Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 16:10:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/04_2023/6n7s_0362_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/04_2023/6n7s_0362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/04_2023/6n7s_0362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/04_2023/6n7s_0362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/04_2023/6n7s_0362_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7s_0362/04_2023/6n7s_0362_updated.pdb" } resolution = 4.6 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 4 5.21 5 S 78 5.16 5 C 7932 2.51 5 N 2253 2.21 5 O 2491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 363": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12783 Number of models: 1 Model: "" Number of chains: 11 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: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2105 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 4, 'TRANS': 268} Chain breaks: 3 Chain: "C" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2121 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 4, 'TRANS': 270} 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: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2003 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1995 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 253} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 260 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "B" 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: "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} Time building chain proxies: 6.92, per 1000 atoms: 0.54 Number of scatterers: 12783 At special positions: 0 Unit cell: (75.97, 129.47, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 25 15.00 Mg 4 11.99 O 2491 8.00 N 2253 7.00 C 7932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.06 Conformation dependent library (CDL) restraints added in 2.0 seconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 11 sheets defined 25.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.515A pdb=" N HIS A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.942A pdb=" N GLY A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.297A pdb=" N GLU A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 378 through 381 No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'B' and resid 272 through 278 removed outlier: 4.076A pdb=" N ARG B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 278' Processing helix chain 'B' and resid 294 through 297 No H-bonds generated for 'chain 'B' and resid 294 through 297' Processing helix chain 'B' and resid 320 through 328 removed outlier: 3.795A pdb=" N GLN B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 4.921A pdb=" N GLU B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 381 No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 405 through 414 removed outlier: 3.591A pdb=" N TYR B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 439 through 453 removed outlier: 3.618A pdb=" N ASP B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'C' and resid 273 through 276 No H-bonds generated for 'chain 'C' and resid 273 through 276' Processing helix chain 'C' and resid 294 through 297 No H-bonds generated for 'chain 'C' and resid 294 through 297' Processing helix chain 'C' and resid 325 through 328 No H-bonds generated for 'chain 'C' and resid 325 through 328' Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 377 through 385 removed outlier: 3.887A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 414 removed outlier: 4.194A pdb=" N TYR C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N MET C 412 " --> pdb=" O LYS C 408 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 440 through 443 No H-bonds generated for 'chain 'C' and resid 440 through 443' Processing helix chain 'C' and resid 446 through 456 removed outlier: 3.786A pdb=" N THR C 456 " --> pdb=" O PHE C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'C' and resid 491 through 493 No H-bonds generated for 'chain 'C' and resid 491 through 493' Processing helix chain 'D' and resid 273 through 276 No H-bonds generated for 'chain 'D' and resid 273 through 276' Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 348 through 357 removed outlier: 3.832A pdb=" N ASP D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'D' and resid 403 through 414 removed outlier: 3.733A pdb=" N ALA D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET D 412 " --> pdb=" O LYS D 408 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 456 removed outlier: 3.755A pdb=" N LYS D 448 " --> pdb=" O ASN D 444 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 273 through 276 No H-bonds generated for 'chain 'E' and resid 273 through 276' Processing helix chain 'E' and resid 325 through 331 removed outlier: 3.885A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 357 removed outlier: 4.866A pdb=" N ASP E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY E 355 " --> pdb=" O GLU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 378 through 386 removed outlier: 3.552A pdb=" N GLU E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 414 removed outlier: 4.276A pdb=" N MET E 412 " --> pdb=" O LYS E 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG E 413 " --> pdb=" O LEU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 446 through 456 removed outlier: 3.915A pdb=" N GLY E 451 " --> pdb=" O THR E 447 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR E 456 " --> pdb=" O PHE E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'F' and resid 268 through 271 removed outlier: 3.747A pdb=" N LEU F 271 " --> pdb=" O ALA F 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 268 through 271' Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 318 through 322 Processing helix chain 'F' and resid 324 through 328 removed outlier: 3.845A pdb=" N GLN F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 324 through 328' Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 367 through 371 Processing helix chain 'F' and resid 378 through 383 Processing helix chain 'F' and resid 405 through 414 removed outlier: 4.955A pdb=" N ALA F 410 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR F 411 " --> pdb=" O LYS F 408 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG F 413 " --> pdb=" O ALA F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 456 Processing helix chain 'F' and resid 490 through 492 No H-bonds generated for 'chain 'F' and resid 490 through 492' Processing sheet with id= A, first strand: chain 'A' and resid 308 through 311 removed outlier: 5.969A pdb=" N THR A 498 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR A 311 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 500 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 520 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 501 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE A 518 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU A 503 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL A 516 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 516 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY A 531 " --> pdb=" O VAL A 516 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 420 through 423 removed outlier: 6.394A pdb=" N VAL A 459 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU A 423 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 461 " --> pdb=" O LEU A 423 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 528 through 534 removed outlier: 7.400A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 515 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 498 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 310 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 461 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 528 through 534 removed outlier: 6.650A pdb=" N VAL C 516 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR C 532 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL C 514 " --> pdb=" O TYR C 532 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 460 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL C 310 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C 462 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 460 through 463 removed outlier: 3.721A pdb=" N VAL D 310 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR D 498 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR D 311 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE D 500 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 515 through 518 removed outlier: 6.123A pdb=" N ILE D 518 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE D 529 " --> pdb=" O ILE D 518 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 337 through 340 removed outlier: 6.689A pdb=" N VAL E 420 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA E 340 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE E 422 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL E 459 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU E 423 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL E 461 " --> pdb=" O LEU E 423 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'E' and resid 498 through 503 removed outlier: 3.574A pdb=" N ILE E 499 " --> pdb=" O LYS E 520 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS E 520 " --> pdb=" O ILE E 499 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA E 501 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE E 518 " --> pdb=" O ALA E 501 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU E 503 " --> pdb=" O VAL E 516 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL E 516 " --> pdb=" O GLU E 503 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY E 531 " --> pdb=" O VAL E 516 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE E 518 " --> pdb=" O ILE E 529 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE E 529 " --> pdb=" O ILE E 518 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 308 through 311 removed outlier: 7.171A pdb=" N THR F 498 " --> pdb=" O MET F 309 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR F 311 " --> pdb=" O THR F 498 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE F 500 " --> pdb=" O THR F 311 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 459 through 462 removed outlier: 6.650A pdb=" N LYS F 336 " --> pdb=" O ASP F 419 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE F 421 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY F 338 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU F 423 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA F 340 " --> pdb=" O LEU F 423 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 532 through 534 removed outlier: 3.750A pdb=" N TYR F 532 " --> pdb=" O SER F 545 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 546 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 5.38 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: 2145 1.31 - 1.43: 3175 1.43 - 1.56: 7456 1.56 - 1.69: 46 1.69 - 1.82: 132 Bond restraints: 12954 Sorted by residual: bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.425 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C2 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.410 1.488 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C2 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.410 1.487 -0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 12949 not shown) Histogram of bond angle deviations from ideal: 96.43 - 103.96: 156 103.96 - 111.49: 5347 111.49 - 119.02: 5311 119.02 - 126.55: 6496 126.55 - 134.08: 147 Bond angle restraints: 17457 Sorted by residual: angle pdb=" N LEU B 356 " pdb=" CA LEU B 356 " pdb=" C LEU B 356 " ideal model delta sigma weight residual 111.02 100.94 10.08 1.52e+00 4.33e-01 4.40e+01 angle pdb=" N PHE B 289 " pdb=" CA PHE B 289 " pdb=" C PHE B 289 " ideal model delta sigma weight residual 109.60 118.52 -8.92 1.53e+00 4.27e-01 3.40e+01 angle pdb=" N HIS C 357 " pdb=" CA HIS C 357 " pdb=" C HIS C 357 " ideal model delta sigma weight residual 111.28 117.55 -6.27 1.09e+00 8.42e-01 3.31e+01 angle pdb=" N ILE F 275 " pdb=" CA ILE F 275 " pdb=" C ILE F 275 " ideal model delta sigma weight residual 111.00 105.42 5.58 1.09e+00 8.42e-01 2.62e+01 angle pdb=" N TYR B 411 " pdb=" CA TYR B 411 " pdb=" C TYR B 411 " ideal model delta sigma weight residual 111.82 117.59 -5.77 1.16e+00 7.43e-01 2.47e+01 ... (remaining 17452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 7594 35.33 - 70.67: 132 70.67 - 106.00: 14 106.00 - 141.33: 5 141.33 - 176.66: 3 Dihedral angle restraints: 7748 sinusoidal: 3275 harmonic: 4473 Sorted by residual: dihedral pdb=" C2 TTP B 700 " pdb=" C1' TTP B 700 " pdb=" N1 TTP B 700 " pdb=" O4' TTP B 700 " ideal model delta sinusoidal sigma weight residual -58.32 118.35 -176.66 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP E 700 " pdb=" C1' TTP E 700 " pdb=" N1 TTP E 700 " pdb=" O4' TTP E 700 " ideal model delta sinusoidal sigma weight residual 301.68 134.74 166.94 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C2 TTP D 700 " pdb=" C1' TTP D 700 " pdb=" N1 TTP D 700 " pdb=" O4' TTP D 700 " ideal model delta sinusoidal sigma weight residual 301.68 150.44 151.24 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 7745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1333 0.059 - 0.117: 519 0.117 - 0.176: 106 0.176 - 0.234: 23 0.234 - 0.293: 9 Chirality restraints: 1990 Sorted by residual: chirality pdb=" CA ASP B 352 " pdb=" N ASP B 352 " pdb=" C ASP B 352 " pdb=" CB ASP B 352 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA HIS B 357 " pdb=" N HIS B 357 " pdb=" C HIS B 357 " pdb=" CB HIS B 357 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' TTP C 700 " pdb=" C2' TTP C 700 " pdb=" C4' TTP C 700 " pdb=" O3' TTP C 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1987 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 515 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU F 515 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU F 515 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL F 516 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 347 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C GLU E 347 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU E 347 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E 348 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 322 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.89e+00 pdb=" C VAL C 322 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL C 322 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG C 323 " 0.015 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 26 2.43 - 3.05: 7287 3.05 - 3.66: 18365 3.66 - 4.28: 28017 4.28 - 4.90: 45286 Nonbonded interactions: 98981 Sorted by model distance: nonbonded pdb=" OE1 GLN C 343 " pdb="MG MG C 701 " model vdw 1.812 2.170 nonbonded pdb=" OE1 GLN E 343 " pdb="MG MG E 701 " model vdw 1.922 2.170 nonbonded pdb=" O1B TTP E 700 " pdb="MG MG E 701 " model vdw 1.987 2.170 nonbonded pdb=" O2G TTP D 700 " pdb="MG MG D 701 " model vdw 2.000 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.121 2.170 ... (remaining 98976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 264 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 506 or resid 510 through 545)) selection = (chain 'B' and (resid 264 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 506 or resid 510 through 545)) selection = (chain 'C' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 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 264 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 through 506 or resid 510 through 545)) selection = (chain 'E' and (resid 264 through 506 or resid 510 through 545)) selection = (chain 'F' and (resid 264 through 506 or resid 510 through 545)) } 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.610 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 33.940 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 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 : 0.008 0.090 12954 Z= 0.500 Angle : 1.198 12.171 17457 Z= 0.636 Chirality : 0.066 0.293 1990 Planarity : 0.005 0.054 2163 Dihedral : 14.865 176.665 4884 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.16), residues: 1555 helix: -4.29 (0.12), residues: 485 sheet: -2.12 (0.30), residues: 276 loop : -3.22 (0.17), residues: 794 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 338 time to evaluate : 1.525 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 349 average time/residue: 0.3155 time to fit residues: 147.4243 Evaluate side-chains 180 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.555 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3783 time to fit residues: 3.1696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 chunk 66 optimal weight: 0.0970 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 425 HIS A 475 HIS A 512 ASN ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 HIS D 358 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN D 475 HIS E 475 HIS F 475 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5544 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 12954 Z= 0.160 Angle : 0.602 9.882 17457 Z= 0.308 Chirality : 0.044 0.182 1990 Planarity : 0.004 0.066 2163 Dihedral : 14.020 145.404 1896 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.18), residues: 1555 helix: -3.37 (0.17), residues: 478 sheet: -1.48 (0.31), residues: 283 loop : -2.81 (0.18), residues: 794 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 1.523 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: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 236 average time/residue: 0.2875 time to fit residues: 94.0861 Evaluate side-chains 162 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1158 time to fit residues: 2.3137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 156 optimal weight: 0.0870 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS F 465 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 12954 Z= 0.168 Angle : 0.595 9.653 17457 Z= 0.297 Chirality : 0.044 0.304 1990 Planarity : 0.004 0.065 2163 Dihedral : 13.054 129.868 1896 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.19), residues: 1555 helix: -2.61 (0.21), residues: 445 sheet: -1.35 (0.30), residues: 304 loop : -2.50 (0.19), residues: 806 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.561 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 outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3057 time to fit residues: 88.8601 Evaluate side-chains 155 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 75 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS A 475 HIS ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 12954 Z= 0.162 Angle : 0.570 9.593 17457 Z= 0.284 Chirality : 0.043 0.173 1990 Planarity : 0.004 0.066 2163 Dihedral : 12.951 137.763 1896 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.19), residues: 1555 helix: -2.14 (0.22), residues: 444 sheet: -1.09 (0.30), residues: 289 loop : -2.30 (0.19), residues: 822 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2810 time to fit residues: 77.5076 Evaluate side-chains 144 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 0.2980 chunk 63 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 51 optimal weight: 0.0970 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 328 GLN ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN D 328 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS E 328 GLN E 536 ASN F 358 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12954 Z= 0.225 Angle : 0.666 9.849 17457 Z= 0.327 Chirality : 0.045 0.212 1990 Planarity : 0.004 0.064 2163 Dihedral : 13.205 133.236 1896 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.19), residues: 1555 helix: -2.21 (0.21), residues: 482 sheet: -1.16 (0.30), residues: 299 loop : -2.25 (0.20), residues: 774 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2903 time to fit residues: 80.4377 Evaluate side-chains 143 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 127 optimal weight: 0.0770 chunk 71 optimal weight: 0.1980 chunk 12 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN F 425 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5812 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 12954 Z= 0.128 Angle : 0.548 9.943 17457 Z= 0.269 Chirality : 0.042 0.179 1990 Planarity : 0.003 0.058 2163 Dihedral : 12.899 137.845 1896 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.20), residues: 1555 helix: -1.76 (0.23), residues: 464 sheet: -0.81 (0.31), residues: 286 loop : -2.05 (0.20), residues: 805 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2595 time to fit residues: 69.0835 Evaluate side-chains 139 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 0.0030 chunk 87 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 153 optimal weight: 9.9990 chunk 95 optimal weight: 0.0870 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 overall best weight: 0.2568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 12954 Z= 0.115 Angle : 0.533 9.505 17457 Z= 0.259 Chirality : 0.042 0.144 1990 Planarity : 0.003 0.071 2163 Dihedral : 12.664 137.512 1896 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.20), residues: 1555 helix: -1.51 (0.24), residues: 458 sheet: -0.52 (0.32), residues: 284 loop : -1.91 (0.20), residues: 813 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2553 time to fit residues: 69.9090 Evaluate side-chains 146 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 6.9990 chunk 46 optimal weight: 0.1980 chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 120 optimal weight: 0.0060 chunk 139 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 HIS D 392 HIS ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12954 Z= 0.194 Angle : 0.620 9.568 17457 Z= 0.302 Chirality : 0.044 0.176 1990 Planarity : 0.004 0.070 2163 Dihedral : 12.929 134.644 1896 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.20), residues: 1555 helix: -1.44 (0.24), residues: 458 sheet: -0.57 (0.32), residues: 286 loop : -2.02 (0.20), residues: 811 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2668 time to fit residues: 70.6771 Evaluate side-chains 148 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 151 optimal weight: 0.0770 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 12954 Z= 0.163 Angle : 0.582 9.594 17457 Z= 0.285 Chirality : 0.043 0.172 1990 Planarity : 0.003 0.068 2163 Dihedral : 12.914 137.607 1896 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.20), residues: 1555 helix: -1.38 (0.24), residues: 463 sheet: -0.49 (0.32), residues: 284 loop : -1.95 (0.20), residues: 808 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2606 time to fit residues: 67.1972 Evaluate side-chains 142 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 HIS ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 12954 Z= 0.206 Angle : 0.633 9.435 17457 Z= 0.311 Chirality : 0.045 0.155 1990 Planarity : 0.004 0.066 2163 Dihedral : 13.117 139.088 1896 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.20), residues: 1555 helix: -1.38 (0.24), residues: 479 sheet: -0.59 (0.32), residues: 273 loop : -2.02 (0.20), residues: 803 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2668 time to fit residues: 66.2669 Evaluate side-chains 136 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 110 optimal weight: 0.0020 chunk 7 optimal weight: 0.9980 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.134994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.121995 restraints weight = 43472.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.123789 restraints weight = 31306.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.125073 restraints weight = 23718.172| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.7574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 12954 Z= 0.155 Angle : 0.588 9.635 17457 Z= 0.285 Chirality : 0.043 0.162 1990 Planarity : 0.003 0.067 2163 Dihedral : 13.005 140.473 1896 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.21), residues: 1555 helix: -1.16 (0.24), residues: 469 sheet: -0.54 (0.32), residues: 283 loop : -1.92 (0.20), residues: 803 =============================================================================== Job complete usr+sys time: 2479.39 seconds wall clock time: 46 minutes 21.70 seconds (2781.70 seconds total)