Starting phenix.real_space_refine on Mon Jul 22 18:17:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpm_14858/07_2024/7zpm_14858.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpm_14858/07_2024/7zpm_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_14858/07_2024/7zpm_14858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpm_14858/07_2024/7zpm_14858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpm_14858/07_2024/7zpm_14858.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpm_14858/07_2024/7zpm_14858.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 10.89, per 1000 atoms: 0.56 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: 7.42 Conformation dependent library (CDL) restraints added in 3.0 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: 2.42 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: 7.21 Time building geometry restraints manager: 8.21 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: 4.370 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 53.180 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.720 ------------------------------------------------------------------------------- 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 % Allowed : 0.47 % Favored : 99.39 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 131 HIS 0.005 0.001 HIS D 713 PHE 0.012 0.001 PHE E 357 TYR 0.018 0.001 TYR E 253 ARG 0.006 0.000 ARG E 334 *********************** 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 : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 206 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6996 (mm-30) outliers start: 3 outliers final: 1 residues processed: 257 average time/residue: 1.7886 time to fit residues: 503.3554 Evaluate side-chains 176 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 MET 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: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19747 Z= 0.297 Angle : 0.583 8.581 26681 Z= 0.298 Chirality : 0.042 0.247 2906 Planarity : 0.004 0.068 3441 Dihedral : 4.035 48.243 2613 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 1.31 % Allowed : 7.24 % Favored : 91.46 % 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 : -0.67 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 580 HIS 0.005 0.001 HIS D 297 PHE 0.024 0.001 PHE B 166 TYR 0.013 0.001 TYR E 253 ARG 0.011 0.001 ARG A 269 *********************** 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: 28 poor density : 175 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 356 MET cc_start: 0.8030 (ttt) cc_final: 0.6090 (tpt) REVERT: B 507 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8125 (mpp) REVERT: D 211 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7980 (mtm) REVERT: E 113 ILE cc_start: 0.9275 (tp) cc_final: 0.9022 (pp) outliers start: 28 outliers final: 7 residues processed: 183 average time/residue: 1.6060 time to fit residues: 325.3777 Evaluate side-chains 176 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain E residue 120 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 218 optimal weight: 0.5980 chunk 235 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 216 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19747 Z= 0.207 Angle : 0.529 8.099 26681 Z= 0.268 Chirality : 0.040 0.249 2906 Planarity : 0.004 0.061 3441 Dihedral : 3.972 48.584 2613 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 1.77 % Allowed : 8.26 % Favored : 89.96 % 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: 0.46 (0.18), residues: 2388 helix: 1.26 (0.16), residues: 1097 sheet: 0.22 (0.33), residues: 247 loop : -0.66 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 580 HIS 0.004 0.001 HIS D 297 PHE 0.010 0.001 PHE E 333 TYR 0.011 0.001 TYR E 253 ARG 0.011 0.000 ARG B 365 *********************** 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 209 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 ILE cc_start: 0.9274 (tp) cc_final: 0.9036 (pp) REVERT: E 409 MET cc_start: 0.6675 (ppp) cc_final: 0.6465 (ppp) outliers start: 38 outliers final: 11 residues processed: 190 average time/residue: 1.5212 time to fit residues: 321.3713 Evaluate side-chains 171 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain F residue 60 ASP 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: 0.5980 chunk 113 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2061 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= 0.222 Angle : 0.542 10.585 26681 Z= 0.269 Chirality : 0.041 0.321 2906 Planarity : 0.004 0.060 3441 Dihedral : 3.841 18.319 2610 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 1.31 % Allowed : 10.60 % Favored : 88.10 % 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: 0.56 (0.18), residues: 2388 helix: 1.34 (0.16), residues: 1100 sheet: 0.30 (0.33), residues: 250 loop : -0.63 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 580 HIS 0.004 0.001 HIS D 297 PHE 0.028 0.001 PHE B 166 TYR 0.011 0.001 TYR E 253 ARG 0.007 0.000 ARG D 213 *********************** 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 191 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 409 MET cc_start: 0.7103 (ptt) cc_final: 0.6819 (ptt) REVERT: B 507 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8125 (mpp) REVERT: D 378 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8591 (tppt) REVERT: E 113 ILE cc_start: 0.9300 (tp) cc_final: 0.9070 (pp) outliers start: 28 outliers final: 12 residues processed: 177 average time/residue: 1.5670 time to fit residues: 308.3914 Evaluate side-chains 168 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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** F 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19747 Z= 0.278 Angle : 0.564 10.395 26681 Z= 0.280 Chirality : 0.041 0.270 2906 Planarity : 0.004 0.058 3441 Dihedral : 3.881 18.818 2610 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 1.59 % Allowed : 11.58 % Favored : 86.83 % 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: 0.59 (0.18), residues: 2388 helix: 1.38 (0.16), residues: 1097 sheet: 0.31 (0.33), residues: 250 loop : -0.62 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 580 HIS 0.004 0.001 HIS D 297 PHE 0.030 0.001 PHE B 166 TYR 0.011 0.001 TYR E 253 ARG 0.006 0.000 ARG C 62 *********************** 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 191 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 378 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8881 (tppt) REVERT: D 423 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.8979 (m) REVERT: E 113 ILE cc_start: 0.9296 (tp) cc_final: 0.9062 (pp) outliers start: 34 outliers final: 16 residues processed: 175 average time/residue: 1.4852 time to fit residues: 289.6809 Evaluate side-chains 172 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19747 Z= 0.290 Angle : 0.579 11.307 26681 Z= 0.286 Chirality : 0.041 0.218 2906 Planarity : 0.004 0.062 3441 Dihedral : 3.941 22.411 2610 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 1.59 % Allowed : 11.81 % Favored : 86.60 % 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: 1.39 (0.16), residues: 1097 sheet: 0.30 (0.33), residues: 250 loop : -0.61 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 580 HIS 0.004 0.001 HIS D 297 PHE 0.018 0.001 PHE B 357 TYR 0.011 0.001 TYR E 253 ARG 0.015 0.000 ARG B 126 *********************** 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 192 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 158 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7945 (tt0) outliers start: 34 outliers final: 18 residues processed: 178 average time/residue: 1.5259 time to fit residues: 306.7009 Evaluate side-chains 172 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 129 optimal weight: 0.0970 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19747 Z= 0.169 Angle : 0.578 13.400 26681 Z= 0.278 Chirality : 0.040 0.295 2906 Planarity : 0.004 0.059 3441 Dihedral : 3.858 26.188 2610 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.39 % Favored : 96.57 % Rotamer: Outliers : 1.17 % Allowed : 12.79 % Favored : 86.04 % 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: 0.69 (0.18), residues: 2388 helix: 1.48 (0.16), residues: 1089 sheet: 0.31 (0.33), residues: 243 loop : -0.55 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 577 HIS 0.004 0.001 HIS A 713 PHE 0.032 0.001 PHE B 166 TYR 0.009 0.001 TYR E 253 ARG 0.008 0.000 ARG C 62 *********************** 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: 25 poor density : 157 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.9085 (ptp) cc_final: 0.8880 (ppp) REVERT: B 372 MET cc_start: 0.8748 (tpp) cc_final: 0.8537 (tpp) REVERT: B 409 MET cc_start: 0.6988 (ptt) cc_final: 0.6735 (ptt) REVERT: D 391 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8513 (pptt) REVERT: E 113 ILE cc_start: 0.9288 (tp) cc_final: 0.8978 (pp) outliers start: 25 outliers final: 9 residues processed: 173 average time/residue: 1.4537 time to fit residues: 281.2860 Evaluate side-chains 163 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 60 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19747 Z= 0.183 Angle : 0.589 13.767 26681 Z= 0.283 Chirality : 0.040 0.259 2906 Planarity : 0.004 0.082 3441 Dihedral : 3.844 27.188 2610 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 1.26 % Allowed : 12.98 % Favored : 85.76 % 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: 0.76 (0.18), residues: 2388 helix: 1.54 (0.16), residues: 1089 sheet: 0.35 (0.33), residues: 245 loop : -0.53 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 577 HIS 0.003 0.001 HIS D 713 PHE 0.037 0.001 PHE B 166 TYR 0.011 0.001 TYR F 118 ARG 0.016 0.000 ARG B 126 *********************** 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 187 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 MET cc_start: 0.7546 (mpp) cc_final: 0.7308 (mpp) REVERT: B 40 MET cc_start: 0.9083 (ptp) cc_final: 0.8868 (ppp) REVERT: B 409 MET cc_start: 0.6847 (ptt) cc_final: 0.6519 (ptt) REVERT: D 391 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8517 (pptt) REVERT: E 113 ILE cc_start: 0.9270 (tp) cc_final: 0.8958 (pp) REVERT: E 407 MET cc_start: 0.7763 (mtp) cc_final: 0.7488 (mmt) REVERT: E 409 MET cc_start: 0.6604 (ppp) cc_final: 0.6144 (ppp) outliers start: 27 outliers final: 17 residues processed: 178 average time/residue: 1.4452 time to fit residues: 288.6455 Evaluate side-chains 172 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.8980 chunk 221 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19747 Z= 0.209 Angle : 0.606 13.503 26681 Z= 0.291 Chirality : 0.040 0.230 2906 Planarity : 0.004 0.057 3441 Dihedral : 3.847 27.506 2610 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.39 % Favored : 96.57 % Rotamer: Outliers : 1.17 % Allowed : 13.91 % Favored : 84.92 % 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: 0.79 (0.18), residues: 2388 helix: 1.57 (0.16), residues: 1088 sheet: 0.31 (0.33), residues: 245 loop : -0.51 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 580 HIS 0.003 0.000 HIS D 297 PHE 0.015 0.001 PHE B 357 TYR 0.011 0.001 TYR E 253 ARG 0.012 0.000 ARG E 126 *********************** 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 181 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 MET cc_start: 0.7578 (mpp) cc_final: 0.7304 (mpp) REVERT: B 174 MET cc_start: 0.8772 (pmm) cc_final: 0.8559 (pmm) REVERT: B 409 MET cc_start: 0.6848 (ptt) cc_final: 0.6417 (ptt) REVERT: D 391 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8543 (pptt) REVERT: E 113 ILE cc_start: 0.9261 (tp) cc_final: 0.8952 (pp) REVERT: E 407 MET cc_start: 0.7784 (mtp) cc_final: 0.7577 (mmt) REVERT: E 409 MET cc_start: 0.6587 (ppp) cc_final: 0.6127 (ppp) outliers start: 25 outliers final: 16 residues processed: 171 average time/residue: 1.4533 time to fit residues: 278.5134 Evaluate side-chains 169 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.0770 chunk 227 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2642 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= 0.168 Angle : 0.617 13.688 26681 Z= 0.291 Chirality : 0.040 0.213 2906 Planarity : 0.004 0.077 3441 Dihedral : 3.816 26.799 2610 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 0.93 % Allowed : 14.19 % Favored : 84.87 % 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: 0.82 (0.18), residues: 2388 helix: 1.59 (0.16), residues: 1090 sheet: 0.33 (0.33), residues: 247 loop : -0.47 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 98 HIS 0.003 0.000 HIS A 713 PHE 0.036 0.001 PHE B 166 TYR 0.012 0.001 TYR E 253 ARG 0.020 0.000 ARG E 126 ********************** 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 182 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 MET cc_start: 0.7557 (mpp) cc_final: 0.7274 (mpp) REVERT: B 40 MET cc_start: 0.9059 (ptp) cc_final: 0.8837 (ppp) REVERT: B 409 MET cc_start: 0.6852 (ptt) cc_final: 0.6337 (ptt) REVERT: D 391 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8585 (pptt) REVERT: E 113 ILE cc_start: 0.9225 (tp) cc_final: 0.8927 (pp) outliers start: 20 outliers final: 14 residues processed: 176 average time/residue: 1.5063 time to fit residues: 295.9098 Evaluate side-chains 169 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.1980 chunk 202 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 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** F 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.062786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.042633 restraints weight = 67091.001| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.19 r_work: 0.2681 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2731 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= 0.163 Angle : 0.625 13.539 26681 Z= 0.294 Chirality : 0.039 0.200 2906 Planarity : 0.004 0.057 3441 Dihedral : 3.785 27.610 2610 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 0.84 % Allowed : 14.24 % Favored : 84.92 % 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: 0.81 (0.18), residues: 2388 helix: 1.56 (0.16), residues: 1097 sheet: 0.36 (0.33), residues: 247 loop : -0.48 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 577 HIS 0.003 0.000 HIS A 713 PHE 0.012 0.001 PHE B 357 TYR 0.010 0.001 TYR E 253 ARG 0.009 0.000 ARG E 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6151.17 seconds wall clock time: 109 minutes 18.86 seconds (6558.86 seconds total)