Starting phenix.real_space_refine on Tue Aug 6 05:30:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ema_19815/08_2024/9ema_19815_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ema_19815/08_2024/9ema_19815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ema_19815/08_2024/9ema_19815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ema_19815/08_2024/9ema_19815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ema_19815/08_2024/9ema_19815_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ema_19815/08_2024/9ema_19815_neut.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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: 8 Type Number sf(0) Gaussians P 18 5.49 5 Mg 4 5.21 5 S 78 5.16 5 Cl 3 4.86 5 C 9735 2.51 5 N 2724 2.21 5 O 2997 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 428": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 426": "OE1" <-> "OE2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 112": "OE1" <-> "OE2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E GLU 420": "OE1" <-> "OE2" Residue "F GLU 246": "OE1" <-> "OE2" Residue "F GLU 282": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15562 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2508 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 2 Chain: "B" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2508 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 2 Chain: "C" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2508 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 2 Chain: "D" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2576 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 9, 'TRANS': 322} Chain breaks: 1 Chain: "E" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2576 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 9, 'TRANS': 322} Chain breaks: 1 Chain: "F" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2576 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 9, 'TRANS': 322} Chain breaks: 1 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'A1H5V': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'A1H5V': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'A1H5V': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.41, per 1000 atoms: 0.60 Number of scatterers: 15562 At special positions: 0 Unit cell: (129.337, 127.689, 75.7896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 3 17.00 S 78 16.00 P 18 15.00 Mg 4 11.99 F 3 9.00 O 2997 8.00 N 2724 7.00 C 9735 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: 5.82 Conformation dependent library (CDL) restraints added in 2.7 seconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 24 sheets defined 54.6% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.731A pdb=" N LYS A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.503A pdb=" N TYR A 102 " --> pdb=" O SER A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 240 through 249 removed outlier: 4.069A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.632A pdb=" N HIS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.774A pdb=" N ARG A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.667A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.669A pdb=" N LYS B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 Processing helix chain 'B' and resid 99 through 102 removed outlier: 3.579A pdb=" N TYR B 102 " --> pdb=" O SER B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 272 through 289 Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 308 through 320 removed outlier: 3.714A pdb=" N HIS B 316 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.717A pdb=" N ARG B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.570A pdb=" N ILE B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 75 through 88 Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.547A pdb=" N TYR C 102 " --> pdb=" O SER C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 272 through 289 removed outlier: 3.534A pdb=" N ARG C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.565A pdb=" N HIS C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 357 removed outlier: 3.613A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 382 Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.512A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.540A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.569A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.637A pdb=" N LEU D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 286 Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.834A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 353 removed outlier: 3.776A pdb=" N ARG D 353 " --> pdb=" O ASP D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 378 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.503A pdb=" N ALA D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 445 Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 95 Processing helix chain 'E' and resid 106 through 109 Processing helix chain 'E' and resid 114 through 126 removed outlier: 3.512A pdb=" N SER E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 253 removed outlier: 4.029A pdb=" N ARG E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 263 removed outlier: 4.212A pdb=" N PHE E 261 " --> pdb=" O PHE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 286 removed outlier: 3.640A pdb=" N ARG E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 304 Processing helix chain 'E' and resid 305 through 316 removed outlier: 3.869A pdb=" N ARG E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 353 removed outlier: 3.779A pdb=" N ARG E 353 " --> pdb=" O ASP E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 379 Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.650A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 435 through 445 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 Processing helix chain 'F' and resid 114 through 126 removed outlier: 3.536A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 253 removed outlier: 4.186A pdb=" N ARG F 253 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 257 No H-bonds generated for 'chain 'F' and resid 255 through 257' Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.600A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.800A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 379 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.720A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.521A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 239 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.320A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 239 Processing sheet with id=AA8, first strand: chain 'B' and resid 336 through 337 removed outlier: 3.617A pdb=" N CYS B 336 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.301A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 337 Processing sheet with id=AB4, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.509A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 77 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N THR D 359 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA D 76 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 240 through 243 Processing sheet with id=AB7, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.535A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY E 77 " --> pdb=" O THR E 328 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR E 359 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA E 76 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 240 through 243 Processing sheet with id=AC2, first strand: chain 'E' and resid 333 through 334 Processing sheet with id=AC3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.298A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY F 77 " --> pdb=" O THR F 328 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 240 through 243 Processing sheet with id=AC6, first strand: chain 'F' and resid 333 through 334 797 hydrogen bonds defined for protein. 2307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 6.34 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: 2634 1.31 - 1.44: 3665 1.44 - 1.56: 9277 1.56 - 1.69: 48 1.69 - 1.82: 141 Bond restraints: 15765 Sorted by residual: bond pdb=" C04 A1H5V B 501 " pdb=" C05 A1H5V B 501 " ideal model delta sigma weight residual 1.371 1.555 -0.184 2.00e-02 2.50e+03 8.51e+01 bond pdb=" C04 A1H5V C 502 " pdb=" C05 A1H5V C 502 " ideal model delta sigma weight residual 1.371 1.554 -0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" C04 A1H5V A 502 " pdb=" C05 A1H5V A 502 " ideal model delta sigma weight residual 1.371 1.553 -0.182 2.00e-02 2.50e+03 8.32e+01 bond pdb=" C05 A1H5V C 502 " pdb=" C28 A1H5V C 502 " ideal model delta sigma weight residual 1.433 1.563 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C05 A1H5V B 501 " pdb=" C28 A1H5V B 501 " ideal model delta sigma weight residual 1.433 1.561 -0.128 2.00e-02 2.50e+03 4.09e+01 ... (remaining 15760 not shown) Histogram of bond angle deviations from ideal: 98.38 - 106.65: 491 106.65 - 114.92: 9469 114.92 - 123.20: 10154 123.20 - 131.47: 1142 131.47 - 139.74: 38 Bond angle restraints: 21294 Sorted by residual: angle pdb=" N LEU E 395 " pdb=" CA LEU E 395 " pdb=" C LEU E 395 " ideal model delta sigma weight residual 112.38 104.89 7.49 1.22e+00 6.72e-01 3.77e+01 angle pdb=" N GLY A 349 " pdb=" CA GLY A 349 " pdb=" C GLY A 349 " ideal model delta sigma weight residual 115.30 106.79 8.51 1.39e+00 5.18e-01 3.74e+01 angle pdb=" C04 A1H5V C 502 " pdb=" N30 A1H5V C 502 " pdb=" C31 A1H5V C 502 " ideal model delta sigma weight residual 131.03 113.52 17.51 3.00e+00 1.11e-01 3.41e+01 angle pdb=" C04 A1H5V B 501 " pdb=" N30 A1H5V B 501 " pdb=" C31 A1H5V B 501 " ideal model delta sigma weight residual 131.03 114.92 16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" C04 A1H5V A 502 " pdb=" N30 A1H5V A 502 " pdb=" C31 A1H5V A 502 " ideal model delta sigma weight residual 131.03 115.02 16.01 3.00e+00 1.11e-01 2.85e+01 ... (remaining 21289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 9494 35.09 - 70.18: 367 70.18 - 105.27: 36 105.27 - 140.37: 0 140.37 - 175.46: 6 Dihedral angle restraints: 9903 sinusoidal: 4248 harmonic: 5655 Sorted by residual: dihedral pdb=" C09 A1H5V C 502 " pdb=" C07 A1H5V C 502 " pdb=" C08 A1H5V C 502 " pdb=" O27 A1H5V C 502 " ideal model delta sinusoidal sigma weight residual -83.32 92.14 -175.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C07 A1H5V C 502 " pdb=" C05 A1H5V C 502 " pdb=" N06 A1H5V C 502 " pdb=" C28 A1H5V C 502 " ideal model delta sinusoidal sigma weight residual 278.01 103.84 174.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C16 A1H5V C 502 " pdb=" C18 A1H5V C 502 " pdb=" O17 A1H5V C 502 " pdb=" C19 A1H5V C 502 " ideal model delta sinusoidal sigma weight residual 75.45 -93.19 168.64 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 9900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1979 0.060 - 0.121: 362 0.121 - 0.181: 112 0.181 - 0.241: 12 0.241 - 0.301: 13 Chirality restraints: 2478 Sorted by residual: chirality pdb=" C3' ATP F 802 " pdb=" C2' ATP F 802 " pdb=" C4' ATP F 802 " pdb=" O3' ATP F 802 " both_signs ideal model delta sigma weight residual False -2.63 -2.94 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C3' ATP D 801 " pdb=" C2' ATP D 801 " pdb=" C4' ATP D 801 " pdb=" O3' ATP D 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ATP E 801 " pdb=" C2' ATP E 801 " pdb=" C4' ATP E 801 " pdb=" O3' ATP E 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2475 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 419 " -0.019 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ILE B 419 " 0.063 2.00e-02 2.50e+03 pdb=" O ILE B 419 " -0.023 2.00e-02 2.50e+03 pdb=" N ASN B 420 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 25 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.86e+00 pdb=" C GLY C 25 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY C 25 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU C 26 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 388 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C THR E 388 " 0.048 2.00e-02 2.50e+03 pdb=" O THR E 388 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL E 389 " -0.016 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 82 2.58 - 3.16: 12262 3.16 - 3.74: 25738 3.74 - 4.32: 36503 4.32 - 4.90: 58703 Nonbonded interactions: 133288 Sorted by model distance: nonbonded pdb=" O3G ATP A 501 " pdb="MG MG F 801 " model vdw 1.999 2.170 nonbonded pdb=" O1A ATP A 501 " pdb="MG MG F 801 " model vdw 2.006 2.170 nonbonded pdb=" O2B ATP F 802 " pdb="MG MG F 803 " model vdw 2.022 2.170 nonbonded pdb=" OG1 THR F 84 " pdb="MG MG F 803 " model vdw 2.037 2.170 nonbonded pdb=" O2B ATP E 801 " pdb="MG MG E 802 " model vdw 2.101 2.170 ... (remaining 133283 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 16 through 451) selection = (chain 'E' and resid 16 through 451) selection = (chain 'F' and resid 16 through 451) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 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: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 45.190 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 0.184 15765 Z= 0.519 Angle : 1.072 17.512 21294 Z= 0.565 Chirality : 0.056 0.301 2478 Planarity : 0.007 0.099 2694 Dihedral : 18.259 175.457 6249 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.34 % Favored : 98.61 % Rotamer: Outliers : 0.42 % Allowed : 12.20 % Favored : 87.38 % 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: -0.24 (0.17), residues: 1944 helix: -0.01 (0.14), residues: 1041 sheet: -0.78 (0.29), residues: 252 loop : 0.22 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 283 HIS 0.005 0.001 HIS E 245 PHE 0.019 0.002 PHE E 257 TYR 0.029 0.002 TYR D 442 ARG 0.019 0.001 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 311 time to evaluate : 2.038 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 314 average time/residue: 1.3179 time to fit residues: 454.8623 Evaluate side-chains 159 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 449 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.0980 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15765 Z= 0.191 Angle : 0.558 9.112 21294 Z= 0.290 Chirality : 0.043 0.238 2478 Planarity : 0.004 0.041 2694 Dihedral : 13.212 179.927 2474 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.36 % Allowed : 15.10 % Favored : 82.55 % 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: 0.99 (0.18), residues: 1944 helix: 1.06 (0.15), residues: 1050 sheet: -0.18 (0.30), residues: 264 loop : 0.62 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 283 HIS 0.005 0.001 HIS C 393 PHE 0.017 0.001 PHE F 257 TYR 0.010 0.001 TYR E 387 ARG 0.006 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.855 Fit side-chains REVERT: A 96 MET cc_start: 0.8008 (ttt) cc_final: 0.7683 (ttt) outliers start: 39 outliers final: 8 residues processed: 223 average time/residue: 1.2766 time to fit residues: 314.6887 Evaluate side-chains 161 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 15765 Z= 0.329 Angle : 0.596 9.301 21294 Z= 0.312 Chirality : 0.045 0.175 2478 Planarity : 0.005 0.051 2694 Dihedral : 14.375 178.086 2472 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.87 % Allowed : 15.82 % Favored : 82.31 % 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: 0.99 (0.18), residues: 1944 helix: 1.12 (0.16), residues: 1071 sheet: -0.09 (0.28), residues: 276 loop : 0.44 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 283 HIS 0.006 0.001 HIS E 344 PHE 0.010 0.002 PHE F 261 TYR 0.011 0.002 TYR B 366 ARG 0.007 0.001 ARG F 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 1.933 Fit side-chains outliers start: 31 outliers final: 5 residues processed: 175 average time/residue: 1.3441 time to fit residues: 259.3587 Evaluate side-chains 140 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15765 Z= 0.184 Angle : 0.464 7.302 21294 Z= 0.247 Chirality : 0.041 0.163 2478 Planarity : 0.004 0.049 2694 Dihedral : 13.737 177.805 2472 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.21 % Allowed : 15.52 % Favored : 83.27 % 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: 1.56 (0.19), residues: 1944 helix: 1.58 (0.16), residues: 1056 sheet: 0.17 (0.28), residues: 276 loop : 0.71 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 283 HIS 0.002 0.001 HIS A 241 PHE 0.009 0.001 PHE F 257 TYR 0.010 0.001 TYR D 446 ARG 0.004 0.000 ARG E 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.920 Fit side-chains outliers start: 20 outliers final: 3 residues processed: 159 average time/residue: 1.4753 time to fit residues: 257.0632 Evaluate side-chains 133 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.6957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15765 Z= 0.337 Angle : 0.525 7.074 21294 Z= 0.277 Chirality : 0.044 0.171 2478 Planarity : 0.004 0.057 2694 Dihedral : 14.313 179.022 2472 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.39 % Allowed : 15.22 % Favored : 83.39 % 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: 1.41 (0.19), residues: 1944 helix: 1.50 (0.16), residues: 1071 sheet: 0.27 (0.28), residues: 276 loop : 0.44 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 283 HIS 0.004 0.001 HIS B 348 PHE 0.008 0.001 PHE D 311 TYR 0.011 0.001 TYR D 362 ARG 0.008 0.001 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 2.105 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 148 average time/residue: 1.4409 time to fit residues: 233.7987 Evaluate side-chains 135 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 437 SER Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.7030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15765 Z= 0.332 Angle : 0.515 6.998 21294 Z= 0.272 Chirality : 0.044 0.168 2478 Planarity : 0.004 0.058 2694 Dihedral : 14.295 178.179 2472 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.15 % Allowed : 15.58 % Favored : 83.27 % 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: 1.40 (0.19), residues: 1944 helix: 1.47 (0.16), residues: 1074 sheet: 0.34 (0.29), residues: 276 loop : 0.41 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 283 HIS 0.005 0.001 HIS B 348 PHE 0.010 0.001 PHE E 257 TYR 0.011 0.001 TYR D 442 ARG 0.007 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.924 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 145 average time/residue: 1.4272 time to fit residues: 227.6405 Evaluate side-chains 137 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.7053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15765 Z= 0.195 Angle : 0.470 7.256 21294 Z= 0.250 Chirality : 0.041 0.156 2478 Planarity : 0.004 0.049 2694 Dihedral : 13.854 179.963 2472 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.91 % Allowed : 15.88 % Favored : 83.21 % 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: 1.55 (0.19), residues: 1944 helix: 1.58 (0.16), residues: 1077 sheet: 0.44 (0.29), residues: 276 loop : 0.49 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 283 HIS 0.002 0.001 HIS B 348 PHE 0.007 0.001 PHE D 311 TYR 0.008 0.001 TYR D 362 ARG 0.011 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.920 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 143 average time/residue: 1.4547 time to fit residues: 227.8113 Evaluate side-chains 136 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15765 Z= 0.296 Angle : 0.505 7.283 21294 Z= 0.266 Chirality : 0.043 0.162 2478 Planarity : 0.004 0.055 2694 Dihedral : 14.105 179.840 2472 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.85 % Allowed : 16.24 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.19), residues: 1944 helix: 1.55 (0.16), residues: 1074 sheet: 0.46 (0.29), residues: 276 loop : 0.44 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 283 HIS 0.004 0.001 HIS B 348 PHE 0.010 0.001 PHE E 257 TYR 0.012 0.001 TYR D 446 ARG 0.009 0.001 ARG F 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 2.036 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 138 average time/residue: 1.4223 time to fit residues: 215.8392 Evaluate side-chains 135 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.7074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15765 Z= 0.332 Angle : 0.520 7.417 21294 Z= 0.274 Chirality : 0.043 0.167 2478 Planarity : 0.004 0.057 2694 Dihedral : 14.183 179.068 2472 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.79 % Allowed : 16.24 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.19), residues: 1944 helix: 1.50 (0.16), residues: 1074 sheet: 0.46 (0.29), residues: 276 loop : 0.42 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 283 HIS 0.005 0.001 HIS B 348 PHE 0.008 0.001 PHE D 311 TYR 0.013 0.001 TYR D 446 ARG 0.009 0.001 ARG F 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.938 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 134 average time/residue: 1.5092 time to fit residues: 221.4820 Evaluate side-chains 130 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 437 SER Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15765 Z= 0.298 Angle : 0.514 7.607 21294 Z= 0.271 Chirality : 0.043 0.164 2478 Planarity : 0.004 0.056 2694 Dihedral : 14.099 179.816 2472 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.48 % Allowed : 16.73 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.19), residues: 1944 helix: 1.49 (0.16), residues: 1077 sheet: 0.45 (0.28), residues: 276 loop : 0.44 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 283 HIS 0.004 0.001 HIS B 348 PHE 0.011 0.001 PHE E 257 TYR 0.013 0.001 TYR D 446 ARG 0.009 0.001 ARG F 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.739 Fit side-chains outliers start: 8 outliers final: 9 residues processed: 128 average time/residue: 1.5044 time to fit residues: 211.5754 Evaluate side-chains 131 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 349 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 136 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.059713 restraints weight = 27693.526| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.30 r_work: 0.2636 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.7137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15765 Z= 0.138 Angle : 0.452 7.971 21294 Z= 0.242 Chirality : 0.040 0.158 2478 Planarity : 0.004 0.052 2694 Dihedral : 13.106 178.445 2472 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.48 % Allowed : 16.49 % Favored : 83.03 % 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: 1.70 (0.19), residues: 1944 helix: 1.67 (0.16), residues: 1074 sheet: 0.52 (0.29), residues: 276 loop : 0.62 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 283 HIS 0.003 0.000 HIS C 316 PHE 0.007 0.001 PHE D 257 TYR 0.019 0.001 TYR F 446 ARG 0.009 0.000 ARG E 414 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 5063.91 seconds wall clock time: 89 minutes 26.88 seconds (5366.88 seconds total)