Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 04:55:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpm_14858/04_2023/7zpm_14858.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpm_14858/04_2023/7zpm_14858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpm_14858/04_2023/7zpm_14858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpm_14858/04_2023/7zpm_14858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpm_14858/04_2023/7zpm_14858.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpm_14858/04_2023/7zpm_14858.pdb" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 12231 2.51 5 N 3309 2.21 5 O 3642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "D PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 581": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 19330 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4142 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 28, 'TRANS': 486} Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4853 Classifications: {'peptide': 610} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 581} Chain breaks: 3 Chain: "C" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 659 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 6, 'TRANS': 73} Chain: "D" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4133 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain: "E" Number of atoms: 4884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4884 Classifications: {'peptide': 613} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 584} Chain breaks: 3 Chain: "F" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 659 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 6, 'TRANS': 73} Time building chain proxies: 9.86, per 1000 atoms: 0.51 Number of scatterers: 19330 At special positions: 0 Unit cell: (115.523, 187.829, 95.5765, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 3642 8.00 N 3309 7.00 C 12231 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: 7.19 Conformation dependent library (CDL) restraints added in 2.8 seconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 23 sheets defined 49.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.634A pdb=" N ARG A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.744A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 345 removed outlier: 3.547A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.718A pdb=" N GLU A 349 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.052A pdb=" N LYS A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 476 removed outlier: 3.597A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.776A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 604 removed outlier: 3.576A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.106A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.596A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.800A pdb=" N GLU B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.594A pdb=" N LEU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.657A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.848A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 275 through 292 removed outlier: 4.033A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.622A pdb=" N VAL B 336 " --> pdb=" O TRP B 332 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.637A pdb=" N ILE B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.506A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.519A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 538 removed outlier: 3.779A pdb=" N MET B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'C' and resid 42 through 53 removed outlier: 3.572A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.729A pdb=" N THR C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.869A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'D' and resid 209 through 216 removed outlier: 3.894A pdb=" N ASP D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 235 removed outlier: 3.633A pdb=" N GLY D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 249 removed outlier: 3.822A pdb=" N GLY D 244 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 312 Processing helix chain 'D' and resid 330 through 345 removed outlier: 3.548A pdb=" N TYR D 334 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 removed outlier: 3.666A pdb=" N GLU D 349 " --> pdb=" O GLN D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 370 Processing helix chain 'D' and resid 380 through 385 removed outlier: 4.043A pdb=" N LYS D 385 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 415 Processing helix chain 'D' and resid 433 through 451 removed outlier: 3.680A pdb=" N GLU D 449 " --> pdb=" O TYR D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 476 Processing helix chain 'D' and resid 533 through 538 removed outlier: 3.738A pdb=" N GLU D 538 " --> pdb=" O HIS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 582 through 603 removed outlier: 3.586A pdb=" N LEU D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL D 602 " --> pdb=" O ALA D 598 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 613 Processing helix chain 'D' and resid 632 through 650 Processing helix chain 'D' and resid 652 through 674 removed outlier: 4.013A pdb=" N LYS D 664 " --> pdb=" O ALA D 660 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 665 " --> pdb=" O GLU D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 692 Processing helix chain 'D' and resid 697 through 715 removed outlier: 3.631A pdb=" N LEU D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 11 Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 84 through 99 Processing helix chain 'E' and resid 101 through 116 removed outlier: 4.275A pdb=" N GLN E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 138 through 153 removed outlier: 3.945A pdb=" N ALA E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 161 removed outlier: 3.884A pdb=" N GLY E 161 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 173 removed outlier: 3.599A pdb=" N PHE E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 213 through 221 Processing helix chain 'E' and resid 248 through 265 removed outlier: 3.557A pdb=" N PHE E 254 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 255 " --> pdb=" O PHE E 251 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS E 265 " --> pdb=" O SER E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 289 removed outlier: 3.811A pdb=" N ALA E 280 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 Processing helix chain 'E' and resid 330 through 338 Processing helix chain 'E' and resid 339 through 346 Processing helix chain 'E' and resid 369 through 373 removed outlier: 3.528A pdb=" N MET E 372 " --> pdb=" O PRO E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 381 removed outlier: 3.665A pdb=" N TYR E 380 " --> pdb=" O ASP E 377 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E 381 " --> pdb=" O LEU E 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 381' Processing helix chain 'E' and resid 382 through 393 removed outlier: 3.774A pdb=" N GLU E 387 " --> pdb=" O LYS E 383 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 426 removed outlier: 3.598A pdb=" N LEU E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 455 through 473 removed outlier: 3.530A pdb=" N VAL E 473 " --> pdb=" O THR E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 538 removed outlier: 3.757A pdb=" N MET E 523 " --> pdb=" O GLU E 519 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER E 524 " --> pdb=" O SER E 520 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP E 538 " --> pdb=" O MET E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 560 Processing helix chain 'E' and resid 572 through 583 Processing helix chain 'E' and resid 590 through 594 Processing helix chain 'E' and resid 607 through 612 Processing helix chain 'E' and resid 617 through 625 Processing helix chain 'F' and resid 42 through 52 removed outlier: 3.585A pdb=" N ALA F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 66 Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.739A pdb=" N THR F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 115 removed outlier: 3.793A pdb=" N TYR F 115 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 294 removed outlier: 4.044A pdb=" N ARG A 496 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 294 removed outlier: 4.044A pdb=" N ARG A 496 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 355 Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.912A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.502A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AB1, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB3, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.752A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 258 through 259 removed outlier: 4.763A pdb=" N ASP E 305 " --> pdb=" O SER E 478 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N LYS E 480 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N THR E 303 " --> pdb=" O LYS E 480 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N SER E 482 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 11.498A pdb=" N THR E 301 " --> pdb=" O SER E 482 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N ILE E 484 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 11.334A pdb=" N SER E 299 " --> pdb=" O ILE E 484 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 290 through 294 removed outlier: 7.444A pdb=" N TYR D 501 " --> pdb=" O PHE D 525 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLY D 555 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG D 551 " --> pdb=" O GLY D 555 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL D 557 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU D 549 " --> pdb=" O VAL D 557 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ARG D 559 " --> pdb=" O ASP D 547 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP D 547 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET D 561 " --> pdb=" O ILE D 545 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 542 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY D 546 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLU D 319 " --> pdb=" O GLY D 546 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N MET D 548 " --> pdb=" O TRP D 317 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N TRP D 317 " --> pdb=" O MET D 548 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 290 through 294 removed outlier: 6.578A pdb=" N MET D 485 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE D 503 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 483 " --> pdb=" O PHE D 503 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE D 505 " --> pdb=" O GLN D 481 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN D 481 " --> pdb=" O ILE D 505 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE D 480 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 391 through 392 Processing sheet with id=AB8, first strand: chain 'D' and resid 628 through 631 removed outlier: 6.806A pdb=" N GLU D 629 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AC1, first strand: chain 'E' and resid 128 through 130 removed outlier: 3.558A pdb=" N ARG E 135 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 179 through 182 Processing sheet with id=AC3, first strand: chain 'E' and resid 223 through 224 removed outlier: 6.642A pdb=" N LEU E 224 " --> pdb=" O ARG E 350 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS E 347 " --> pdb=" O LEU E 403 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 489 through 491 Processing sheet with id=AC5, first strand: chain 'E' and resid 667 through 668 removed outlier: 4.631A pdb=" N ILE E 667 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THR F 81 " --> pdb=" O MET F 90 " (cutoff:3.500A) 927 hydrogen bonds defined for protein. 2514 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: 6.08 Time building geometry restraints manager: 7.82 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: 6319 1.34 - 1.46: 3423 1.46 - 1.57: 9749 1.57 - 1.69: 0 1.69 - 1.81: 256 Bond restraints: 19747 Sorted by residual: bond pdb=" CG1 ILE B 389 " pdb=" CD1 ILE B 389 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.13e+00 bond pdb=" CG GLU E 109 " pdb=" CD GLU E 109 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.67e-01 bond pdb=" CB PRO B 272 " pdb=" CG PRO B 272 " ideal model delta sigma weight residual 1.506 1.536 -0.030 3.90e-02 6.57e+02 5.93e-01 bond pdb=" CB PRO A 376 " pdb=" CG PRO A 376 " ideal model delta sigma weight residual 1.492 1.455 0.037 5.00e-02 4.00e+02 5.44e-01 bond pdb=" CB GLU A 449 " pdb=" CG GLU A 449 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.64e-01 ... (remaining 19742 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.89: 530 105.89 - 112.93: 10481 112.93 - 119.96: 6821 119.96 - 127.00: 8590 127.00 - 134.03: 259 Bond angle restraints: 26681 Sorted by residual: angle pdb=" N GLU E 109 " pdb=" CA GLU E 109 " pdb=" CB GLU E 109 " ideal model delta sigma weight residual 110.28 114.78 -4.50 1.55e+00 4.16e-01 8.43e+00 angle pdb=" C GLU D 298 " pdb=" N GLY D 299 " pdb=" CA GLY D 299 " ideal model delta sigma weight residual 121.41 126.79 -5.38 1.96e+00 2.60e-01 7.52e+00 angle pdb=" N GLY D 299 " pdb=" CA GLY D 299 " pdb=" C GLY D 299 " ideal model delta sigma weight residual 113.18 119.56 -6.38 2.37e+00 1.78e-01 7.24e+00 angle pdb=" C ARG B 386 " pdb=" N GLU B 387 " pdb=" CA GLU B 387 " ideal model delta sigma weight residual 120.72 116.27 4.45 1.67e+00 3.59e-01 7.09e+00 angle pdb=" N GLU B 387 " pdb=" CA GLU B 387 " pdb=" CB GLU B 387 " ideal model delta sigma weight residual 110.39 114.55 -4.16 1.66e+00 3.63e-01 6.27e+00 ... (remaining 26676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 10971 17.43 - 34.87: 885 34.87 - 52.30: 140 52.30 - 69.73: 36 69.73 - 87.17: 16 Dihedral angle restraints: 12048 sinusoidal: 5022 harmonic: 7026 Sorted by residual: dihedral pdb=" CA MET A 523 " pdb=" C MET A 523 " pdb=" N GLU A 524 " pdb=" CA GLU A 524 " ideal model delta harmonic sigma weight residual 180.00 -162.56 -17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA TYR D 540 " pdb=" C TYR D 540 " pdb=" N CYS D 541 " pdb=" CA CYS D 541 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA TRP E 613 " pdb=" C TRP E 613 " pdb=" N GLU E 614 " pdb=" CA GLU E 614 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 12045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1904 0.035 - 0.069: 762 0.069 - 0.104: 174 0.104 - 0.138: 62 0.138 - 0.173: 4 Chirality restraints: 2906 Sorted by residual: chirality pdb=" CB VAL D 450 " pdb=" CA VAL D 450 " pdb=" CG1 VAL D 450 " pdb=" CG2 VAL D 450 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CB VAL A 450 " pdb=" CA VAL A 450 " pdb=" CG1 VAL A 450 " pdb=" CG2 VAL A 450 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CG LEU D 641 " pdb=" CB LEU D 641 " pdb=" CD1 LEU D 641 " pdb=" CD2 LEU D 641 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 2903 not shown) Planarity restraints: 3441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 111 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO C 112 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 598 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C ALA A 598 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA A 598 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU A 599 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 583 " -0.179 9.50e-02 1.11e+02 8.05e-02 3.99e+00 pdb=" NE ARG A 583 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 583 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 583 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 583 " -0.006 2.00e-02 2.50e+03 ... (remaining 3438 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 54 2.44 - 3.05: 12041 3.05 - 3.67: 28880 3.67 - 4.28: 44741 4.28 - 4.90: 74460 Nonbonded interactions: 160176 Sorted by model distance: nonbonded pdb=" NE2 GLN A 217 " pdb=" OD1 ASN B 58 " model vdw 1.820 2.520 nonbonded pdb=" O THR E 323 " pdb=" NH2 ARG E 334 " model vdw 2.171 2.520 nonbonded pdb=" OH TYR E 129 " pdb=" OD1 ASN E 134 " model vdw 2.194 2.440 nonbonded pdb=" OE1 GLU E 267 " pdb=" NZ LYS E 288 " model vdw 2.209 2.520 nonbonded pdb=" O ILE B 18 " pdb=" OG1 THR B 21 " model vdw 2.231 2.440 ... (remaining 160171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 203 through 716) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 1 through 633 or resid 657 through 670)) selection = (chain 'E' and (resid 1 through 183 or resid 209 through 633 or resid 657 throug \ h 670)) } ncs_group { reference = chain 'C' 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=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: 7.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.250 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 47.520 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 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 : 0.002 0.041 19747 Z= 0.152 Angle : 0.494 8.666 26681 Z= 0.255 Chirality : 0.040 0.173 2906 Planarity : 0.004 0.080 3441 Dihedral : 13.141 87.166 7500 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.40 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.23 (0.17), residues: 2388 helix: 0.60 (0.16), residues: 1074 sheet: -0.20 (0.32), residues: 243 loop : -0.86 (0.19), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 254 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 257 average time/residue: 1.8447 time to fit residues: 518.0094 Evaluate side-chains 177 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.1350 time to fit residues: 4.3628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 392 GLN B 367 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN D 392 GLN E 367 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 19747 Z= 0.298 Angle : 0.586 8.682 26681 Z= 0.299 Chirality : 0.042 0.249 2906 Planarity : 0.004 0.067 3441 Dihedral : 3.917 16.926 2610 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.31 (0.17), residues: 2388 helix: 1.11 (0.16), residues: 1090 sheet: 0.07 (0.32), residues: 246 loop : -0.68 (0.19), residues: 1052 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 7 residues processed: 183 average time/residue: 1.7167 time to fit residues: 348.0286 Evaluate side-chains 171 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 2.279 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 5 average time/residue: 0.6574 time to fit residues: 7.1844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.0670 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 overall best weight: 0.7922 ------------------------------------------------------------------------------- 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** B 47 HIS ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN E 329 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN F 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 19747 Z= 0.173 Angle : 0.526 9.028 26681 Z= 0.266 Chirality : 0.040 0.253 2906 Planarity : 0.004 0.062 3441 Dihedral : 3.813 17.490 2610 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.48 (0.18), residues: 2388 helix: 1.27 (0.16), residues: 1097 sheet: 0.28 (0.33), residues: 247 loop : -0.65 (0.19), residues: 1044 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 170 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 7 residues processed: 187 average time/residue: 1.6279 time to fit residues: 339.2378 Evaluate side-chains 167 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 2.490 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.9849 time to fit residues: 6.8690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 231 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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** B 312 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 ASN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.041 19747 Z= 0.458 Angle : 0.643 9.299 26681 Z= 0.324 Chirality : 0.044 0.221 2906 Planarity : 0.004 0.059 3441 Dihedral : 4.129 20.276 2610 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.38 (0.18), residues: 2388 helix: 1.22 (0.16), residues: 1096 sheet: 0.19 (0.34), residues: 247 loop : -0.73 (0.19), residues: 1045 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 11 residues processed: 182 average time/residue: 1.6143 time to fit residues: 326.7487 Evaluate side-chains 169 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 2.283 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 5 average time/residue: 0.6639 time to fit residues: 7.2076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 197 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.0870 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN F 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 19747 Z= 0.177 Angle : 0.561 11.597 26681 Z= 0.277 Chirality : 0.040 0.312 2906 Planarity : 0.004 0.061 3441 Dihedral : 3.953 20.794 2610 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.60 (0.18), residues: 2388 helix: 1.37 (0.16), residues: 1100 sheet: 0.32 (0.33), residues: 252 loop : -0.60 (0.20), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 176 average time/residue: 1.6365 time to fit residues: 322.1922 Evaluate side-chains 167 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 2.445 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 4 average time/residue: 0.8202 time to fit residues: 7.3425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.043 19747 Z= 0.470 Angle : 0.659 13.414 26681 Z= 0.326 Chirality : 0.045 0.208 2906 Planarity : 0.004 0.058 3441 Dihedral : 4.176 25.101 2610 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.43 (0.18), residues: 2388 helix: 1.28 (0.16), residues: 1097 sheet: 0.16 (0.33), residues: 250 loop : -0.72 (0.19), residues: 1041 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 174 average time/residue: 1.6377 time to fit residues: 319.1001 Evaluate side-chains 172 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 2.623 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 6 average time/residue: 0.6710 time to fit residues: 8.6008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 129 optimal weight: 0.0870 chunk 231 optimal weight: 0.0980 chunk 144 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 19747 Z= 0.152 Angle : 0.572 11.880 26681 Z= 0.279 Chirality : 0.040 0.172 2906 Planarity : 0.004 0.064 3441 Dihedral : 3.956 26.176 2610 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.63 (0.18), residues: 2388 helix: 1.41 (0.16), residues: 1101 sheet: 0.33 (0.33), residues: 250 loop : -0.59 (0.20), residues: 1037 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 178 average time/residue: 1.5288 time to fit residues: 306.6159 Evaluate side-chains 168 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 2.387 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 2 average time/residue: 0.3549 time to fit residues: 4.2838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 147 optimal weight: 0.1980 chunk 157 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 19747 Z= 0.184 Angle : 0.591 14.529 26681 Z= 0.285 Chirality : 0.040 0.347 2906 Planarity : 0.004 0.056 3441 Dihedral : 3.909 28.592 2610 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.67 (0.18), residues: 2388 helix: 1.46 (0.16), residues: 1101 sheet: 0.32 (0.33), residues: 245 loop : -0.59 (0.20), residues: 1042 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 176 average time/residue: 1.5100 time to fit residues: 298.6646 Evaluate side-chains 168 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 2.347 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 2 average time/residue: 0.3343 time to fit residues: 4.3160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.4980 chunk 221 optimal weight: 0.8980 chunk 202 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 0.0970 chunk 66 optimal weight: 6.9990 chunk 194 optimal weight: 0.4980 chunk 203 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19747 Z= 0.165 Angle : 0.603 13.745 26681 Z= 0.289 Chirality : 0.040 0.345 2906 Planarity : 0.004 0.077 3441 Dihedral : 3.892 29.839 2610 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.70 (0.18), residues: 2388 helix: 1.47 (0.16), residues: 1102 sheet: 0.37 (0.33), residues: 243 loop : -0.56 (0.20), residues: 1043 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 180 average time/residue: 1.4892 time to fit residues: 302.9394 Evaluate side-chains 167 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 2.675 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 3 average time/residue: 0.3935 time to fit residues: 5.2745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 19747 Z= 0.273 Angle : 0.655 13.640 26681 Z= 0.311 Chirality : 0.042 0.379 2906 Planarity : 0.004 0.054 3441 Dihedral : 3.982 29.095 2610 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.75 (0.18), residues: 2388 helix: 1.58 (0.16), residues: 1089 sheet: 0.28 (0.33), residues: 248 loop : -0.57 (0.20), residues: 1051 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 168 average time/residue: 1.5324 time to fit residues: 290.6543 Evaluate side-chains 167 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 2.453 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 3 average time/residue: 0.7227 time to fit residues: 6.2362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 190 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.061856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.041791 restraints weight = 66783.275| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.16 r_work: 0.2656 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19747 Z= 0.184 Angle : 0.643 13.878 26681 Z= 0.303 Chirality : 0.041 0.365 2906 Planarity : 0.004 0.058 3441 Dihedral : 3.921 28.557 2610 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.52 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.72 (0.18), residues: 2388 helix: 1.50 (0.16), residues: 1103 sheet: 0.30 (0.33), residues: 245 loop : -0.54 (0.20), residues: 1040 =============================================================================== Job complete usr+sys time: 6153.58 seconds wall clock time: 111 minutes 14.75 seconds (6674.75 seconds total)