen bonds : bond 0.04685 ( 1246) hydrogen bonds : angle 4.61905 ( 3546) Misc. bond : bond 0.05654 ( 38) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 194 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 14 ASN cc_start: 0.9389 (t0) cc_final: 0.9069 (OUTLIER) REVERT: B 246 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8872 (p90) REVERT: C 71 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8932 (mt-10) REVERT: C 158 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8211 (mm) REVERT: C 365 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8818 (tp) REVERT: C 451 ASP cc_start: 0.8529 (m-30) cc_final: 0.8080 (p0) REVERT: D 8 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7975 (t80) REVERT: D 323 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8498 (mt-10) REVERT: E 12 ASP cc_start: 0.7168 (t0) cc_final: 0.6729 (t0) REVERT: H 79 MET cc_start: 0.8843 (mmm) cc_final: 0.8082 (tpp) REVERT: I 34 LYS cc_start: 0.8204 (tptt) cc_final: 0.7971 (tptt) REVERT: L 8 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8408 (tptt) REVERT: L 9 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8340 (mm-40) REVERT: O 58 GLN cc_start: 0.9002 (mm110) cc_final: 0.8703 (mp10) REVERT: P 107 GLU cc_start: 0.8953 (pt0) cc_final: 0.8715 (tt0) REVERT: P 126 LYS cc_start: 0.9214 (mppt) cc_final: 0.8983 (mmmt) REVERT: P 176 THR cc_start: 0.8993 (t) cc_final: 0.8593 (p) REVERT: Q 118 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8626 (mptt) REVERT: Q 177 GLN cc_start: 0.9138 (tt0) cc_final: 0.8889 (tt0) REVERT: T 24 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8050 (ptt180) REVERT: U 97 LYS cc_start: 0.8659 (tmtt) cc_final: 0.8320 (tptt) REVERT: U 105 SER cc_start: 0.8974 (t) cc_final: 0.8753 (p) REVERT: U 110 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8666 (tpp80) REVERT: W 86 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7816 (tm) outliers start: 81 outliers final: 36 residues processed: 256 average time/residue: 0.6006 time to fit residues: 178.8768 Evaluate side-chains 233 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain X residue 90 ILE Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 110 ARG Chi-restraints excluded: chain W residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 36 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 160 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 GLN L 38 ASN Q 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.069300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.056442 restraints weight = 64239.076| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.20 r_work: 0.2714 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.219 25637 Z= 0.138 Angle : 0.564 9.162 35213 Z= 0.270 Chirality : 0.040 0.194 3542 Planarity : 0.004 0.055 4409 Dihedral : 15.090 128.768 4428 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.93 % Allowed : 15.55 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.16), residues: 2692 helix: 1.97 (0.13), residues: 1483 sheet: 0.10 (0.35), residues: 181 loop : -0.15 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 127 TYR 0.013 0.001 TYR A 246 PHE 0.019 0.001 PHE B 246 TRP 0.016 0.001 TRP A 131 HIS 0.004 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00315 (25599) covalent geometry : angle 0.56369 (35213) hydrogen bonds : bond 0.04165 ( 1246) hydrogen bonds : angle 4.45756 ( 3546) Misc. bond : bond 0.04718 ( 38) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 198 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8376 (mt) REVERT: B 246 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8836 (p90) REVERT: C 71 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8925 (mt-10) REVERT: C 158 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8232 (mm) REVERT: C 451 ASP cc_start: 0.8531 (m-30) cc_final: 0.8183 (p0) REVERT: D 8 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8280 (m-10) REVERT: E 12 ASP cc_start: 0.7218 (t0) cc_final: 0.6761 (t0) REVERT: E 59 ASP cc_start: 0.9449 (t0) cc_final: 0.9223 (t0) REVERT: E 77 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8282 (tmtt) REVERT: H 39 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8228 (mtmm) REVERT: H 79 MET cc_start: 0.8844 (mmm) cc_final: 0.8537 (tpp) REVERT: I 34 LYS cc_start: 0.8195 (tptt) cc_final: 0.7964 (tptt) REVERT: L 8 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8304 (tptt) REVERT: L 9 GLN cc_start: 0.8685 (mm-40) cc_final: 0.7632 (mp10) REVERT: O 58 GLN cc_start: 0.8878 (mm110) cc_final: 0.8592 (mp10) REVERT: O 230 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8806 (tm) REVERT: P 107 GLU cc_start: 0.8965 (pt0) cc_final: 0.8724 (tt0) REVERT: P 176 THR cc_start: 0.8926 (t) cc_final: 0.8623 (p) REVERT: Q 118 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8591 (mptt) REVERT: Q 174 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8102 (mt-10) REVERT: Q 177 GLN cc_start: 0.9108 (tt0) cc_final: 0.8841 (tt0) REVERT: U 97 LYS cc_start: 0.8668 (tmtt) cc_final: 0.8301 (tptt) outliers start: 65 outliers final: 31 residues processed: 246 average time/residue: 0.6184 time to fit residues: 177.5048 Evaluate side-chains 227 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain W residue 65 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 ASN D 61 HIS L 38 ASN Q 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.066979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.054078 restraints weight = 65261.065| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.21 r_work: 0.2652 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.291 25637 Z= 0.227 Angle : 0.631 8.756 35213 Z= 0.301 Chirality : 0.043 0.230 3542 Planarity : 0.005 0.056 4409 Dihedral : 15.280 121.298 4428 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.57 % Allowed : 16.14 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.16), residues: 2692 helix: 1.84 (0.13), residues: 1481 sheet: 0.20 (0.36), residues: 183 loop : -0.17 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 127 TYR 0.013 0.001 TYR O 157 PHE 0.021 0.002 PHE B 246 TRP 0.016 0.001 TRP A 131 HIS 0.007 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00535 (25599) covalent geometry : angle 0.63052 (35213) hydrogen bonds : bond 0.04793 ( 1246) hydrogen bonds : angle 4.59350 ( 3546) Misc. bond : bond 0.05981 ( 38) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8410 (mp) REVERT: B 73 GLN cc_start: 0.8238 (mt0) cc_final: 0.7682 (mt0) REVERT: B 246 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8837 (p90) REVERT: C 158 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8206 (mm) REVERT: C 451 ASP cc_start: 0.8579 (m-30) cc_final: 0.8183 (p0) REVERT: D 8 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8015 (t80) REVERT: D 323 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8527 (mt-10) REVERT: E 12 ASP cc_start: 0.7214 (t0) cc_final: 0.6782 (t0) REVERT: H 79 MET cc_start: 0.8857 (mmm) cc_final: 0.8580 (tpp) REVERT: I 34 LYS cc_start: 0.8195 (tptt) cc_final: 0.7991 (tptt) REVERT: L 8 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8545 (tptt) REVERT: L 9 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8361 (mm-40) REVERT: O 58 GLN cc_start: 0.9081 (mm110) cc_final: 0.8772 (mp10) REVERT: P 176 THR cc_start: 0.8877 (t) cc_final: 0.8591 (p) REVERT: Q 118 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8614 (mptt) REVERT: Q 177 GLN cc_start: 0.9149 (tt0) cc_final: 0.8915 (tt0) REVERT: T 24 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8284 (ptt180) REVERT: W 65 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7940 (ttm) outliers start: 57 outliers final: 33 residues processed: 237 average time/residue: 0.6342 time to fit residues: 174.5930 Evaluate side-chains 226 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 214 TYR Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain W residue 65 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 56 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 ASN L 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.066656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.053685 restraints weight = 65133.233| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.22 r_work: 0.2644 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.269 25637 Z= 0.224 Angle : 0.637 8.967 35213 Z= 0.306 Chirality : 0.043 0.229 3542 Planarity : 0.005 0.057 4409 Dihedral : 15.180 121.417 4428 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.52 % Allowed : 16.68 % Favored : 80.79 % 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: 1.34 (0.16), residues: 2692 helix: 1.75 (0.13), residues: 1484 sheet: 0.24 (0.37), residues: 183 loop : -0.20 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 225 TYR 0.014 0.001 TYR A 246 PHE 0.021 0.002 PHE B 246 TRP 0.016 0.001 TRP A 131 HIS 0.006 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00526 (25599) covalent geometry : angle 0.63747 (35213) hydrogen bonds : bond 0.04776 ( 1246) hydrogen bonds : angle 4.61448 ( 3546) Misc. bond : bond 0.05618 ( 38) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 73 GLN cc_start: 0.8254 (mt0) cc_final: 0.7680 (mt0) REVERT: B 246 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8938 (p90) REVERT: C 158 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8188 (mm) REVERT: C 451 ASP cc_start: 0.8598 (m-30) cc_final: 0.8176 (p0) REVERT: D 8 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8334 (m-10) REVERT: D 323 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: E 12 ASP cc_start: 0.7284 (t0) cc_final: 0.6843 (t0) REVERT: H 39 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8184 (mtmm) REVERT: H 79 MET cc_start: 0.8778 (mmm) cc_final: 0.8558 (tpp) REVERT: L 8 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8606 (tptt) REVERT: L 9 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8358 (mm-40) REVERT: M 20 SER cc_start: 0.8444 (t) cc_final: 0.8133 (m) REVERT: O 58 GLN cc_start: 0.9141 (mm110) cc_final: 0.8835 (mp10) REVERT: P 107 GLU cc_start: 0.8870 (pt0) cc_final: 0.8605 (tt0) REVERT: P 176 THR cc_start: 0.8861 (t) cc_final: 0.8553 (p) REVERT: Q 118 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8620 (mptt) REVERT: Q 174 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8092 (mt-10) REVERT: Q 177 GLN cc_start: 0.9138 (tt0) cc_final: 0.8903 (tt0) REVERT: X 96 PHE cc_start: 0.4893 (OUTLIER) cc_final: 0.3832 (t80) REVERT: W 65 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7983 (ttm) outliers start: 56 outliers final: 34 residues processed: 236 average time/residue: 0.6530 time to fit residues: 179.4894 Evaluate side-chains 228 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain D residue 8 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 214 TYR Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain P residue 183 THR Chi-restraints excluded: chain P residue 189 LEU Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain W residue 65 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 56 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 281 GLN C 403 ASN L 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.068464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.055538 restraints weight = 64672.987| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.24 r_work: 0.2689 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.204 25637 Z= 0.134 Angle : 0.591 9.420 35213 Z= 0.283 Chirality : 0.040 0.198 3542 Planarity : 0.004 0.056 4409 Dihedral : 14.755 120.178 4428 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.34 % Allowed : 17.36 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.16), residues: 2692 helix: 1.90 (0.13), residues: 1484 sheet: 0.48 (0.37), residues: 177 loop : -0.18 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 127 TYR 0.012 0.001 TYR A 254 PHE 0.018 0.001 PHE B 246 TRP 0.018 0.001 TRP A 131 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00308 (25599) covalent geometry : angle 0.59092 (35213) hydrogen bonds : bond 0.04204 ( 1246) hydrogen bonds : angle 4.45562 ( 3546) Misc. bond : bond 0.03981 ( 38) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8389 (mt) REVERT: B 73 GLN cc_start: 0.8302 (mt0) cc_final: 0.7732 (mt0) REVERT: B 246 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8821 (p90) REVERT: C 71 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8934 (mt-10) REVERT: C 158 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8202 (mm) REVERT: C 451 ASP cc_start: 0.8536 (m-30) cc_final: 0.8212 (p0) REVERT: E 12 ASP cc_start: 0.7321 (t0) cc_final: 0.6893 (t0) REVERT: L 8 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8554 (tptt) REVERT: L 9 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8370 (mm-40) REVERT: M 20 SER cc_start: 0.8432 (t) cc_final: 0.8123 (m) REVERT: O 58 GLN cc_start: 0.8992 (mm110) cc_final: 0.8699 (mp10) REVERT: P 107 GLU cc_start: 0.8906 (pt0) cc_final: 0.8669 (tt0) REVERT: P 176 THR cc_start: 0.8827 (t) cc_final: 0.8549 (p) REVERT: Q 118 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8602 (mptt) REVERT: Q 174 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8085 (mt-10) REVERT: Q 177 GLN cc_start: 0.9124 (tt0) cc_final: 0.8862 (tt0) REVERT: W 65 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7945 (ttm) outliers start: 52 outliers final: 32 residues processed: 238 average time/residue: 0.6491 time to fit residues: 180.1850 Evaluate side-chains 224 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain W residue 65 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 166 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 250 optimal weight: 30.0000 chunk 184 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 281 GLN C 403 ASN L 38 ASN P 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.055048 restraints weight = 64910.180| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.18 r_work: 0.2682 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.229 25637 Z= 0.163 Angle : 0.612 10.560 35213 Z= 0.292 Chirality : 0.041 0.208 3542 Planarity : 0.004 0.056 4409 Dihedral : 14.714 120.456 4428 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.03 % Allowed : 17.81 % Favored : 80.16 % 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: 1.46 (0.16), residues: 2692 helix: 1.87 (0.13), residues: 1485 sheet: 0.24 (0.37), residues: 183 loop : -0.17 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 177 TYR 0.013 0.001 TYR A 254 PHE 0.020 0.001 PHE B 246 TRP 0.017 0.001 TRP A 131 HIS 0.005 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00382 (25599) covalent geometry : angle 0.61225 (35213) hydrogen bonds : bond 0.04336 ( 1246) hydrogen bonds : angle 4.47266 ( 3546) Misc. bond : bond 0.04456 ( 38) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8427 (mp) REVERT: B 73 GLN cc_start: 0.8300 (mt0) cc_final: 0.7724 (mt0) REVERT: B 246 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8822 (p90) REVERT: C 71 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8938 (mt-10) REVERT: C 158 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8217 (mm) REVERT: C 451 ASP cc_start: 0.8512 (m-30) cc_final: 0.8174 (p0) REVERT: E 12 ASP cc_start: 0.7338 (t0) cc_final: 0.6903 (t0) REVERT: L 8 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8554 (tptt) REVERT: L 9 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8385 (mm-40) REVERT: O 58 GLN cc_start: 0.9011 (mm110) cc_final: 0.8709 (mp10) REVERT: P 107 GLU cc_start: 0.8903 (pt0) cc_final: 0.8656 (tt0) REVERT: P 176 THR cc_start: 0.8844 (t) cc_final: 0.8567 (p) REVERT: Q 118 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8627 (mptt) REVERT: Q 174 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8077 (mt-10) REVERT: Q 177 GLN cc_start: 0.9124 (tt0) cc_final: 0.8896 (tt0) REVERT: W 65 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7990 (ttm) REVERT: W 86 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7853 (tm) outliers start: 45 outliers final: 29 residues processed: 226 average time/residue: 0.6550 time to fit residues: 172.2940 Evaluate side-chains 219 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 262 PHE Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 229 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 ASN D 9 GLN L 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.055849 restraints weight = 64427.781| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.17 r_work: 0.2703 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.207 25637 Z= 0.135 Angle : 0.593 12.394 35213 Z= 0.283 Chirality : 0.040 0.196 3542 Planarity : 0.004 0.056 4409 Dihedral : 14.432 120.090 4428 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.85 % Allowed : 17.99 % Favored : 80.16 % 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: 1.53 (0.16), residues: 2692 helix: 1.94 (0.13), residues: 1481 sheet: 0.44 (0.37), residues: 177 loop : -0.19 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 127 TYR 0.013 0.001 TYR A 254 PHE 0.018 0.001 PHE B 246 TRP 0.018 0.001 TRP A 131 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00314 (25599) covalent geometry : angle 0.59261 (35213) hydrogen bonds : bond 0.04107 ( 1246) hydrogen bonds : angle 4.39958 ( 3546) Misc. bond : bond 0.03897 ( 38) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7513.81 seconds wall clock time: 129 minutes 23.16 seconds (7763.16 seconds total)