Starting phenix.real_space_refine (version: dev) on Sat Feb 18 09:34:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzw_8941/02_2023/6dzw_8941_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzw_8941/02_2023/6dzw_8941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzw_8941/02_2023/6dzw_8941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzw_8941/02_2023/6dzw_8941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzw_8941/02_2023/6dzw_8941_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzw_8941/02_2023/6dzw_8941_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 Process input model Symmetric amino acids flipped Residue "A GLU 80": "OE1" <-> "OE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "V TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 209": "OD1" <-> "OD2" Residue "V PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 219": "OD1" <-> "OD2" Residue "V TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 254": "OE1" <-> "OE2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "L PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7829 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4279 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 22, 'TRANS': 514} Chain: "V" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1743 Classifications: {'peptide': 223} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 212} Chain breaks: 1 Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'8PR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.02, per 1000 atoms: 0.64 Number of scatterers: 7829 At special positions: 0 Unit cell: (86.652, 107.532, 123.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 F 1 9.00 O 1429 8.00 N 1250 7.00 C 5109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS V 37 " - pdb=" SG CYS V 111 " distance=2.03 Simple disulfide: pdb=" SG CYS V 172 " - pdb=" SG CYS V 237 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 704 " - " ASN A 217 " " NAG B 1 " - " ASN A 208 " Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 11 sheets defined 37.8% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.949A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.650A pdb=" N VAL A 102 " --> pdb=" O LEU A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 104 through 111 removed outlier: 4.188A pdb=" N ILE A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.623A pdb=" N PHE A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Proline residue: A 120 - end of helix removed outlier: 3.744A pdb=" N ILE A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N MET A 124 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA A 125 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 126 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 127 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 removed outlier: 3.885A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 189 removed outlier: 3.692A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 163 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 165 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS A 166 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A 172 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 173 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 174 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 185 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 188 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 189 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 253 through 270 removed outlier: 3.856A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 removed outlier: 4.042A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.792A pdb=" N SER A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 3.544A pdb=" N PHE A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.650A pdb=" N ILE A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.632A pdb=" N VAL A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 389 removed outlier: 3.503A pdb=" N THR A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 397 No H-bonds generated for 'chain 'A' and resid 394 through 397' Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.841A pdb=" N LEU A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 407' Processing helix chain 'A' and resid 409 through 415 removed outlier: 3.787A pdb=" N ALA A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 414 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 415' Processing helix chain 'A' and resid 420 through 447 removed outlier: 3.976A pdb=" N ILE A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.909A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 453' Processing helix chain 'A' and resid 462 through 465 No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 467 through 479 removed outlier: 3.618A pdb=" N ILE A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.672A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 513 removed outlier: 3.776A pdb=" N VAL A 501 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.721A pdb=" N CYS A 522 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.709A pdb=" N ILE A 539 " --> pdb=" O TRP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 4.171A pdb=" N LEU A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 555 " --> pdb=" O PHE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 599 removed outlier: 3.972A pdb=" N ILE A 575 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 577 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 579 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 580 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 581 " --> pdb=" O GLY A 578 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 583 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 585 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A 587 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 589 " --> pdb=" O PHE A 586 " (cutoff:3.500A) Proline residue: A 590 - end of helix removed outlier: 4.006A pdb=" N ILE A 593 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 595 " --> pdb=" O TYR A 592 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 596 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 597 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 598 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 599 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 removed outlier: 3.843A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 79 No H-bonds generated for 'chain 'V' and resid 77 through 79' Processing helix chain 'V' and resid 103 through 105 No H-bonds generated for 'chain 'V' and resid 103 through 105' Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'L' and resid 73 through 75 No H-bonds generated for 'chain 'L' and resid 73 through 75' Processing helix chain 'L' and resid 104 through 106 No H-bonds generated for 'chain 'L' and resid 104 through 106' Processing sheet with id= A, first strand: chain 'V' and resid 33 through 38 removed outlier: 3.811A pdb=" N LEU V 98 " --> pdb=" O VAL V 33 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE V 35 " --> pdb=" O MET V 96 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET V 96 " --> pdb=" O ILE V 35 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS V 37 " --> pdb=" O ALA V 94 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA V 94 " --> pdb=" O CYS V 37 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU V 97 " --> pdb=" O THR V 84 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR V 84 " --> pdb=" O GLU V 97 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'V' and resid 128 through 130 removed outlier: 3.912A pdb=" N ALA V 107 " --> pdb=" O LEU V 130 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET V 49 " --> pdb=" O ILE V 66 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE V 66 " --> pdb=" O MET V 49 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP V 51 " --> pdb=" O GLY V 64 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY V 64 " --> pdb=" O TRP V 51 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LYS V 53 " --> pdb=" O TRP V 62 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N TRP V 62 " --> pdb=" O LYS V 53 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER V 55 " --> pdb=" O LEU V 60 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU V 60 " --> pdb=" O SER V 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'V' and resid 153 through 155 removed outlier: 3.518A pdb=" N VAL V 168 " --> pdb=" O ILE V 224 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE V 224 " --> pdb=" O VAL V 168 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE V 220 " --> pdb=" O CYS V 172 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP V 219 " --> pdb=" O SER V 216 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER V 216 " --> pdb=" O ASP V 219 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR V 221 " --> pdb=" O SER V 214 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER V 214 " --> pdb=" O THR V 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR V 223 " --> pdb=" O THR V 212 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR V 212 " --> pdb=" O THR V 223 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'V' and resid 184 through 187 removed outlier: 3.516A pdb=" N TYR V 185 " --> pdb=" O TYR V 236 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR V 236 " --> pdb=" O TYR V 185 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 22 through 25 removed outlier: 3.866A pdb=" N GLN H 22 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER H 44 " --> pdb=" O GLN H 22 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN H 24 " --> pdb=" O LYS H 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE H 39 " --> pdb=" O MET H 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS H 41 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR H 97 " --> pdb=" O ASP H 92 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP H 92 " --> pdb=" O THR H 97 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.689A pdb=" N TYR H 113 " --> pdb=" O THR H 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE H 114 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL H 56 " --> pdb=" O PHE H 114 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP H 55 " --> pdb=" O GLY H 68 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N TRP H 66 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG H 69 " --> pdb=" O LYS H 78 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS H 78 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP H 76 " --> pdb=" O TYR H 71 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 116 through 118 removed outlier: 4.362A pdb=" N TYR H 129 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 24 through 27 removed outlier: 4.224A pdb=" N SER L 27 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER L 42 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 30 through 32 removed outlier: 6.504A pdb=" N LYS L 127 " --> pdb=" O LEU L 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'L' and resid 39 through 41 removed outlier: 4.320A pdb=" N ALA L 39 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE L 99 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE L 41 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR L 94 " --> pdb=" O SER L 91 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER L 91 " --> pdb=" O TYR L 94 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER L 89 " --> pdb=" O SER L 96 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 109 through 114 removed outlier: 3.580A pdb=" N PHE L 111 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE L 60 " --> pdb=" O PHE L 111 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN L 113 " --> pdb=" O ASN L 58 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 420 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: 2.27 Time building geometry restraints manager: 3.42 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: 2288 1.34 - 1.46: 1607 1.46 - 1.57: 4098 1.57 - 1.69: 1 1.69 - 1.81: 59 Bond restraints: 8053 Sorted by residual: bond pdb=" CAT 8PR A 701 " pdb=" CAX 8PR A 701 " ideal model delta sigma weight residual 1.509 1.577 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CAV 8PR A 701 " pdb=" OAQ 8PR A 701 " ideal model delta sigma weight residual 1.354 1.415 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" CAI 8PR A 701 " pdb=" NAN 8PR A 701 " ideal model delta sigma weight residual 1.452 1.508 -0.056 2.00e-02 2.50e+03 7.86e+00 bond pdb=" CAU 8PR A 701 " pdb=" OAP 8PR A 701 " ideal model delta sigma weight residual 1.362 1.416 -0.054 2.00e-02 2.50e+03 7.16e+00 bond pdb=" CAK 8PR A 701 " pdb=" NAN 8PR A 701 " ideal model delta sigma weight residual 1.451 1.502 -0.051 2.00e-02 2.50e+03 6.39e+00 ... (remaining 8048 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.85: 230 106.85 - 113.76: 4269 113.76 - 120.66: 3468 120.66 - 127.57: 2890 127.57 - 134.48: 97 Bond angle restraints: 10954 Sorted by residual: angle pdb=" N GLY A 249 " pdb=" CA GLY A 249 " pdb=" C GLY A 249 " ideal model delta sigma weight residual 111.02 122.35 -11.33 1.86e+00 2.89e-01 3.71e+01 angle pdb=" N ILE A 251 " pdb=" CA ILE A 251 " pdb=" C ILE A 251 " ideal model delta sigma weight residual 109.30 115.39 -6.09 1.25e+00 6.40e-01 2.37e+01 angle pdb=" C GLY A 129 " pdb=" N ILE A 130 " pdb=" CA ILE A 130 " ideal model delta sigma weight residual 120.33 124.05 -3.72 8.00e-01 1.56e+00 2.16e+01 angle pdb=" C GLY H 81 " pdb=" N LYS H 82 " pdb=" CA LYS H 82 " ideal model delta sigma weight residual 122.08 128.69 -6.61 1.47e+00 4.63e-01 2.02e+01 angle pdb=" N ILE A 612 " pdb=" CA ILE A 612 " pdb=" C ILE A 612 " ideal model delta sigma weight residual 111.90 108.33 3.57 8.10e-01 1.52e+00 1.94e+01 ... (remaining 10949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4213 17.96 - 35.91: 312 35.91 - 53.86: 73 53.86 - 71.82: 10 71.82 - 89.77: 4 Dihedral angle restraints: 4612 sinusoidal: 1767 harmonic: 2845 Sorted by residual: dihedral pdb=" CA GLU L 47 " pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta harmonic sigma weight residual 0.00 32.90 -32.90 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA GLY A 249 " pdb=" C GLY A 249 " pdb=" N GLY A 250 " pdb=" CA GLY A 250 " ideal model delta harmonic sigma weight residual -180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA GLU V 254 " pdb=" C GLU V 254 " pdb=" N ILE V 255 " pdb=" CA ILE V 255 " ideal model delta harmonic sigma weight residual 0.00 20.71 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 4609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.472: 1207 0.472 - 0.943: 1 0.943 - 1.415: 0 1.415 - 1.886: 0 1.886 - 2.358: 1 Chirality restraints: 1209 Sorted by residual: chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 217 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -0.04 -2.36 2.00e-01 2.50e+01 1.39e+02 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.92e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 208 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.52e+01 ... (remaining 1206 not shown) Planarity restraints: 1354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 217 " -0.179 2.00e-02 2.50e+03 1.66e-01 3.44e+02 pdb=" CG ASN A 217 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A 217 " 0.067 2.00e-02 2.50e+03 pdb=" ND2 ASN A 217 " 0.248 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " -0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 208 " 0.100 2.00e-02 2.50e+03 1.05e-01 1.39e+02 pdb=" CG ASN A 208 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 208 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 208 " -0.162 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.095 2.00e-02 2.50e+03 7.83e-02 7.66e+01 pdb=" C7 NAG B 2 " 0.025 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.071 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.125 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.016 2.00e-02 2.50e+03 ... (remaining 1351 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 54 2.62 - 3.19: 6185 3.19 - 3.76: 11788 3.76 - 4.33: 16149 4.33 - 4.90: 25726 Nonbonded interactions: 59902 Sorted by model distance: nonbonded pdb=" O3 NAG B 2 " pdb=" O7 NAG B 2 " model vdw 2.052 2.440 nonbonded pdb=" OH TYR A 495 " pdb=" O PRO A 561 " model vdw 2.317 2.440 nonbonded pdb=" OG SER V 59 " pdb=" O GLY V 248 " model vdw 2.337 2.440 nonbonded pdb=" OG1 THR V 112 " pdb=" O TYR V 123 " model vdw 2.339 2.440 nonbonded pdb=" O SER H 96 " pdb=" OG SER H 96 " model vdw 2.340 2.440 ... (remaining 59897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 5109 2.51 5 N 1250 2.21 5 O 1429 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.570 Check model and map are aligned: 0.120 Process input model: 23.460 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.080 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5316 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 : 0.004 0.068 8053 Z= 0.236 Angle : 0.863 11.483 10954 Z= 0.466 Chirality : 0.087 2.358 1209 Planarity : 0.006 0.078 1352 Dihedral : 13.511 89.773 2793 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.19), residues: 978 helix: -4.98 (0.08), residues: 313 sheet: -1.85 (0.34), residues: 156 loop : -2.64 (0.21), residues: 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 293 time to evaluate : 0.890 Fit side-chains 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: 293 average time/residue: 0.2278 time to fit residues: 87.7895 Evaluate side-chains 196 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0747 time to fit residues: 1.3911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 0.0270 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN A 145 ASN A 223 HIS ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN V 239 GLN H 58 GLN L 58 ASN L 78 GLN L 100 HIS L 114 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8053 Z= 0.187 Angle : 0.643 17.178 10954 Z= 0.319 Chirality : 0.045 0.444 1209 Planarity : 0.005 0.038 1352 Dihedral : 4.375 20.317 1097 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.22), residues: 978 helix: -3.67 (0.18), residues: 331 sheet: -1.08 (0.37), residues: 169 loop : -1.95 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 255 time to evaluate : 0.822 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 outliers start: 2 outliers final: 0 residues processed: 256 average time/residue: 0.1725 time to fit residues: 61.8780 Evaluate side-chains 202 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 316 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 GLN V 67 ASN V 69 ASN V 157 HIS ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 114 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 8053 Z= 0.349 Angle : 0.805 18.300 10954 Z= 0.414 Chirality : 0.050 0.439 1209 Planarity : 0.005 0.048 1352 Dihedral : 5.080 28.025 1097 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.25), residues: 978 helix: -2.17 (0.25), residues: 332 sheet: -1.09 (0.35), residues: 189 loop : -1.53 (0.28), residues: 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.1877 time to fit residues: 58.2565 Evaluate side-chains 173 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 25 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 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 359 GLN A 368 ASN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN L 61 GLN L 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8053 Z= 0.158 Angle : 0.606 18.466 10954 Z= 0.293 Chirality : 0.044 0.379 1209 Planarity : 0.004 0.064 1352 Dihedral : 4.581 28.008 1097 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.26), residues: 978 helix: -1.66 (0.27), residues: 330 sheet: -0.57 (0.37), residues: 177 loop : -1.34 (0.28), residues: 471 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1941 time to fit residues: 61.3205 Evaluate side-chains 177 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 23 optimal weight: 0.0000 overall best weight: 1.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 211 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 8053 Z= 0.214 Angle : 0.658 18.878 10954 Z= 0.320 Chirality : 0.045 0.376 1209 Planarity : 0.004 0.052 1352 Dihedral : 4.705 30.900 1097 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.26), residues: 978 helix: -1.38 (0.27), residues: 332 sheet: -0.46 (0.36), residues: 183 loop : -1.29 (0.28), residues: 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1919 time to fit residues: 56.9644 Evaluate side-chains 174 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 0.3980 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 0.0070 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 391 ASN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8053 Z= 0.157 Angle : 0.602 18.440 10954 Z= 0.293 Chirality : 0.043 0.352 1209 Planarity : 0.004 0.049 1352 Dihedral : 4.533 30.713 1097 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.26), residues: 978 helix: -1.23 (0.28), residues: 330 sheet: -0.25 (0.38), residues: 180 loop : -1.10 (0.29), residues: 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1933 time to fit residues: 59.0140 Evaluate side-chains 178 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 235 HIS A 238 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** V 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8053 Z= 0.191 Angle : 0.617 18.448 10954 Z= 0.304 Chirality : 0.043 0.343 1209 Planarity : 0.004 0.045 1352 Dihedral : 4.629 31.936 1097 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.26), residues: 978 helix: -1.18 (0.28), residues: 329 sheet: -0.31 (0.37), residues: 183 loop : -1.05 (0.29), residues: 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.1982 time to fit residues: 59.2249 Evaluate side-chains 166 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 0.0770 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 81 optimal weight: 0.0270 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 368 ASN V 176 GLN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 8053 Z= 0.150 Angle : 0.614 18.071 10954 Z= 0.296 Chirality : 0.043 0.346 1209 Planarity : 0.004 0.057 1352 Dihedral : 4.517 30.790 1097 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.27), residues: 978 helix: -1.23 (0.28), residues: 330 sheet: -0.06 (0.39), residues: 180 loop : -1.02 (0.29), residues: 468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1989 time to fit residues: 58.2180 Evaluate side-chains 175 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 52 optimal weight: 0.0030 chunk 37 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 0.0270 chunk 57 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 2.0054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN V 176 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8053 Z= 0.216 Angle : 0.644 18.285 10954 Z= 0.320 Chirality : 0.043 0.336 1209 Planarity : 0.004 0.061 1352 Dihedral : 4.784 33.113 1097 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.27), residues: 978 helix: -1.15 (0.28), residues: 326 sheet: -0.21 (0.37), residues: 184 loop : -0.96 (0.30), residues: 468 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1977 time to fit residues: 56.7257 Evaluate side-chains 168 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 8053 Z= 0.151 Angle : 0.622 18.103 10954 Z= 0.299 Chirality : 0.043 0.351 1209 Planarity : 0.004 0.062 1352 Dihedral : 4.595 31.958 1097 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.27), residues: 978 helix: -1.18 (0.28), residues: 331 sheet: 0.11 (0.40), residues: 180 loop : -0.94 (0.30), residues: 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 211 average time/residue: 0.1873 time to fit residues: 54.7126 Evaluate side-chains 176 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0777 time to fit residues: 1.4077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.0030 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN L 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.184618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.147876 restraints weight = 16407.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.154044 restraints weight = 11738.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.159217 restraints weight = 8799.629| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 8053 Z= 0.158 Angle : 0.630 18.121 10954 Z= 0.304 Chirality : 0.043 0.373 1209 Planarity : 0.004 0.062 1352 Dihedral : 4.615 30.050 1097 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.27), residues: 978 helix: -1.25 (0.27), residues: 335 sheet: 0.16 (0.41), residues: 180 loop : -0.93 (0.30), residues: 463 =============================================================================== Job complete usr+sys time: 2087.17 seconds wall clock time: 39 minutes 4.87 seconds (2344.87 seconds total)