Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 13:04:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/04_2023/7cmh_30406_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/04_2023/7cmh_30406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/04_2023/7cmh_30406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/04_2023/7cmh_30406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/04_2023/7cmh_30406_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/04_2023/7cmh_30406_updated.pdb" } resolution = 3.4 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= -0.000 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 4830 2.51 5 N 1179 2.21 5 O 1330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B ARG 361": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7368 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "B" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3480 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 25, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 126 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3, 111 Unusual residues: {'3PH': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Conformer: "B" Number of residues, atoms: 3, 111 Unusual residues: {'3PH': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} bond proxies already assigned to first conformer: 94 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP B 601 " occ=0.50 ... (28 atoms not shown) pdb=" OXTBTRP B 601 " occ=0.50 Time building chain proxies: 4.63, per 1000 atoms: 0.63 Number of scatterers: 7368 At special positions: 0 Unit cell: (82.916, 84.007, 127.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 1330 8.00 N 1179 7.00 C 4830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 154 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1702 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 5 sheets defined 49.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.584A pdb=" N VAL A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 207 removed outlier: 3.581A pdb=" N TRP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 195 " --> pdb=" O TRP A 191 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.704A pdb=" N LYS A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.548A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 341 removed outlier: 3.723A pdb=" N ALA A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.313A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.585A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.927A pdb=" N GLN A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 removed outlier: 3.701A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.974A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.501A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 No H-bonds generated for 'chain 'A' and resid 535 through 538' Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'B' and resid 42 through 53 removed outlier: 3.860A pdb=" N GLY B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 72 through 99 removed outlier: 3.657A pdb=" N ILE B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.734A pdb=" N VAL B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 removed outlier: 3.554A pdb=" N LEU B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 128 " --> pdb=" O TRP B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 146 removed outlier: 3.634A pdb=" N GLN B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 138 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.628A pdb=" N TRP B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 187 through 209 removed outlier: 3.592A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 218 No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'B' and resid 231 through 239 removed outlier: 3.850A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 264 through 288 removed outlier: 3.954A pdb=" N ILE B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) Proline residue: B 274 - end of helix removed outlier: 3.521A pdb=" N TYR B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 302 through 308 Processing helix chain 'B' and resid 314 through 317 No H-bonds generated for 'chain 'B' and resid 314 through 317' Processing helix chain 'B' and resid 320 through 335 removed outlier: 4.036A pdb=" N SER B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.660A pdb=" N ALA B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 368 No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 370 through 379 removed outlier: 4.049A pdb=" N THR B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 378 " --> pdb=" O SER B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 411 removed outlier: 4.025A pdb=" N ASN B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 394 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR B 402 " --> pdb=" O PHE B 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 403 " --> pdb=" O TYR B 399 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 444 removed outlier: 3.553A pdb=" N VAL B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 removed outlier: 3.836A pdb=" N GLY B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 455 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.506A pdb=" N PHE B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 490 removed outlier: 3.707A pdb=" N ASP B 478 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 479 " --> pdb=" O CYS B 475 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 225 through 227 Processing sheet with id= B, first strand: chain 'A' and resid 259 through 262 removed outlier: 7.224A pdb=" N ARG A 304 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 262 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 306 " --> pdb=" O LEU A 262 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.525A pdb=" N LEU A 400 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 432 through 434 Processing sheet with id= E, first strand: chain 'A' and resid 541 through 544 removed outlier: 5.988A pdb=" N ARG A 626 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU A 596 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 610 " --> pdb=" O ALA A 594 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 705 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: 1.90 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2161 1.34 - 1.45: 1262 1.45 - 1.57: 4079 1.57 - 1.69: 2 1.69 - 1.81: 41 Bond restraints: 7545 Sorted by residual: bond pdb=" C31 3PH B 603 " pdb=" O31 3PH B 603 " ideal model delta sigma weight residual 1.325 1.452 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C21 3PH B 603 " pdb=" O21 3PH B 603 " ideal model delta sigma weight residual 1.328 1.455 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C31 3PH B 602 " pdb=" O31 3PH B 602 " ideal model delta sigma weight residual 1.325 1.451 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C21 3PH B 602 " pdb=" O21 3PH B 602 " ideal model delta sigma weight residual 1.328 1.452 -0.124 2.00e-02 2.50e+03 3.81e+01 bond pdb=" O11 3PH B 602 " pdb=" P 3PH B 602 " ideal model delta sigma weight residual 1.703 1.608 0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 7540 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.68: 237 106.68 - 113.62: 4236 113.62 - 120.56: 3101 120.56 - 127.50: 2591 127.50 - 134.44: 94 Bond angle restraints: 10259 Sorted by residual: angle pdb=" C GLY A 175 " pdb=" N SER A 176 " pdb=" CA SER A 176 " ideal model delta sigma weight residual 122.83 129.01 -6.18 1.08e+00 8.57e-01 3.28e+01 angle pdb=" N ASN B 176 " pdb=" CA ASN B 176 " pdb=" C ASN B 176 " ideal model delta sigma weight residual 111.28 116.28 -5.00 1.09e+00 8.42e-01 2.10e+01 angle pdb=" N SER B 61 " pdb=" CA SER B 61 " pdb=" C SER B 61 " ideal model delta sigma weight residual 113.25 118.96 -5.71 1.30e+00 5.92e-01 1.93e+01 angle pdb=" N SER B 178 " pdb=" CA SER B 178 " pdb=" C SER B 178 " ideal model delta sigma weight residual 110.28 116.55 -6.27 1.48e+00 4.57e-01 1.80e+01 angle pdb=" CA SER A 176 " pdb=" C SER A 176 " pdb=" N PRO A 177 " ideal model delta sigma weight residual 118.09 121.55 -3.46 8.20e-01 1.49e+00 1.78e+01 ... (remaining 10254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 3811 16.95 - 33.89: 420 33.89 - 50.84: 105 50.84 - 67.78: 11 67.78 - 84.73: 8 Dihedral angle restraints: 4355 sinusoidal: 1701 harmonic: 2654 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 154 " pdb=" CB CYS B 154 " ideal model delta sinusoidal sigma weight residual -86.00 -37.22 -48.78 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CA SER A 176 " pdb=" C SER A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA THR B 381 " pdb=" C THR B 381 " pdb=" N SER B 382 " pdb=" CA SER B 382 " ideal model delta harmonic sigma weight residual 180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 4352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1088 0.089 - 0.178: 103 0.178 - 0.267: 8 0.267 - 0.356: 1 0.356 - 0.445: 1 Chirality restraints: 1201 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CB VAL B 492 " pdb=" CA VAL B 492 " pdb=" CG1 VAL B 492 " pdb=" CG2 VAL B 492 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 425 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1198 not shown) Planarity restraints: 1265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 228 " -0.054 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 229 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 131 " -0.041 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 132 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 460 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.69e+00 pdb=" N PRO B 461 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 461 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 461 " -0.034 5.00e-02 4.00e+02 ... (remaining 1262 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1087 2.75 - 3.29: 6706 3.29 - 3.83: 11675 3.83 - 4.36: 14043 4.36 - 4.90: 23689 Nonbonded interactions: 57200 Sorted by model distance: nonbonded pdb=" O PHE B 243 " pdb=" CE3ATRP B 601 " model vdw 2.214 3.340 nonbonded pdb=" OD1 ASN B 134 " pdb=" N ATRP B 601 " model vdw 2.224 2.520 nonbonded pdb=" O PHE B 59 " pdb=" OH TYR B 145 " model vdw 2.251 2.440 nonbonded pdb=" O VAL B 129 " pdb=" OG1 THR B 133 " model vdw 2.257 2.440 nonbonded pdb=" O PHE B 243 " pdb=" N BTRP B 601 " model vdw 2.279 2.520 ... (remaining 57195 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.50 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: 0.720 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: 0.000 Extract box with map and model: 4.250 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 22.950 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.127 7545 Z= 0.398 Angle : 1.060 10.434 10259 Z= 0.558 Chirality : 0.056 0.445 1201 Planarity : 0.007 0.081 1261 Dihedral : 15.202 84.727 2650 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.56 % Favored : 90.68 % Rotamer Outliers : 1.18 % 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: -5.98 (0.17), residues: 923 helix: -4.53 (0.10), residues: 463 sheet: -1.57 (0.58), residues: 70 loop : -3.54 (0.22), residues: 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 191 time to evaluate : 0.805 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 197 average time/residue: 0.2067 time to fit residues: 54.1688 Evaluate side-chains 137 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0727 time to fit residues: 1.4651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN A 296 GLN A 317 ASN A 353 ASN A 388 GLN ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 601 GLN A 620 HIS B 284 ASN B 331 ASN B 349 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7545 Z= 0.215 Angle : 0.679 10.440 10259 Z= 0.335 Chirality : 0.043 0.261 1201 Planarity : 0.006 0.061 1261 Dihedral : 7.558 59.188 1057 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer Outliers : 2.49 % 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: -4.09 (0.22), residues: 923 helix: -2.64 (0.18), residues: 484 sheet: -0.52 (0.67), residues: 57 loop : -3.04 (0.25), residues: 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 0.935 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 157 average time/residue: 0.1799 time to fit residues: 39.6837 Evaluate side-chains 140 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0813 time to fit residues: 2.8018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 68 optimal weight: 0.0040 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 89 optimal weight: 0.0570 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.0470 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 overall best weight: 0.2608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 7545 Z= 0.156 Angle : 0.609 8.957 10259 Z= 0.296 Chirality : 0.041 0.264 1201 Planarity : 0.004 0.052 1261 Dihedral : 7.034 58.935 1057 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer Outliers : 2.49 % 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: -2.92 (0.25), residues: 923 helix: -1.58 (0.22), residues: 477 sheet: -0.49 (0.69), residues: 57 loop : -2.54 (0.28), residues: 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 0.878 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 156 average time/residue: 0.1777 time to fit residues: 38.5562 Evaluate side-chains 139 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0782 time to fit residues: 2.4143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7545 Z= 0.218 Angle : 0.621 9.393 10259 Z= 0.302 Chirality : 0.042 0.245 1201 Planarity : 0.004 0.050 1261 Dihedral : 6.905 58.414 1057 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.83 % Favored : 93.07 % Rotamer Outliers : 3.80 % 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: -2.25 (0.26), residues: 923 helix: -0.92 (0.23), residues: 469 sheet: -0.35 (0.69), residues: 57 loop : -2.33 (0.29), residues: 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 0.829 Fit side-chains outliers start: 29 outliers final: 15 residues processed: 158 average time/residue: 0.1885 time to fit residues: 40.9736 Evaluate side-chains 149 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0711 time to fit residues: 3.1541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7545 Z= 0.178 Angle : 0.590 8.394 10259 Z= 0.286 Chirality : 0.041 0.236 1201 Planarity : 0.004 0.050 1261 Dihedral : 6.688 58.502 1057 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.42 % Rotamer Outliers : 2.23 % 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: -1.83 (0.27), residues: 923 helix: -0.53 (0.24), residues: 476 sheet: -0.32 (0.69), residues: 57 loop : -2.18 (0.30), residues: 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 0.884 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 157 average time/residue: 0.1833 time to fit residues: 40.0562 Evaluate side-chains 143 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0737 time to fit residues: 2.2757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.0070 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 0.0020 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 530 GLN B 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7545 Z= 0.166 Angle : 0.594 9.211 10259 Z= 0.285 Chirality : 0.041 0.224 1201 Planarity : 0.004 0.049 1261 Dihedral : 6.507 58.535 1057 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer Outliers : 1.96 % 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: -1.53 (0.28), residues: 923 helix: -0.27 (0.24), residues: 476 sheet: -0.31 (0.69), residues: 57 loop : -2.06 (0.30), residues: 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 0.969 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 147 average time/residue: 0.1790 time to fit residues: 37.0928 Evaluate side-chains 137 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0741 time to fit residues: 1.9811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7545 Z= 0.170 Angle : 0.592 9.403 10259 Z= 0.283 Chirality : 0.041 0.222 1201 Planarity : 0.004 0.050 1261 Dihedral : 6.329 58.282 1057 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.80 % Favored : 92.09 % Rotamer Outliers : 1.44 % 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: -1.33 (0.28), residues: 923 helix: -0.03 (0.25), residues: 473 sheet: -0.29 (0.69), residues: 57 loop : -2.03 (0.30), residues: 393 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.903 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 141 average time/residue: 0.1819 time to fit residues: 35.7954 Evaluate side-chains 138 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0737 time to fit residues: 1.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7545 Z= 0.163 Angle : 0.588 9.333 10259 Z= 0.281 Chirality : 0.041 0.217 1201 Planarity : 0.004 0.049 1261 Dihedral : 6.203 58.236 1057 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer Outliers : 0.92 % 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: -1.19 (0.28), residues: 923 helix: 0.14 (0.25), residues: 476 sheet: -0.33 (0.69), residues: 57 loop : -2.04 (0.30), residues: 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 0.914 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 144 average time/residue: 0.1881 time to fit residues: 37.6578 Evaluate side-chains 138 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0735 time to fit residues: 1.3451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 7545 Z= 0.157 Angle : 0.583 9.129 10259 Z= 0.279 Chirality : 0.041 0.216 1201 Planarity : 0.004 0.048 1261 Dihedral : 6.091 58.311 1057 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.37 % Favored : 92.52 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.05 (0.28), residues: 923 helix: 0.30 (0.25), residues: 475 sheet: -0.42 (0.69), residues: 52 loop : -1.98 (0.30), residues: 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 0.929 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 145 average time/residue: 0.1819 time to fit residues: 37.0334 Evaluate side-chains 139 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0693 time to fit residues: 1.6974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 8.9990 chunk 60 optimal weight: 0.0040 chunk 90 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7545 Z= 0.176 Angle : 0.616 10.307 10259 Z= 0.295 Chirality : 0.042 0.211 1201 Planarity : 0.004 0.049 1261 Dihedral : 6.131 58.062 1057 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer Outliers : 0.39 % 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: -0.97 (0.28), residues: 923 helix: 0.37 (0.25), residues: 473 sheet: -0.41 (0.70), residues: 52 loop : -1.94 (0.30), residues: 398 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 0.853 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 137 average time/residue: 0.1772 time to fit residues: 34.1912 Evaluate side-chains 132 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0701 time to fit residues: 1.4317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.0470 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.109565 restraints weight = 11771.928| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.81 r_work: 0.3171 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7545 Z= 0.167 Angle : 0.622 11.700 10259 Z= 0.298 Chirality : 0.041 0.211 1201 Planarity : 0.004 0.049 1261 Dihedral : 6.110 57.870 1057 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer Outliers : 1.18 % 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: -0.85 (0.28), residues: 923 helix: 0.49 (0.25), residues: 471 sheet: -0.42 (0.69), residues: 52 loop : -1.90 (0.30), residues: 400 =============================================================================== Job complete usr+sys time: 1884.76 seconds wall clock time: 34 minutes 38.02 seconds (2078.02 seconds total)