Starting phenix.real_space_refine on Mon Oct 26 06:21:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n9x_0382/10_2026/6n9x_0382_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n9x_0382/10_2026/6n9x_0382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6n9x_0382/10_2026/6n9x_0382_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n9x_0382/10_2026/6n9x_0382_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n9x_0382/10_2026/6n9x_0382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n9x_0382/10_2026/6n9x_0382.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 45 5.49 5 Mg 6 5.21 5 S 112 5.16 5 C 12237 2.51 5 N 3432 2.21 5 O 3825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19658 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2093 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3880 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 489} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3680 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 9, 'TRANS': 464} Chain breaks: 3 Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2086 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1861 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 236} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "H" Number of atoms: 5144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5144 Classifications: {'peptide': 645} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {'DOC': 1} Classifications: {'RNA': 5, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 4, None: 1} Not linked: pdbres=" G P 5 " pdbres="DOC P 6 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 506 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 1, ' ZN': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2162 SG CYS B 17 86.829 42.707 47.451 1.00 83.88 S ATOM 2184 SG CYS B 20 84.808 40.498 45.781 1.00 88.35 S ATOM 2297 SG CYS B 36 83.303 42.356 48.342 1.00 63.37 S ATOM 2322 SG CYS B 39 85.429 40.011 49.438 1.00 74.62 S Time building chain proxies: 4.31, per 1000 atoms: 0.22 Number of scatterers: 19658 At special positions: 0 Unit cell: (118.68, 129, 196.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 112 16.00 P 45 15.00 Mg 6 11.99 O 3825 8.00 N 3432 7.00 C 12237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 235 " - pdb=" SG CYS C 241 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 790.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 39 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 20 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 17 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 36 " Number of angles added : 6 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 17 sheets defined 36.8% alpha, 13.3% beta 5 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.892A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.818A pdb=" N THR A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 4.002A pdb=" N GLN A 364 " --> pdb=" O ARG A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.534A pdb=" N ILE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.946A pdb=" N ASP A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 379 through 384' Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.727A pdb=" N ASN A 388 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.632A pdb=" N GLU A 477 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 478 " --> pdb=" O HIS A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 478' Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.706A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 486 " --> pdb=" O ILE A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'B' and resid 87 through 95 removed outlier: 3.807A pdb=" N CYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 4.070A pdb=" N GLY B 103 " --> pdb=" O LYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.685A pdb=" N GLN B 198 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 199 " --> pdb=" O PHE B 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 195 through 199' Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.668A pdb=" N GLN B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 280 Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.708A pdb=" N LEU B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 removed outlier: 3.615A pdb=" N PHE B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.777A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 373 removed outlier: 3.584A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 386 removed outlier: 3.725A pdb=" N TRP B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 removed outlier: 3.550A pdb=" N ALA B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 454 Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'C' and resid 87 through 95 removed outlier: 3.737A pdb=" N CYS C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 168 removed outlier: 4.039A pdb=" N LEU C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 191 removed outlier: 3.618A pdb=" N THR C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 199 removed outlier: 3.923A pdb=" N GLN C 198 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C 199 " --> pdb=" O PHE C 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 199' Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 237 through 244 removed outlier: 3.741A pdb=" N CYS C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.926A pdb=" N TRP C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 279 removed outlier: 3.601A pdb=" N LEU C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.717A pdb=" N THR C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 345 through 350' Processing helix chain 'C' and resid 351 through 358 removed outlier: 4.128A pdb=" N GLY C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 removed outlier: 3.919A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 removed outlier: 4.049A pdb=" N GLN C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 removed outlier: 3.704A pdb=" N ALA C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.520A pdb=" N ILE C 428 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 457 removed outlier: 4.124A pdb=" N MET C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 removed outlier: 4.194A pdb=" N GLY C 478 " --> pdb=" O HIS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 3.621A pdb=" N ASP C 485 " --> pdb=" O SER C 482 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C 486 " --> pdb=" O ILE C 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 482 through 486' Processing helix chain 'D' and resid 271 through 279 removed outlier: 3.833A pdb=" N LEU D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 299 Processing helix chain 'D' and resid 317 through 331 removed outlier: 3.611A pdb=" N GLN D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 removed outlier: 3.588A pdb=" N THR D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 376 removed outlier: 3.652A pdb=" N ILE D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 removed outlier: 3.890A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 417 Processing helix chain 'D' and resid 440 through 457 removed outlier: 3.554A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 removed outlier: 3.545A pdb=" N GLU D 477 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY D 478 " --> pdb=" O HIS D 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 474 through 478' Processing helix chain 'E' and resid 294 through 299 Processing helix chain 'E' and resid 317 through 328 removed outlier: 3.503A pdb=" N GLN E 325 " --> pdb=" O PHE E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.811A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN E 358 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.604A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 386 removed outlier: 4.143A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 415 Processing helix chain 'E' and resid 440 through 457 removed outlier: 3.637A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 478 removed outlier: 3.992A pdb=" N GLY E 478 " --> pdb=" O HIS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 494 removed outlier: 3.855A pdb=" N ARG E 493 " --> pdb=" O GLY E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'H' and resid 38 through 52 Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.508A pdb=" N LYS H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 124 through 132 Processing helix chain 'H' and resid 138 through 151 Processing helix chain 'H' and resid 165 through 186 removed outlier: 3.830A pdb=" N LYS H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 231 removed outlier: 3.576A pdb=" N GLU H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 246 removed outlier: 3.889A pdb=" N LEU H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 259 removed outlier: 4.032A pdb=" N GLU H 259 " --> pdb=" O ARG H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 348 Processing helix chain 'H' and resid 378 through 400 removed outlier: 4.480A pdb=" N ASP H 384 " --> pdb=" O GLN H 380 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 409 removed outlier: 3.638A pdb=" N ARG H 408 " --> pdb=" O ALA H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 453 Processing helix chain 'H' and resid 478 through 488 removed outlier: 3.628A pdb=" N ALA H 485 " --> pdb=" O LEU H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 514 removed outlier: 3.989A pdb=" N LYS H 508 " --> pdb=" O ASP H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 530 removed outlier: 3.683A pdb=" N TYR H 526 " --> pdb=" O LYS H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 555 removed outlier: 4.027A pdb=" N LYS H 552 " --> pdb=" O GLY H 548 " (cutoff:3.500A) Processing helix chain 'H' and resid 561 through 573 Processing helix chain 'H' and resid 608 through 637 removed outlier: 4.088A pdb=" N SER H 616 " --> pdb=" O THR H 612 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 617 " --> pdb=" O LEU H 613 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU H 620 " --> pdb=" O SER H 616 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE H 621 " --> pdb=" O ALA H 617 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS H 622 " --> pdb=" O GLY H 618 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE H 627 " --> pdb=" O LYS H 623 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU H 630 " --> pdb=" O ILE H 626 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU H 633 " --> pdb=" O THR H 629 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU H 635 " --> pdb=" O GLU H 631 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY H 637 " --> pdb=" O LEU H 633 " (cutoff:3.500A) Processing helix chain 'H' and resid 662 through 684 removed outlier: 4.573A pdb=" N GLN H 674 " --> pdb=" O ILE H 670 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU H 675 " --> pdb=" O GLU H 671 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP H 684 " --> pdb=" O VAL H 680 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.225A pdb=" N GLU B 306 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL B 462 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE B 308 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N CYS B 464 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL B 310 " --> pdb=" O CYS B 464 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 498 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 543 through 544 removed outlier: 7.096A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 307 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE A 500 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET A 309 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU A 502 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR A 311 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ARG A 504 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 393 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL F 266 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 15 removed outlier: 3.918A pdb=" N TYR B 13 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.533A pdb=" N SER B 120 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 133 " --> pdb=" O GLN B 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 123 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 175 through 177 removed outlier: 7.885A pdb=" N VAL B 176 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL B 154 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE B 153 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE B 202 " --> pdb=" O ARG B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 266 through 267 removed outlier: 3.658A pdb=" N VAL B 266 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 337 " --> pdb=" O HIS C 392 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE C 308 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY C 531 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE C 518 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE C 529 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.561A pdb=" N SER C 120 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 175 through 176 removed outlier: 6.047A pdb=" N VAL C 154 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 265 through 267 removed outlier: 6.571A pdb=" N VAL D 337 " --> pdb=" O HIS D 392 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N TYR D 394 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER D 312 " --> pdb=" O CYS D 464 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL D 307 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE D 500 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET D 309 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU D 502 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR D 311 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 543 " --> pdb=" O GLU D 534 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 265 through 267 removed outlier: 3.722A pdb=" N VAL D 266 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR E 394 " --> pdb=" O LEU E 339 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY E 338 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL E 310 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS E 464 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL E 307 " --> pdb=" O THR E 498 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE E 500 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET E 309 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU E 502 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR E 311 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY E 528 " --> pdb=" O ILE E 518 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.148A pdb=" N GLY H 21 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE H 2 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE H 56 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 232 through 233 Processing sheet with id=AB4, first strand: chain 'H' and resid 264 through 267 Processing sheet with id=AB5, first strand: chain 'H' and resid 419 through 421 Processing sheet with id=AB6, first strand: chain 'H' and resid 646 through 651 removed outlier: 7.106A pdb=" N GLN H 657 " --> pdb=" O MET H 649 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 574 through 579 removed outlier: 3.928A pdb=" N SER H 576 " --> pdb=" O LYS H 587 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 592 through 594 644 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue (no planarity definition) Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3278 1.31 - 1.44: 5265 1.44 - 1.56: 11238 1.56 - 1.69: 82 1.69 - 1.82: 182 Bond restraints: 20045 Sorted by residual: bond pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " ideal model delta sigma weight residual 1.748 1.591 0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" O3B TTP C 700 " pdb=" PG TTP C 700 " ideal model delta sigma weight residual 1.748 1.591 0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" O3B TTP B 602 " pdb=" PG TTP B 602 " ideal model delta sigma weight residual 1.748 1.593 0.155 2.00e-02 2.50e+03 5.97e+01 bond pdb=" O3B TTP H 801 " pdb=" PG TTP H 801 " ideal model delta sigma weight residual 1.748 1.599 0.149 2.00e-02 2.50e+03 5.51e+01 bond pdb=" O3B TTP E 700 " pdb=" PG TTP E 700 " ideal model delta sigma weight residual 1.748 1.600 0.148 2.00e-02 2.50e+03 5.45e+01 ... (remaining 20040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 26761 2.90 - 5.80: 305 5.80 - 8.70: 39 8.70 - 11.60: 23 11.60 - 14.50: 23 Bond angle restraints: 27151 Sorted by residual: angle pdb=" O4' DT T2037 " pdb=" C4' DT T2037 " pdb=" C3' DT T2037 " ideal model delta sigma weight residual 106.00 102.51 3.49 6.00e-01 2.78e+00 3.39e+01 angle pdb=" O4' DT T2039 " pdb=" C4' DT T2039 " pdb=" C3' DT T2039 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.34e+01 angle pdb=" C ASN A 388 " pdb=" N ASP A 389 " pdb=" CA ASP A 389 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C2 TTP D 700 " pdb=" N3 TTP D 700 " pdb=" C4 TTP D 700 " ideal model delta sigma weight residual 128.28 113.78 14.50 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C2 TTP B 602 " pdb=" N3 TTP B 602 " pdb=" C4 TTP B 602 " ideal model delta sigma weight residual 128.28 113.84 14.44 3.00e+00 1.11e-01 2.32e+01 ... (remaining 27146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 11238 18.09 - 36.19: 528 36.19 - 54.28: 155 54.28 - 72.38: 63 72.38 - 90.47: 9 Dihedral angle restraints: 11993 sinusoidal: 5167 harmonic: 6826 Sorted by residual: dihedral pdb=" CD ARG H 604 " pdb=" NE ARG H 604 " pdb=" CZ ARG H 604 " pdb=" NH1 ARG H 604 " ideal model delta sinusoidal sigma weight residual 0.00 -73.14 73.14 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CD ARG E 323 " pdb=" NE ARG E 323 " pdb=" CZ ARG E 323 " pdb=" NH1 ARG E 323 " ideal model delta sinusoidal sigma weight residual 0.00 72.85 -72.85 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CA TYR H 64 " pdb=" C TYR H 64 " pdb=" N ASP H 65 " pdb=" CA ASP H 65 " ideal model delta harmonic sigma weight residual -180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 11990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2566 0.075 - 0.151: 393 0.151 - 0.226: 28 0.226 - 0.302: 7 0.302 - 0.377: 1 Chirality restraints: 2995 Sorted by residual: chirality pdb=" CB ILE C 261 " pdb=" CA ILE C 261 " pdb=" CG1 ILE C 261 " pdb=" CG2 ILE C 261 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C4' TTP D 700 " pdb=" C3' TTP D 700 " pdb=" C5' TTP D 700 " pdb=" O4' TTP D 700 " both_signs ideal model delta sigma weight residual False -2.46 -2.76 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C4' TTP B 602 " pdb=" C3' TTP B 602 " pdb=" C5' TTP B 602 " pdb=" O4' TTP B 602 " both_signs ideal model delta sigma weight residual False -2.46 -2.74 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 2992 not shown) Planarity restraints: 3357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 604 " 1.051 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG H 604 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG H 604 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 604 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG H 604 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 323 " -1.047 9.50e-02 1.11e+02 4.69e-01 1.33e+02 pdb=" NE ARG E 323 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG E 323 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 323 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG E 323 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 229 " -0.575 9.50e-02 1.11e+02 2.58e-01 4.06e+01 pdb=" NE ARG C 229 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG C 229 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 229 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 229 " -0.019 2.00e-02 2.50e+03 ... (remaining 3354 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 301 2.68 - 3.24: 16655 3.24 - 3.79: 28691 3.79 - 4.35: 38060 4.35 - 4.90: 62997 Nonbonded interactions: 146704 Sorted by model distance: nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.131 2.170 nonbonded pdb=" O2B TTP E 700 " pdb="MG MG E 701 " model vdw 2.184 2.170 nonbonded pdb=" O1G TTP B 602 " pdb="MG MG B 603 " model vdw 2.185 2.170 nonbonded pdb=" OG SER C 319 " pdb="MG MG C 701 " model vdw 2.191 2.170 nonbonded pdb=" OD2 ASP H 654 " pdb="MG MG H 802 " model vdw 2.202 2.170 ... (remaining 146699 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 545)) selection = (chain 'D' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 through 545)) selection = (chain 'E' and resid 285 through 545) } ncs_group { reference = (chain 'B' and (resid 65 through 506 or resid 510 through 547 or resid 602 throu \ gh 603)) selection = (chain 'C' and (resid 65 through 208 or resid 219 through 396 or resid 402 throu \ gh 431 or resid 436 through 701)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.020 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.241 20051 Z= 0.332 Angle : 0.954 16.541 27159 Z= 0.508 Chirality : 0.054 0.377 2995 Planarity : 0.015 0.471 3357 Dihedral : 12.770 90.474 7622 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 0.60 % Allowed : 3.62 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -4.04 (0.13), residues: 2367 helix: -3.02 (0.12), residues: 838 sheet: -1.22 (0.27), residues: 372 loop : -2.90 (0.14), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.013 0.001 TYR H 648 PHE 0.024 0.002 PHE H 686 TRP 0.046 0.002 TRP H 700 HIS 0.009 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.32 (20045) covalent geometry : angle 0.94536 / 0.51 (27151) SS BOND : bond 0.00013 / 0.01 ( 1) SS BOND : angle 1.44315 / 0.63 ( 2) hydrogen bonds : bond 0.15937 / 10.47 ( 656) hydrogen bonds : angle 6.92037 / 4.80 ( 1875) metal coordination : bond 0.16909 / 12.75 ( 4) metal coordination : angle 8.59010 / 3.74 ( 6) Misc. bond : bond 0.04214 / 2.63 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 686 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 GLN cc_start: 0.6865 (mm-40) cc_final: 0.6043 (mm-40) REVERT: A 347 GLU cc_start: 0.7261 (mp0) cc_final: 0.6891 (mt-10) REVERT: A 539 THR cc_start: 0.7350 (p) cc_final: 0.7118 (p) REVERT: B 255 TRP cc_start: 0.7885 (m100) cc_final: 0.7658 (m100) REVERT: B 309 MET cc_start: 0.8748 (tpp) cc_final: 0.8276 (tpp) REVERT: B 329 TRP cc_start: 0.7546 (m-10) cc_final: 0.7256 (m-10) REVERT: B 424 ASP cc_start: 0.8259 (t0) cc_final: 0.8037 (p0) REVERT: C 105 MET cc_start: 0.7782 (mmm) cc_final: 0.7403 (mmp) REVERT: C 117 ASN cc_start: 0.5633 (m110) cc_final: 0.5030 (p0) REVERT: C 236 LYS cc_start: 0.8513 (tmtt) cc_final: 0.8087 (mmmm) REVERT: C 249 GLU cc_start: 0.7439 (mp0) cc_final: 0.7044 (mp0) REVERT: C 314 SER cc_start: 0.9114 (m) cc_final: 0.8850 (p) REVERT: C 425 HIS cc_start: 0.8299 (t-90) cc_final: 0.8053 (t-90) REVERT: C 476 GLU cc_start: 0.7132 (mp0) cc_final: 0.6824 (mp0) REVERT: D 352 ASP cc_start: 0.8175 (t0) cc_final: 0.7706 (t0) REVERT: D 494 GLN cc_start: 0.7910 (mt0) cc_final: 0.7443 (mt0) REVERT: E 323 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6780 (mtt180) REVERT: E 356 LEU cc_start: 0.8213 (tp) cc_final: 0.7969 (tp) REVERT: H 6 ILE cc_start: 0.8969 (tt) cc_final: 0.8650 (tt) REVERT: H 75 LEU cc_start: 0.8506 (mt) cc_final: 0.8276 (tp) REVERT: H 90 ASP cc_start: 0.9253 (t0) cc_final: 0.8691 (t70) REVERT: H 101 ASN cc_start: 0.7657 (p0) cc_final: 0.7319 (p0) REVERT: H 626 ILE cc_start: 0.9384 (pt) cc_final: 0.8971 (tp) REVERT: H 649 MET cc_start: 0.8077 (mtm) cc_final: 0.7847 (mtt) REVERT: H 669 VAL cc_start: 0.8254 (t) cc_final: 0.8049 (p) outliers start: 12 outliers final: 0 residues processed: 691 average time/residue: 0.1663 time to fit residues: 165.8467 Evaluate side-chains 323 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 322 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.0370 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN B 169 GLN B 198 GLN B 256 ASN B 278 HIS B 296 ASN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN C 296 ASN C 325 GLN C 358 ASN C 392 HIS ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS D 278 HIS D 325 GLN D 343 GLN D 507 GLN E 325 GLN E 425 HIS H 62 HIS H 150 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN H 439 GLN H 450 GLN H 520 ASN H 615 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.141476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117067 restraints weight = 41364.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118305 restraints weight = 31919.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119789 restraints weight = 22734.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119934 restraints weight = 18698.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120133 restraints weight = 17656.237| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20051 Z= 0.136 Angle : 0.596 8.615 27159 Z= 0.314 Chirality : 0.044 0.165 2995 Planarity : 0.005 0.071 3357 Dihedral : 11.587 85.045 3120 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.15 % Allowed : 3.18 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -2.83 (0.15), residues: 2367 helix: -1.39 (0.16), residues: 824 sheet: -1.20 (0.26), residues: 379 loop : -2.48 (0.15), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 604 TYR 0.023 0.001 TYR C 411 PHE 0.015 0.002 PHE A 378 TRP 0.020 0.001 TRP B 69 HIS 0.006 0.001 HIS E 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (20045) covalent geometry : angle 0.59458 / 0.31 (27151) SS BOND : bond 0.00176 / 0.11 ( 1) SS BOND : angle 1.52614 / 0.71 ( 2) hydrogen bonds : bond 0.04474 / 2.95 ( 656) hydrogen bonds : angle 5.03145 / 3.51 ( 1875) metal coordination : bond 0.00386 / 0.20 ( 4) metal coordination : angle 2.51041 / 1.32 ( 6) Misc. bond : bond 0.00276 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 433 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5818 (ttm) cc_final: 0.5413 (ttm) REVERT: A 392 HIS cc_start: 0.7589 (m-70) cc_final: 0.7346 (m-70) REVERT: A 526 ASP cc_start: 0.7211 (m-30) cc_final: 0.5828 (t0) REVERT: A 539 THR cc_start: 0.7549 (p) cc_final: 0.7253 (p) REVERT: A 543 GLU cc_start: 0.7868 (mp0) cc_final: 0.7611 (mp0) REVERT: B 205 MET cc_start: 0.8963 (tpp) cc_final: 0.7930 (mtt) REVERT: B 255 TRP cc_start: 0.7932 (m100) cc_final: 0.7625 (m100) REVERT: B 309 MET cc_start: 0.8625 (tpp) cc_final: 0.8308 (tpp) REVERT: B 329 TRP cc_start: 0.7460 (m-10) cc_final: 0.7256 (m-10) REVERT: C 105 MET cc_start: 0.7783 (mmm) cc_final: 0.7440 (mmp) REVERT: C 117 ASN cc_start: 0.5579 (m110) cc_final: 0.4914 (p0) REVERT: C 126 LYS cc_start: 0.7130 (mttt) cc_final: 0.6910 (mmtp) REVERT: C 203 ILE cc_start: 0.9500 (mm) cc_final: 0.9287 (mm) REVERT: C 236 LYS cc_start: 0.8599 (tmtt) cc_final: 0.8235 (mmmm) REVERT: C 333 MET cc_start: 0.8284 (mpp) cc_final: 0.7795 (mpp) REVERT: C 476 GLU cc_start: 0.7154 (mp0) cc_final: 0.6846 (mp0) REVERT: D 352 ASP cc_start: 0.8003 (t0) cc_final: 0.7616 (t0) REVERT: D 404 ARG cc_start: 0.7178 (ptt-90) cc_final: 0.6951 (ptt90) REVERT: D 494 GLN cc_start: 0.7693 (mt0) cc_final: 0.7438 (mt0) REVERT: E 292 CYS cc_start: 0.7218 (p) cc_final: 0.6955 (p) REVERT: E 356 LEU cc_start: 0.8124 (tp) cc_final: 0.7879 (tp) REVERT: H 75 LEU cc_start: 0.8564 (mt) cc_final: 0.8287 (tp) REVERT: H 101 ASN cc_start: 0.7444 (p0) cc_final: 0.7079 (p0) REVERT: H 168 MET cc_start: 0.8108 (mmm) cc_final: 0.7838 (tpt) REVERT: H 253 LEU cc_start: 0.8199 (mt) cc_final: 0.7912 (mt) REVERT: H 335 ASN cc_start: 0.8401 (t0) cc_final: 0.8195 (t0) REVERT: H 626 ILE cc_start: 0.9261 (pt) cc_final: 0.8903 (tp) outliers start: 3 outliers final: 0 residues processed: 435 average time/residue: 0.1412 time to fit residues: 94.3140 Evaluate side-chains 283 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: [197, 45, 180, 39, 181, 63, 237, 28, 186, 142, 134] chunk 197 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 39 optimal weight: 0.0470 chunk 181 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 28 optimal weight: 0.0170 chunk 186 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN B 136 HIS B 145 HIS B 169 GLN B 343 GLN B 358 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 358 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS E 506 GLN E 512 ASN H 173 GLN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 509 ASN H 611 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119529 restraints weight = 42194.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120175 restraints weight = 38638.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121216 restraints weight = 33556.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121427 restraints weight = 25617.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121675 restraints weight = 24710.549| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20051 Z= 0.115 Angle : 0.534 8.032 27159 Z= 0.283 Chirality : 0.043 0.176 2995 Planarity : 0.003 0.051 3357 Dihedral : 11.324 85.534 3120 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -2.17 (0.16), residues: 2367 helix: -0.60 (0.18), residues: 829 sheet: -1.05 (0.25), residues: 401 loop : -2.24 (0.16), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 429 TYR 0.011 0.001 TYR A 532 PHE 0.017 0.001 PHE B 378 TRP 0.015 0.001 TRP C 97 HIS 0.007 0.001 HIS E 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (20045) covalent geometry : angle 0.53288 / 0.28 (27151) SS BOND : bond 0.00189 / 0.12 ( 1) SS BOND : angle 1.45094 / 0.68 ( 2) hydrogen bonds : bond 0.03676 / 2.45 ( 656) hydrogen bonds : angle 4.60498 / 3.21 ( 1875) metal coordination : bond 0.00522 / 0.32 ( 4) metal coordination : angle 2.22256 / 0.95 ( 6) Misc. bond : bond 0.00183 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 398 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5957 (ttm) cc_final: 0.5594 (ttm) REVERT: A 424 ASP cc_start: 0.7312 (t0) cc_final: 0.7041 (t0) REVERT: A 448 LYS cc_start: 0.7316 (mmtp) cc_final: 0.7030 (mmtp) REVERT: A 526 ASP cc_start: 0.7059 (m-30) cc_final: 0.5779 (t0) REVERT: B 112 ARG cc_start: 0.8811 (mtt90) cc_final: 0.8571 (mtt-85) REVERT: B 255 TRP cc_start: 0.8015 (m100) cc_final: 0.7627 (m100) REVERT: B 309 MET cc_start: 0.8538 (tpp) cc_final: 0.8309 (tpp) REVERT: B 329 TRP cc_start: 0.7545 (m-10) cc_final: 0.7259 (m-10) REVERT: C 105 MET cc_start: 0.7725 (mmm) cc_final: 0.7450 (mmp) REVERT: C 117 ASN cc_start: 0.5510 (m110) cc_final: 0.4978 (p0) REVERT: C 126 LYS cc_start: 0.6942 (mttt) cc_final: 0.6741 (mmtp) REVERT: C 162 MET cc_start: 0.7727 (tmm) cc_final: 0.7354 (tmm) REVERT: C 166 MET cc_start: 0.8132 (mtp) cc_final: 0.7898 (ttm) REVERT: C 203 ILE cc_start: 0.9537 (mm) cc_final: 0.9260 (mm) REVERT: C 236 LYS cc_start: 0.8682 (tmtt) cc_final: 0.8193 (mmmm) REVERT: C 306 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8121 (mt-10) REVERT: C 333 MET cc_start: 0.8364 (mpp) cc_final: 0.7742 (mpp) REVERT: C 352 ASP cc_start: 0.7544 (m-30) cc_final: 0.6770 (m-30) REVERT: D 352 ASP cc_start: 0.7941 (t0) cc_final: 0.7589 (t0) REVERT: D 494 GLN cc_start: 0.7809 (mt0) cc_final: 0.7464 (mt0) REVERT: E 295 ILE cc_start: 0.8413 (mm) cc_final: 0.8115 (mm) REVERT: H 75 LEU cc_start: 0.8561 (mt) cc_final: 0.8207 (tp) REVERT: H 101 ASN cc_start: 0.7396 (p0) cc_final: 0.7057 (p0) REVERT: H 125 LEU cc_start: 0.8554 (tp) cc_final: 0.8263 (tp) REVERT: H 168 MET cc_start: 0.8091 (mmm) cc_final: 0.7857 (tpt) REVERT: H 458 GLU cc_start: 0.7429 (pm20) cc_final: 0.7122 (pt0) REVERT: H 626 ILE cc_start: 0.9233 (pt) cc_final: 0.8931 (tp) outliers start: 2 outliers final: 0 residues processed: 399 average time/residue: 0.1338 time to fit residues: 83.9908 Evaluate side-chains 266 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: [116, 230, 152, 199, 223, 194, 107, 160, 40, 148, 19] chunk 116 optimal weight: 0.4980 chunk 230 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.0870 chunk 160 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 148 optimal weight: 0.0470 chunk 19 optimal weight: 5.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN B 169 GLN B 198 GLN B 358 ASN C 465 HIS D 343 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 509 ASN H 653 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.118837 restraints weight = 42165.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119095 restraints weight = 41064.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120257 restraints weight = 35979.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.120574 restraints weight = 27121.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120814 restraints weight = 24706.822| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20051 Z= 0.103 Angle : 0.519 7.992 27159 Z= 0.272 Chirality : 0.042 0.168 2995 Planarity : 0.003 0.053 3357 Dihedral : 11.074 85.362 3120 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.15 % Allowed : 2.28 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.79 (0.17), residues: 2367 helix: -0.15 (0.18), residues: 833 sheet: -0.96 (0.25), residues: 424 loop : -2.10 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 413 TYR 0.016 0.001 TYR C 193 PHE 0.018 0.001 PHE B 378 TRP 0.013 0.001 TRP C 97 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (20045) covalent geometry : angle 0.51814 / 0.27 (27151) SS BOND : bond 0.00145 / 0.09 ( 1) SS BOND : angle 1.50497 / 0.68 ( 2) hydrogen bonds : bond 0.03319 / 2.22 ( 656) hydrogen bonds : angle 4.40690 / 3.07 ( 1875) metal coordination : bond 0.00380 / 0.23 ( 4) metal coordination : angle 1.94186 / 0.83 ( 6) Misc. bond : bond 0.00098 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 371 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5996 (ttm) cc_final: 0.5548 (ttm) REVERT: A 359 ARG cc_start: 0.7035 (mmt-90) cc_final: 0.6736 (tpp-160) REVERT: A 392 HIS cc_start: 0.7418 (m-70) cc_final: 0.7141 (m90) REVERT: A 448 LYS cc_start: 0.7256 (mmtp) cc_final: 0.6929 (mmtp) REVERT: A 526 ASP cc_start: 0.7142 (m-30) cc_final: 0.5853 (t0) REVERT: B 112 ARG cc_start: 0.8746 (mtt90) cc_final: 0.8476 (mtt-85) REVERT: B 167 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8213 (mm-30) REVERT: B 309 MET cc_start: 0.8543 (tpp) cc_final: 0.8257 (tpp) REVERT: B 329 TRP cc_start: 0.7538 (m-10) cc_final: 0.7249 (m-10) REVERT: C 117 ASN cc_start: 0.5513 (m110) cc_final: 0.4934 (p0) REVERT: C 126 LYS cc_start: 0.7000 (mttt) cc_final: 0.6799 (mmtp) REVERT: C 166 MET cc_start: 0.8202 (mtp) cc_final: 0.7847 (ttm) REVERT: C 203 ILE cc_start: 0.9555 (mm) cc_final: 0.9264 (mm) REVERT: C 236 LYS cc_start: 0.8645 (tmtt) cc_final: 0.8169 (mmmm) REVERT: C 306 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8094 (mt-10) REVERT: C 333 MET cc_start: 0.8387 (mpp) cc_final: 0.7734 (mpp) REVERT: D 352 ASP cc_start: 0.7988 (t0) cc_final: 0.7613 (t0) REVERT: E 295 ILE cc_start: 0.8335 (mm) cc_final: 0.8023 (mm) REVERT: H 75 LEU cc_start: 0.8511 (mt) cc_final: 0.8158 (tp) REVERT: H 101 ASN cc_start: 0.7394 (p0) cc_final: 0.7068 (p0) REVERT: H 168 MET cc_start: 0.8081 (mmm) cc_final: 0.7852 (mmm) REVERT: H 335 ASN cc_start: 0.8498 (t0) cc_final: 0.8221 (t0) REVERT: H 458 GLU cc_start: 0.7604 (pm20) cc_final: 0.7111 (pt0) REVERT: H 626 ILE cc_start: 0.9245 (pt) cc_final: 0.8939 (tp) outliers start: 3 outliers final: 1 residues processed: 373 average time/residue: 0.1338 time to fit residues: 78.4467 Evaluate side-chains 261 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: [72, 194, 209, 89, 145, 84, 28, 162, 31, 7, 18] chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 89 optimal weight: 0.0270 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 31 optimal weight: 0.0270 chunk 7 optimal weight: 0.0010 chunk 18 optimal weight: 3.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 475 HIS C 246 HIS ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 ASN H 439 GLN H 509 ASN H 653 HIS H 674 GLN H 683 HIS H 704 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.137016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114720 restraints weight = 42414.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115405 restraints weight = 41951.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116373 restraints weight = 32794.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117086 restraints weight = 24967.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117392 restraints weight = 23185.451| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20051 Z= 0.148 Angle : 0.552 8.287 27159 Z= 0.290 Chirality : 0.044 0.176 2995 Planarity : 0.003 0.050 3357 Dihedral : 11.019 85.272 3120 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.59 (0.17), residues: 2367 helix: 0.10 (0.18), residues: 843 sheet: -0.96 (0.25), residues: 425 loop : -2.03 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 493 TYR 0.016 0.001 TYR C 78 PHE 0.022 0.002 PHE H 143 TRP 0.021 0.001 TRP C 97 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (20045) covalent geometry : angle 0.55113 / 0.29 (27151) SS BOND : bond 0.00020 / 0.01 ( 1) SS BOND : angle 2.10034 / 0.87 ( 2) hydrogen bonds : bond 0.03651 / 2.46 ( 656) hydrogen bonds : angle 4.30115 / 3.00 ( 1875) metal coordination : bond 0.00513 / 0.36 ( 4) metal coordination : angle 1.94890 / 0.85 ( 6) Misc. bond : bond 0.00043 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5931 (ttm) cc_final: 0.5511 (ttm) REVERT: A 526 ASP cc_start: 0.7179 (m-30) cc_final: 0.5898 (t0) REVERT: B 309 MET cc_start: 0.8653 (tpp) cc_final: 0.8245 (tpp) REVERT: B 329 TRP cc_start: 0.7589 (m-10) cc_final: 0.7230 (m-10) REVERT: C 117 ASN cc_start: 0.5497 (m110) cc_final: 0.4926 (p0) REVERT: C 203 ILE cc_start: 0.9589 (mm) cc_final: 0.9290 (mm) REVERT: C 236 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8200 (mmmm) REVERT: C 306 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8070 (mt-10) REVERT: C 333 MET cc_start: 0.8499 (mpp) cc_final: 0.7796 (mpp) REVERT: D 352 ASP cc_start: 0.7999 (t0) cc_final: 0.7614 (t0) REVERT: E 295 ILE cc_start: 0.8330 (mm) cc_final: 0.8000 (mm) REVERT: H 75 LEU cc_start: 0.8581 (mt) cc_final: 0.8132 (tp) REVERT: H 101 ASN cc_start: 0.7384 (p0) cc_final: 0.7056 (p0) REVERT: H 125 LEU cc_start: 0.8669 (tp) cc_final: 0.8378 (tp) REVERT: H 168 MET cc_start: 0.8172 (mmm) cc_final: 0.7947 (tpt) REVERT: H 217 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6978 (mm-30) REVERT: H 335 ASN cc_start: 0.8543 (t0) cc_final: 0.8341 (t0) REVERT: H 458 GLU cc_start: 0.7794 (pm20) cc_final: 0.7176 (pt0) REVERT: H 626 ILE cc_start: 0.9257 (pt) cc_final: 0.8962 (tp) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1256 time to fit residues: 69.3129 Evaluate side-chains 243 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: [150, 107, 87, 1, 108, 171, 187, 141, 223, 129, 75] chunk 150 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 0.0060 chunk 108 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 223 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 198 GLN B 358 ASN ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115171 restraints weight = 42280.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116131 restraints weight = 41677.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117099 restraints weight = 32646.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117807 restraints weight = 25648.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117978 restraints weight = 23891.786| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20051 Z= 0.111 Angle : 0.514 7.432 27159 Z= 0.270 Chirality : 0.042 0.173 2995 Planarity : 0.003 0.052 3357 Dihedral : 10.940 85.178 3120 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.05 % Allowed : 1.64 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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 (0.17), residues: 2367 helix: 0.31 (0.19), residues: 849 sheet: -0.91 (0.25), residues: 426 loop : -1.95 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 323 TYR 0.018 0.001 TYR C 193 PHE 0.033 0.001 PHE B 142 TRP 0.036 0.001 TRP B 147 HIS 0.005 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (20045) covalent geometry : angle 0.51311 / 0.27 (27151) SS BOND : bond 0.00165 / 0.10 ( 1) SS BOND : angle 1.14018 / 0.53 ( 2) hydrogen bonds : bond 0.03342 / 2.25 ( 656) hydrogen bonds : angle 4.22070 / 2.95 ( 1875) metal coordination : bond 0.00345 / 0.22 ( 4) metal coordination : angle 1.81724 / 0.76 ( 6) Misc. bond : bond 0.00025 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5869 (ttm) cc_final: 0.5412 (ttm) REVERT: A 448 LYS cc_start: 0.7237 (mmtp) cc_final: 0.7001 (mmtp) REVERT: B 271 LEU cc_start: 0.8525 (mt) cc_final: 0.8307 (mt) REVERT: B 309 MET cc_start: 0.8540 (tpp) cc_final: 0.8244 (tpp) REVERT: B 316 MET cc_start: 0.9073 (mmm) cc_final: 0.8518 (mmm) REVERT: B 329 TRP cc_start: 0.7604 (m-10) cc_final: 0.7252 (m-10) REVERT: C 117 ASN cc_start: 0.5418 (m110) cc_final: 0.4787 (p0) REVERT: C 162 MET cc_start: 0.7846 (tmm) cc_final: 0.7302 (tmm) REVERT: C 203 ILE cc_start: 0.9578 (mm) cc_final: 0.9268 (mm) REVERT: C 236 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8195 (mmmm) REVERT: C 251 MET cc_start: 0.7875 (mmp) cc_final: 0.7612 (mmp) REVERT: C 333 MET cc_start: 0.8493 (mpp) cc_final: 0.7801 (mpp) REVERT: D 352 ASP cc_start: 0.7973 (t0) cc_final: 0.7575 (t0) REVERT: E 295 ILE cc_start: 0.8346 (mm) cc_final: 0.8003 (mm) REVERT: H 75 LEU cc_start: 0.8480 (mt) cc_final: 0.8095 (tp) REVERT: H 101 ASN cc_start: 0.7382 (p0) cc_final: 0.7071 (p0) REVERT: H 125 LEU cc_start: 0.8642 (tp) cc_final: 0.8358 (tp) REVERT: H 168 MET cc_start: 0.8258 (mmm) cc_final: 0.8023 (tpt) REVERT: H 217 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6876 (mm-30) REVERT: H 458 GLU cc_start: 0.7885 (pm20) cc_final: 0.7199 (pt0) REVERT: H 626 ILE cc_start: 0.9232 (pt) cc_final: 0.8856 (tp) outliers start: 1 outliers final: 0 residues processed: 332 average time/residue: 0.1261 time to fit residues: 66.9516 Evaluate side-chains 255 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: [15, 40, 139, 175, 148, 103, 91, 217, 97, 13, 31] chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 91 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 180 HIS B 343 GLN B 358 ASN B 425 HIS ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114529 restraints weight = 42418.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115610 restraints weight = 38489.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116764 restraints weight = 29070.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117260 restraints weight = 22771.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117519 restraints weight = 21631.272| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20051 Z= 0.103 Angle : 0.509 9.143 27159 Z= 0.267 Chirality : 0.042 0.168 2995 Planarity : 0.003 0.054 3357 Dihedral : 10.869 84.912 3120 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.05 % Allowed : 1.09 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.28 (0.17), residues: 2367 helix: 0.44 (0.19), residues: 850 sheet: -0.83 (0.25), residues: 424 loop : -1.91 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 363 TYR 0.013 0.001 TYR C 96 PHE 0.022 0.001 PHE B 378 TRP 0.017 0.001 TRP B 147 HIS 0.004 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (20045) covalent geometry : angle 0.50793 / 0.27 (27151) SS BOND : bond 0.00162 / 0.10 ( 1) SS BOND : angle 1.16565 / 0.53 ( 2) hydrogen bonds : bond 0.03198 / 2.16 ( 656) hydrogen bonds : angle 4.16388 / 2.90 ( 1875) metal coordination : bond 0.00296 / 0.19 ( 4) metal coordination : angle 1.60190 / 0.66 ( 6) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5745 (ttm) cc_final: 0.5332 (ttm) REVERT: A 448 LYS cc_start: 0.7228 (mmtp) cc_final: 0.6978 (mmtp) REVERT: A 493 ARG cc_start: 0.7786 (ptt180) cc_final: 0.7544 (ptt180) REVERT: B 162 MET cc_start: 0.8418 (ttp) cc_final: 0.7873 (tmm) REVERT: B 309 MET cc_start: 0.8588 (tpp) cc_final: 0.8278 (tpp) REVERT: B 316 MET cc_start: 0.9055 (mmm) cc_final: 0.8629 (mmm) REVERT: B 329 TRP cc_start: 0.7659 (m-10) cc_final: 0.7318 (m-10) REVERT: B 515 LEU cc_start: 0.8723 (pp) cc_final: 0.8426 (tp) REVERT: C 117 ASN cc_start: 0.5520 (m110) cc_final: 0.4808 (p0) REVERT: C 203 ILE cc_start: 0.9568 (mm) cc_final: 0.9255 (mm) REVERT: C 236 LYS cc_start: 0.8765 (tmtt) cc_final: 0.8153 (mmmm) REVERT: C 251 MET cc_start: 0.7944 (mmp) cc_final: 0.7716 (mmp) REVERT: C 333 MET cc_start: 0.8492 (mpp) cc_final: 0.7774 (mpp) REVERT: D 352 ASP cc_start: 0.8021 (t0) cc_final: 0.7596 (t0) REVERT: E 502 LEU cc_start: 0.8481 (mp) cc_final: 0.8034 (tp) REVERT: E 534 GLU cc_start: 0.6950 (mp0) cc_final: 0.6718 (pm20) REVERT: H 75 LEU cc_start: 0.8438 (mt) cc_final: 0.8088 (tp) REVERT: H 101 ASN cc_start: 0.7391 (p0) cc_final: 0.7093 (p0) REVERT: H 125 LEU cc_start: 0.8592 (tp) cc_final: 0.8301 (tp) REVERT: H 168 MET cc_start: 0.8229 (mmm) cc_final: 0.8000 (tpt) REVERT: H 217 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6942 (mm-30) REVERT: H 458 GLU cc_start: 0.7962 (pm20) cc_final: 0.7297 (pt0) REVERT: H 626 ILE cc_start: 0.9255 (pt) cc_final: 0.8854 (tp) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.1231 time to fit residues: 66.2550 Evaluate side-chains 254 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: [37, 139, 181, 78, 185, 20, 51, 46, 166, 102, 7] chunk 37 optimal weight: 9.9990 chunk 139 optimal weight: 0.5980 chunk 181 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 185 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 46 optimal weight: 0.0070 chunk 166 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 198 GLN B 358 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS H 585 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115393 restraints weight = 42145.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116466 restraints weight = 38086.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117517 restraints weight = 29546.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117980 restraints weight = 23123.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118185 restraints weight = 21537.153| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20051 Z= 0.094 Angle : 0.498 8.336 27159 Z= 0.261 Chirality : 0.042 0.161 2995 Planarity : 0.003 0.056 3357 Dihedral : 10.775 84.429 3120 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.13 (0.17), residues: 2367 helix: 0.54 (0.19), residues: 855 sheet: -0.65 (0.25), residues: 410 loop : -1.85 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 274 TYR 0.019 0.001 TYR C 193 PHE 0.021 0.001 PHE B 378 TRP 0.040 0.001 TRP H 264 HIS 0.003 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (20045) covalent geometry : angle 0.49757 / 0.26 (27151) SS BOND : bond 0.00115 / 0.07 ( 1) SS BOND : angle 1.23675 / 0.55 ( 2) hydrogen bonds : bond 0.03009 / 2.04 ( 656) hydrogen bonds : angle 4.07200 / 2.83 ( 1875) metal coordination : bond 0.00261 / 0.15 ( 4) metal coordination : angle 1.48030 / 0.60 ( 6) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5636 (ttm) cc_final: 0.5262 (ttm) REVERT: A 448 LYS cc_start: 0.7237 (mmtp) cc_final: 0.6972 (mmtp) REVERT: A 493 ARG cc_start: 0.7830 (ptt180) cc_final: 0.7589 (ptt180) REVERT: A 543 GLU cc_start: 0.7902 (mp0) cc_final: 0.7504 (mp0) REVERT: B 309 MET cc_start: 0.8539 (tpp) cc_final: 0.8280 (tpp) REVERT: B 316 MET cc_start: 0.9052 (mmm) cc_final: 0.8646 (mmm) REVERT: B 329 TRP cc_start: 0.7651 (m-10) cc_final: 0.7296 (m-10) REVERT: B 515 LEU cc_start: 0.8738 (pp) cc_final: 0.8454 (tp) REVERT: C 117 ASN cc_start: 0.5431 (m110) cc_final: 0.4818 (p0) REVERT: C 203 ILE cc_start: 0.9562 (mm) cc_final: 0.9241 (mm) REVERT: C 236 LYS cc_start: 0.8756 (tmtt) cc_final: 0.8146 (mmmm) REVERT: C 251 MET cc_start: 0.7903 (mmp) cc_final: 0.7676 (mmp) REVERT: C 333 MET cc_start: 0.8503 (mpp) cc_final: 0.7799 (mpp) REVERT: D 352 ASP cc_start: 0.8048 (t0) cc_final: 0.7644 (t0) REVERT: E 427 SER cc_start: 0.7625 (m) cc_final: 0.7286 (t) REVERT: E 534 GLU cc_start: 0.6918 (mp0) cc_final: 0.6580 (mp0) REVERT: H 75 LEU cc_start: 0.8389 (mt) cc_final: 0.8058 (tp) REVERT: H 101 ASN cc_start: 0.7361 (p0) cc_final: 0.7070 (p0) REVERT: H 136 LYS cc_start: 0.7327 (mmmt) cc_final: 0.7112 (pttm) REVERT: H 168 MET cc_start: 0.8213 (mmm) cc_final: 0.7991 (tpt) REVERT: H 253 LEU cc_start: 0.8678 (mt) cc_final: 0.8465 (mt) REVERT: H 391 MET cc_start: 0.8581 (tmm) cc_final: 0.8273 (tmm) REVERT: H 458 GLU cc_start: 0.7992 (pm20) cc_final: 0.7327 (pt0) REVERT: H 626 ILE cc_start: 0.9240 (pt) cc_final: 0.8917 (tp) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.1250 time to fit residues: 68.3259 Evaluate side-chains 255 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: [194, 111, 109, 17, 43, 154, 71, 112, 11, 141, 82] chunk 194 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 141 optimal weight: 0.0970 chunk 82 optimal weight: 0.0040 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 475 HIS ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 653 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.134450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110297 restraints weight = 42137.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111626 restraints weight = 36095.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112794 restraints weight = 27218.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113030 restraints weight = 21534.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113224 restraints weight = 20802.560| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20051 Z= 0.169 Angle : 0.563 9.617 27159 Z= 0.296 Chirality : 0.044 0.178 2995 Planarity : 0.003 0.056 3357 Dihedral : 10.906 84.627 3120 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.12 (0.17), residues: 2367 helix: 0.59 (0.19), residues: 852 sheet: -0.75 (0.25), residues: 426 loop : -1.84 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 274 TYR 0.015 0.001 TYR C 96 PHE 0.021 0.002 PHE B 378 TRP 0.022 0.002 TRP C 97 HIS 0.010 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (20045) covalent geometry : angle 0.56238 / 0.30 (27151) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 1.26663 / 0.55 ( 2) hydrogen bonds : bond 0.03707 / 2.52 ( 656) hydrogen bonds : angle 4.18352 / 2.90 ( 1875) metal coordination : bond 0.00508 / 0.38 ( 4) metal coordination : angle 1.82031 / 0.88 ( 6) Misc. bond : bond 0.00070 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5625 (ttm) cc_final: 0.5255 (ttm) REVERT: A 448 LYS cc_start: 0.7180 (mmtp) cc_final: 0.6960 (mmtp) REVERT: A 493 ARG cc_start: 0.7971 (ptt180) cc_final: 0.7638 (ptt180) REVERT: B 309 MET cc_start: 0.8656 (tpp) cc_final: 0.8213 (tpp) REVERT: B 316 MET cc_start: 0.9075 (mmm) cc_final: 0.8706 (mmm) REVERT: B 329 TRP cc_start: 0.7692 (m-10) cc_final: 0.7317 (m-10) REVERT: B 515 LEU cc_start: 0.8833 (pp) cc_final: 0.8515 (tp) REVERT: C 117 ASN cc_start: 0.5612 (m110) cc_final: 0.4828 (p0) REVERT: C 203 ILE cc_start: 0.9574 (mm) cc_final: 0.9253 (mm) REVERT: C 236 LYS cc_start: 0.8806 (tmtt) cc_final: 0.8104 (mmmm) REVERT: C 251 MET cc_start: 0.8036 (mmp) cc_final: 0.7808 (mmp) REVERT: C 333 MET cc_start: 0.8589 (mpp) cc_final: 0.7803 (mpp) REVERT: D 352 ASP cc_start: 0.8115 (t0) cc_final: 0.7676 (t0) REVERT: E 427 SER cc_start: 0.7735 (m) cc_final: 0.7461 (t) REVERT: E 502 LEU cc_start: 0.8482 (mp) cc_final: 0.8050 (tp) REVERT: E 534 GLU cc_start: 0.6937 (mp0) cc_final: 0.6583 (mp0) REVERT: H 75 LEU cc_start: 0.8431 (mt) cc_final: 0.8125 (tp) REVERT: H 101 ASN cc_start: 0.7461 (p0) cc_final: 0.7146 (p0) REVERT: H 136 LYS cc_start: 0.7404 (mmmt) cc_final: 0.7128 (pttm) REVERT: H 253 LEU cc_start: 0.8849 (mt) cc_final: 0.8495 (mt) REVERT: H 458 GLU cc_start: 0.8084 (pm20) cc_final: 0.7450 (pt0) REVERT: H 597 ASP cc_start: 0.8630 (p0) cc_final: 0.8297 (p0) REVERT: H 626 ILE cc_start: 0.9339 (pt) cc_final: 0.8955 (tp) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1272 time to fit residues: 66.3954 Evaluate side-chains 246 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: [47, 17, 214, 158, 168, 26, 3, 238, 230, 241, 94] chunk 47 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 238 optimal weight: 0.2980 chunk 230 optimal weight: 4.9990 chunk 241 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 358 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 509 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109826 restraints weight = 42165.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111445 restraints weight = 35484.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112302 restraints weight = 26455.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112911 restraints weight = 20949.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113151 restraints weight = 19101.055| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20051 Z= 0.136 Angle : 0.549 9.410 27159 Z= 0.287 Chirality : 0.044 0.233 2995 Planarity : 0.003 0.059 3357 Dihedral : 10.892 85.194 3120 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.03 (0.17), residues: 2367 helix: 0.72 (0.19), residues: 844 sheet: -0.77 (0.25), residues: 423 loop : -1.79 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 274 TYR 0.019 0.001 TYR H 648 PHE 0.025 0.001 PHE B 378 TRP 0.041 0.001 TRP B 147 HIS 0.012 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (20045) covalent geometry : angle 0.54822 / 0.29 (27151) SS BOND : bond 0.00142 / 0.09 ( 1) SS BOND : angle 1.75324 / 0.78 ( 2) hydrogen bonds : bond 0.03561 / 2.41 ( 656) hydrogen bonds : angle 4.17110 / 2.89 ( 1875) metal coordination : bond 0.00387 / 0.28 ( 4) metal coordination : angle 1.73357 / 0.78 ( 6) Misc. bond : bond 0.00040 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.5758 (ttm) cc_final: 0.5315 (ttm) REVERT: A 448 LYS cc_start: 0.7249 (mmtp) cc_final: 0.6938 (mmtp) REVERT: B 309 MET cc_start: 0.8658 (tpp) cc_final: 0.8274 (tpp) REVERT: B 316 MET cc_start: 0.9064 (mmm) cc_final: 0.8716 (mmm) REVERT: B 329 TRP cc_start: 0.7682 (m-10) cc_final: 0.7314 (m-10) REVERT: B 515 LEU cc_start: 0.8805 (pp) cc_final: 0.8505 (tp) REVERT: C 203 ILE cc_start: 0.9584 (mm) cc_final: 0.9270 (mm) REVERT: C 236 LYS cc_start: 0.8918 (tmtt) cc_final: 0.8082 (mmmm) REVERT: C 237 ASP cc_start: 0.9077 (p0) cc_final: 0.8698 (p0) REVERT: C 251 MET cc_start: 0.7956 (mmp) cc_final: 0.7730 (mmp) REVERT: C 333 MET cc_start: 0.8603 (mpp) cc_final: 0.7753 (mpp) REVERT: D 352 ASP cc_start: 0.8096 (t0) cc_final: 0.7663 (t0) REVERT: E 292 CYS cc_start: 0.7379 (p) cc_final: 0.7126 (p) REVERT: E 427 SER cc_start: 0.7757 (m) cc_final: 0.7521 (t) REVERT: H 75 LEU cc_start: 0.8422 (mt) cc_final: 0.8103 (tp) REVERT: H 101 ASN cc_start: 0.7450 (p0) cc_final: 0.7143 (p0) REVERT: H 136 LYS cc_start: 0.7435 (mmmt) cc_final: 0.7219 (pttm) REVERT: H 253 LEU cc_start: 0.8895 (mt) cc_final: 0.8574 (mt) REVERT: H 458 GLU cc_start: 0.8143 (pm20) cc_final: 0.7530 (pt0) REVERT: H 597 ASP cc_start: 0.8622 (p0) cc_final: 0.8290 (p0) REVERT: H 626 ILE cc_start: 0.9347 (pt) cc_final: 0.8973 (tp) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1300 time to fit residues: 66.7107 Evaluate side-chains 246 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: [139, 6, 91, 108, 118, 9, 60, 235, 69, 24, 13] chunk 139 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 91 optimal weight: 0.0970 chunk 108 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 69 optimal weight: 0.0000 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 358 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN H 162 ASN H 509 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.134299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110212 restraints weight = 42233.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112229 restraints weight = 37099.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113070 restraints weight = 26933.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113362 restraints weight = 20972.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113585 restraints weight = 20017.171| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20051 Z= 0.115 Angle : 0.537 8.833 27159 Z= 0.281 Chirality : 0.043 0.177 2995 Planarity : 0.003 0.059 3357 Dihedral : 10.859 85.149 3120 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.94 (0.17), residues: 2367 helix: 0.77 (0.19), residues: 844 sheet: -0.69 (0.25), residues: 421 loop : -1.72 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 274 TYR 0.013 0.001 TYR H 154 PHE 0.024 0.001 PHE B 378 TRP 0.025 0.001 TRP C 97 HIS 0.006 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (20045) covalent geometry : angle 0.53620 / 0.28 (27151) SS BOND : bond 0.00197 / 0.12 ( 1) SS BOND : angle 2.77187 / 1.07 ( 2) hydrogen bonds : bond 0.03359 / 2.27 ( 656) hydrogen bonds : angle 4.12499 / 2.87 ( 1875) metal coordination : bond 0.00267 / 0.19 ( 4) metal coordination : angle 1.52227 / 0.65 ( 6) Misc. bond : bond 0.00023 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.41 seconds wall clock time: 53 minutes 20.71 seconds (3200.71 seconds total)