Starting phenix.real_space_refine on Mon Mar 11 09:17:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzw_8941/03_2024/6dzw_8941_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzw_8941/03_2024/6dzw_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_8941/03_2024/6dzw_8941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzw_8941/03_2024/6dzw_8941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzw_8941/03_2024/6dzw_8941_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzw_8941/03_2024/6dzw_8941_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 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. 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-5265/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.68, per 1000 atoms: 0.60 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: 2.85 Conformation dependent library (CDL) restraints added in 1.3 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: 1.52 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: 2.00 Time building geometry restraints manager: 3.13 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=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta sigma weight residual 121.70 134.48 -12.78 1.80e+00 3.09e-01 5.04e+01 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 ... (remaining 10949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.27: 4481 27.27 - 54.54: 178 54.54 - 81.80: 11 81.80 - 109.07: 3 109.07 - 136.34: 1 Dihedral angle restraints: 4674 sinusoidal: 1829 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=" CAX 8PR A 701 " pdb=" CAM 8PR A 701 " pdb=" CAW 8PR A 701 " pdb=" OAO 8PR A 701 " ideal model delta sinusoidal sigma weight residual 182.60 46.26 136.34 1 3.00e+01 1.11e-03 1.84e+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 ... (remaining 4671 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 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: 1.010 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: 3.400 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.910 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5450 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= 0.246 Angle : 0.870 12.783 10954 Z= 0.468 Chirality : 0.087 2.358 1209 Planarity : 0.006 0.078 1352 Dihedral : 13.751 136.338 2855 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 % Allowed : 5.54 % Favored : 94.10 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 151 HIS 0.001 0.000 HIS V 240 PHE 0.012 0.001 PHE A 423 TYR 0.008 0.001 TYR V 48 ARG 0.005 0.000 ARG A 596 *********************** 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 : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6967 (mp0) cc_final: 0.5820 (tt0) REVERT: A 103 TRP cc_start: 0.8712 (p-90) cc_final: 0.8297 (p-90) REVERT: A 104 ARG cc_start: 0.8278 (tpt170) cc_final: 0.7907 (tpp80) REVERT: A 111 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8359 (mm-40) REVERT: A 136 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8251 (tm-30) REVERT: A 158 PHE cc_start: 0.8517 (m-80) cc_final: 0.7924 (m-80) REVERT: A 172 ILE cc_start: 0.9383 (mt) cc_final: 0.9086 (tt) REVERT: A 187 LEU cc_start: 0.9220 (tp) cc_final: 0.9007 (tp) REVERT: A 229 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8326 (tm-30) REVERT: A 230 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8047 (mm-30) REVERT: A 253 TRP cc_start: 0.5958 (m100) cc_final: 0.5680 (p-90) REVERT: A 260 MET cc_start: 0.3788 (ttt) cc_final: 0.3560 (ttt) REVERT: A 317 TRP cc_start: 0.7144 (p-90) cc_final: 0.6853 (m-10) REVERT: A 344 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7732 (tt) REVERT: A 392 GLU cc_start: 0.5982 (mp0) cc_final: 0.5334 (mp0) REVERT: A 407 PHE cc_start: 0.8610 (m-80) cc_final: 0.8173 (m-80) REVERT: A 430 MET cc_start: 0.7831 (ttt) cc_final: 0.7181 (ttp) REVERT: A 490 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8578 (mmmt) REVERT: A 595 TYR cc_start: 0.6293 (t80) cc_final: 0.5651 (t80) REVERT: A 596 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7633 (mtt-85) REVERT: A 607 ARG cc_start: 0.7349 (ptm160) cc_final: 0.6689 (mtp180) REVERT: V 20 GLN cc_start: 0.8034 (mp10) cc_final: 0.7832 (mp10) REVERT: V 49 MET cc_start: 0.8074 (tpt) cc_final: 0.7618 (tpt) REVERT: V 63 ILE cc_start: 0.7694 (mt) cc_final: 0.7373 (mt) REVERT: V 76 ASN cc_start: 0.8140 (t0) cc_final: 0.7574 (t0) REVERT: V 244 PRO cc_start: 0.8263 (Cg_exo) cc_final: 0.8062 (Cg_endo) REVERT: L 100 HIS cc_start: 0.6117 (m170) cc_final: 0.5726 (m-70) REVERT: L 127 LYS cc_start: 0.6752 (mttt) cc_final: 0.6121 (tttm) outliers start: 3 outliers final: 1 residues processed: 293 average time/residue: 0.2323 time to fit residues: 89.1311 Evaluate side-chains 215 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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: 0.5980 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 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 114 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8053 Z= 0.193 Angle : 0.629 11.168 10954 Z= 0.318 Chirality : 0.043 0.388 1209 Planarity : 0.005 0.037 1352 Dihedral : 6.655 125.681 1159 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.24 % Allowed : 4.57 % Favored : 95.19 % 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: -3.70 (0.22), residues: 978 helix: -3.63 (0.18), residues: 332 sheet: -1.08 (0.37), residues: 173 loop : -1.99 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP V 184 HIS 0.005 0.001 HIS A 235 PHE 0.027 0.001 PHE A 191 TYR 0.018 0.001 TYR V 204 ARG 0.005 0.000 ARG H 69 *********************** 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 266 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 264 time to evaluate : 0.868 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: A 80 GLU cc_start: 0.7165 (mp0) cc_final: 0.5809 (tt0) REVERT: A 90 LEU cc_start: 0.9328 (tp) cc_final: 0.9080 (tp) REVERT: A 103 TRP cc_start: 0.8758 (p-90) cc_final: 0.8374 (p-90) REVERT: A 104 ARG cc_start: 0.8507 (tpt170) cc_final: 0.7926 (tpp80) REVERT: A 111 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8210 (mm-40) REVERT: A 132 LEU cc_start: 0.9152 (tp) cc_final: 0.8917 (tp) REVERT: A 136 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8312 (tm-30) REVERT: A 144 ARG cc_start: 0.5821 (ptm160) cc_final: 0.5519 (ptt180) REVERT: A 158 PHE cc_start: 0.8600 (m-80) cc_final: 0.8045 (m-80) REVERT: A 166 CYS cc_start: 0.8465 (t) cc_final: 0.7574 (t) REVERT: A 168 ILE cc_start: 0.9280 (mm) cc_final: 0.8935 (mm) REVERT: A 171 TYR cc_start: 0.8384 (m-10) cc_final: 0.8010 (m-10) REVERT: A 238 GLN cc_start: 0.8235 (mt0) cc_final: 0.7733 (mt0) REVERT: A 253 TRP cc_start: 0.5839 (m100) cc_final: 0.5213 (p-90) REVERT: A 260 MET cc_start: 0.4264 (ttt) cc_final: 0.4031 (ttt) REVERT: A 317 TRP cc_start: 0.7641 (p-90) cc_final: 0.6896 (m-10) REVERT: A 332 GLN cc_start: 0.7779 (tp40) cc_final: 0.7491 (tp40) REVERT: A 344 LEU cc_start: 0.8279 (tt) cc_final: 0.7553 (tt) REVERT: A 358 TYR cc_start: 0.7580 (t80) cc_final: 0.6750 (t80) REVERT: A 407 PHE cc_start: 0.9004 (m-80) cc_final: 0.8438 (m-10) REVERT: A 423 PHE cc_start: 0.8749 (m-10) cc_final: 0.8518 (m-10) REVERT: A 430 MET cc_start: 0.7621 (ttt) cc_final: 0.6712 (ttp) REVERT: A 595 TYR cc_start: 0.6355 (t80) cc_final: 0.5626 (t80) REVERT: A 596 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.7927 (mtt-85) REVERT: V 63 ILE cc_start: 0.8237 (mt) cc_final: 0.7430 (mt) REVERT: V 76 ASN cc_start: 0.7979 (t0) cc_final: 0.7759 (p0) REVERT: V 176 GLN cc_start: 0.7017 (mt0) cc_final: 0.6736 (mt0) REVERT: V 241 TYR cc_start: 0.8325 (t80) cc_final: 0.8080 (t80) REVERT: H 21 VAL cc_start: 0.7487 (t) cc_final: 0.5762 (t) REVERT: L 100 HIS cc_start: 0.5983 (m170) cc_final: 0.5640 (m-70) REVERT: L 110 TYR cc_start: 0.7978 (m-10) cc_final: 0.7302 (m-80) REVERT: L 127 LYS cc_start: 0.6872 (mttt) cc_final: 0.6230 (tttm) outliers start: 2 outliers final: 0 residues processed: 265 average time/residue: 0.1719 time to fit residues: 63.6998 Evaluate side-chains 208 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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: 3.9990 chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 0.1980 chunk 88 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 0.0000 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** 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 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8053 Z= 0.215 Angle : 0.633 9.989 10954 Z= 0.322 Chirality : 0.045 0.359 1209 Planarity : 0.004 0.057 1352 Dihedral : 6.566 127.511 1159 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.24 % Allowed : 4.69 % Favored : 95.07 % 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: -2.76 (0.24), residues: 978 helix: -2.43 (0.23), residues: 336 sheet: -0.97 (0.37), residues: 189 loop : -1.60 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP V 62 HIS 0.003 0.001 HIS A 240 PHE 0.021 0.001 PHE A 133 TYR 0.017 0.001 TYR H 120 ARG 0.003 0.000 ARG H 69 *********************** 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 240 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7298 (mp0) cc_final: 0.5721 (tt0) REVERT: A 90 LEU cc_start: 0.9362 (tp) cc_final: 0.9144 (tp) REVERT: A 104 ARG cc_start: 0.8599 (tpt170) cc_final: 0.8155 (ttm-80) REVERT: A 134 TYR cc_start: 0.7589 (t80) cc_final: 0.7388 (t80) REVERT: A 136 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8275 (tm-30) REVERT: A 166 CYS cc_start: 0.8606 (t) cc_final: 0.7693 (t) REVERT: A 168 ILE cc_start: 0.9353 (mm) cc_final: 0.8977 (mm) REVERT: A 171 TYR cc_start: 0.8515 (m-10) cc_final: 0.8031 (m-10) REVERT: A 229 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8708 (tm-30) REVERT: A 230 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8149 (mm-30) REVERT: A 238 GLN cc_start: 0.8378 (mt0) cc_final: 0.7830 (mt0) REVERT: A 253 TRP cc_start: 0.5426 (m100) cc_final: 0.4675 (p-90) REVERT: A 260 MET cc_start: 0.4079 (ttt) cc_final: 0.3792 (ttt) REVERT: A 302 LEU cc_start: 0.7740 (tt) cc_final: 0.7539 (mt) REVERT: A 317 TRP cc_start: 0.7686 (p-90) cc_final: 0.6993 (m-10) REVERT: A 343 VAL cc_start: 0.9044 (t) cc_final: 0.8821 (t) REVERT: A 358 TYR cc_start: 0.7556 (t80) cc_final: 0.6564 (t80) REVERT: A 407 PHE cc_start: 0.9109 (m-80) cc_final: 0.8640 (m-10) REVERT: A 430 MET cc_start: 0.7753 (ttt) cc_final: 0.6780 (ttp) REVERT: A 473 CYS cc_start: 0.8141 (p) cc_final: 0.7893 (p) REVERT: A 595 TYR cc_start: 0.6625 (t80) cc_final: 0.5783 (t80) REVERT: A 596 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8330 (mtt-85) REVERT: V 45 THR cc_start: 0.7490 (p) cc_final: 0.6732 (t) REVERT: V 49 MET cc_start: 0.8600 (tpt) cc_final: 0.8143 (tpt) REVERT: V 63 ILE cc_start: 0.8657 (mt) cc_final: 0.8308 (mt) REVERT: V 76 ASN cc_start: 0.7898 (t0) cc_final: 0.7582 (t0) REVERT: V 159 PHE cc_start: 0.6742 (m-10) cc_final: 0.6516 (m-10) REVERT: V 241 TYR cc_start: 0.8556 (t80) cc_final: 0.8305 (t80) REVERT: H 21 VAL cc_start: 0.7157 (t) cc_final: 0.5682 (t) REVERT: H 46 TYR cc_start: 0.8358 (p90) cc_final: 0.7943 (p90) REVERT: H 52 TRP cc_start: 0.7918 (m100) cc_final: 0.7229 (m100) REVERT: H 71 TYR cc_start: 0.8496 (t80) cc_final: 0.8284 (t80) REVERT: L 85 ARG cc_start: 0.6927 (ptm160) cc_final: 0.6603 (ptm160) REVERT: L 97 LEU cc_start: 0.6235 (pt) cc_final: 0.6011 (pt) REVERT: L 100 HIS cc_start: 0.6296 (m170) cc_final: 0.5962 (m-70) REVERT: L 127 LYS cc_start: 0.7088 (mttt) cc_final: 0.6330 (tttt) outliers start: 2 outliers final: 0 residues processed: 240 average time/residue: 0.1831 time to fit residues: 60.4432 Evaluate side-chains 196 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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: 4.9990 chunk 66 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8053 Z= 0.161 Angle : 0.587 12.546 10954 Z= 0.289 Chirality : 0.043 0.327 1209 Planarity : 0.004 0.058 1352 Dihedral : 6.383 126.758 1159 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % 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: -2.18 (0.25), residues: 978 helix: -1.80 (0.26), residues: 334 sheet: -0.51 (0.39), residues: 179 loop : -1.45 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 182 HIS 0.003 0.001 HIS V 240 PHE 0.018 0.001 PHE A 133 TYR 0.018 0.001 TYR H 120 ARG 0.003 0.000 ARG H 69 *********************** 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 239 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 0.887 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: A 80 GLU cc_start: 0.7407 (mp0) cc_final: 0.5798 (tt0) REVERT: A 90 LEU cc_start: 0.9344 (tp) cc_final: 0.9109 (tp) REVERT: A 104 ARG cc_start: 0.8650 (tpt170) cc_final: 0.8174 (ttm-80) REVERT: A 132 LEU cc_start: 0.9035 (tp) cc_final: 0.8752 (tp) REVERT: A 133 PHE cc_start: 0.7951 (m-80) cc_final: 0.7442 (m-80) REVERT: A 136 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8457 (tm-30) REVERT: A 166 CYS cc_start: 0.8541 (t) cc_final: 0.7641 (t) REVERT: A 168 ILE cc_start: 0.9354 (mm) cc_final: 0.8945 (mm) REVERT: A 171 TYR cc_start: 0.8603 (m-10) cc_final: 0.8160 (m-10) REVERT: A 238 GLN cc_start: 0.8347 (mt0) cc_final: 0.7772 (mt0) REVERT: A 260 MET cc_start: 0.4090 (ttt) cc_final: 0.3809 (ttt) REVERT: A 306 TRP cc_start: 0.8507 (p90) cc_final: 0.8258 (p90) REVERT: A 317 TRP cc_start: 0.7561 (p-90) cc_final: 0.6834 (m-10) REVERT: A 341 PHE cc_start: 0.8256 (t80) cc_final: 0.8032 (t80) REVERT: A 343 VAL cc_start: 0.8970 (t) cc_final: 0.8706 (t) REVERT: A 407 PHE cc_start: 0.9187 (m-80) cc_final: 0.8716 (m-10) REVERT: A 430 MET cc_start: 0.7889 (ttt) cc_final: 0.6957 (ttp) REVERT: A 444 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 473 CYS cc_start: 0.8170 (p) cc_final: 0.7917 (p) REVERT: A 537 TRP cc_start: 0.7927 (m-90) cc_final: 0.7581 (m100) REVERT: A 596 ARG cc_start: 0.8619 (mtm-85) cc_final: 0.8392 (mpt-90) REVERT: V 45 THR cc_start: 0.7388 (p) cc_final: 0.6587 (t) REVERT: V 63 ILE cc_start: 0.8896 (mt) cc_final: 0.8101 (mt) REVERT: V 76 ASN cc_start: 0.7785 (t0) cc_final: 0.7569 (t0) REVERT: V 151 ILE cc_start: 0.8175 (mt) cc_final: 0.7940 (mt) REVERT: V 241 TYR cc_start: 0.8553 (t80) cc_final: 0.8291 (t80) REVERT: H 21 VAL cc_start: 0.7376 (t) cc_final: 0.6541 (m) REVERT: H 52 TRP cc_start: 0.8034 (m100) cc_final: 0.7750 (m100) REVERT: H 71 TYR cc_start: 0.8405 (t80) cc_final: 0.8145 (t80) REVERT: L 85 ARG cc_start: 0.6852 (ptm160) cc_final: 0.6604 (ptm160) REVERT: L 97 LEU cc_start: 0.6021 (pt) cc_final: 0.5744 (pt) REVERT: L 100 HIS cc_start: 0.6142 (m170) cc_final: 0.5785 (m-70) REVERT: L 102 MET cc_start: 0.5109 (ptt) cc_final: 0.4830 (ptt) REVERT: L 127 LYS cc_start: 0.7092 (mttt) cc_final: 0.6377 (tttt) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.1829 time to fit residues: 60.0665 Evaluate side-chains 198 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 80 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- 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 316 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 70 ASN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 GLN L 114 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8053 Z= 0.320 Angle : 0.731 10.406 10954 Z= 0.379 Chirality : 0.047 0.348 1209 Planarity : 0.005 0.075 1352 Dihedral : 7.208 140.784 1159 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % 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: -2.10 (0.25), residues: 978 helix: -1.71 (0.26), residues: 325 sheet: -0.74 (0.36), residues: 185 loop : -1.31 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP V 62 HIS 0.009 0.002 HIS A 143 PHE 0.021 0.002 PHE A 133 TYR 0.025 0.002 TYR H 120 ARG 0.006 0.001 ARG H 69 *********************** 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 234 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 0.814 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: A 80 GLU cc_start: 0.7432 (mp0) cc_final: 0.7164 (mp0) REVERT: A 104 ARG cc_start: 0.8789 (tpt170) cc_final: 0.8277 (ttm-80) REVERT: A 132 LEU cc_start: 0.9144 (tp) cc_final: 0.8894 (tp) REVERT: A 133 PHE cc_start: 0.7969 (m-80) cc_final: 0.7756 (m-80) REVERT: A 136 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8486 (tm-30) REVERT: A 166 CYS cc_start: 0.8831 (t) cc_final: 0.7891 (t) REVERT: A 168 ILE cc_start: 0.9429 (mm) cc_final: 0.9105 (mm) REVERT: A 171 TYR cc_start: 0.8657 (m-10) cc_final: 0.8202 (m-10) REVERT: A 229 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 260 MET cc_start: 0.3997 (ttt) cc_final: 0.3732 (ttt) REVERT: A 306 TRP cc_start: 0.8600 (p90) cc_final: 0.8353 (p90) REVERT: A 317 TRP cc_start: 0.7582 (p-90) cc_final: 0.6882 (m-10) REVERT: A 341 PHE cc_start: 0.8286 (t80) cc_final: 0.7970 (t80) REVERT: A 382 VAL cc_start: 0.9210 (t) cc_final: 0.9009 (t) REVERT: A 407 PHE cc_start: 0.9276 (m-80) cc_final: 0.8858 (m-10) REVERT: A 417 MET cc_start: 0.7776 (mmp) cc_final: 0.7562 (tpp) REVERT: A 430 MET cc_start: 0.7906 (ttt) cc_final: 0.7108 (ttp) REVERT: A 444 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7854 (mt-10) REVERT: A 473 CYS cc_start: 0.8269 (p) cc_final: 0.8011 (p) REVERT: A 596 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8337 (mpt180) REVERT: V 45 THR cc_start: 0.7513 (p) cc_final: 0.7276 (p) REVERT: V 76 ASN cc_start: 0.7737 (t0) cc_final: 0.7514 (t0) REVERT: V 151 ILE cc_start: 0.8182 (mt) cc_final: 0.7967 (mt) REVERT: H 32 LYS cc_start: 0.7127 (pttt) cc_final: 0.6823 (pptt) REVERT: H 38 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7476 (ttt180) REVERT: H 117 ARG cc_start: 0.8346 (tmt170) cc_final: 0.7842 (tmt170) REVERT: L 85 ARG cc_start: 0.7897 (ptm160) cc_final: 0.7488 (ptm160) REVERT: L 97 LEU cc_start: 0.7165 (pt) cc_final: 0.6890 (pt) REVERT: L 100 HIS cc_start: 0.6418 (m170) cc_final: 0.5952 (m-70) REVERT: L 127 LYS cc_start: 0.7253 (mttt) cc_final: 0.6725 (tttt) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.1886 time to fit residues: 59.4578 Evaluate side-chains 192 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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: 7.9990 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 368 ASN A 391 ASN ** V 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.5604 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= 0.160 Angle : 0.604 12.491 10954 Z= 0.296 Chirality : 0.043 0.296 1209 Planarity : 0.004 0.069 1352 Dihedral : 6.747 133.701 1159 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.12 % Allowed : 1.93 % Favored : 97.95 % 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: -1.73 (0.26), residues: 978 helix: -1.39 (0.27), residues: 330 sheet: -0.35 (0.37), residues: 179 loop : -1.17 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 182 HIS 0.005 0.001 HIS V 240 PHE 0.017 0.001 PHE A 133 TYR 0.022 0.001 TYR H 120 ARG 0.003 0.000 ARG A 596 *********************** 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 246 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7415 (mp0) cc_final: 0.5760 (tt0) REVERT: A 103 TRP cc_start: 0.9195 (p-90) cc_final: 0.8952 (p-90) REVERT: A 104 ARG cc_start: 0.8868 (tpt170) cc_final: 0.8340 (ttm-80) REVERT: A 111 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7619 (mm-40) REVERT: A 132 LEU cc_start: 0.9124 (tp) cc_final: 0.8856 (tp) REVERT: A 133 PHE cc_start: 0.7906 (m-80) cc_final: 0.7539 (m-80) REVERT: A 136 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 166 CYS cc_start: 0.8595 (t) cc_final: 0.7736 (t) REVERT: A 168 ILE cc_start: 0.9451 (mm) cc_final: 0.9070 (mm) REVERT: A 171 TYR cc_start: 0.8668 (m-10) cc_final: 0.8183 (m-10) REVERT: A 237 LEU cc_start: 0.9396 (mm) cc_final: 0.8853 (mm) REVERT: A 238 GLN cc_start: 0.8725 (mt0) cc_final: 0.8191 (mp10) REVERT: A 260 MET cc_start: 0.3661 (ttt) cc_final: 0.3376 (ttt) REVERT: A 306 TRP cc_start: 0.8521 (p90) cc_final: 0.8097 (p90) REVERT: A 317 TRP cc_start: 0.7524 (p-90) cc_final: 0.6855 (m-10) REVERT: A 341 PHE cc_start: 0.8208 (t80) cc_final: 0.7829 (t80) REVERT: A 407 PHE cc_start: 0.9226 (m-80) cc_final: 0.8815 (m-10) REVERT: A 430 MET cc_start: 0.7784 (ttt) cc_final: 0.7016 (ttp) REVERT: A 444 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7718 (mt-10) REVERT: A 447 ILE cc_start: 0.6697 (pt) cc_final: 0.6410 (tt) REVERT: A 473 CYS cc_start: 0.8252 (p) cc_final: 0.7991 (p) REVERT: V 45 THR cc_start: 0.7454 (p) cc_final: 0.6607 (t) REVERT: V 151 ILE cc_start: 0.8014 (mt) cc_final: 0.7785 (mt) REVERT: V 158 LYS cc_start: 0.8227 (ptmm) cc_final: 0.7924 (tmtt) REVERT: V 241 TYR cc_start: 0.8232 (t80) cc_final: 0.7919 (t80) REVERT: H 38 ARG cc_start: 0.7842 (ttm170) cc_final: 0.7389 (ttt180) REVERT: H 117 ARG cc_start: 0.8244 (tmt170) cc_final: 0.7687 (tmt170) REVERT: H 127 MET cc_start: 0.5556 (ptp) cc_final: 0.5341 (ptp) REVERT: H 129 TYR cc_start: 0.8957 (m-10) cc_final: 0.8751 (m-10) REVERT: L 97 LEU cc_start: 0.6854 (pt) cc_final: 0.6556 (pt) REVERT: L 100 HIS cc_start: 0.6418 (m170) cc_final: 0.5922 (m-70) REVERT: L 127 LYS cc_start: 0.7236 (mttt) cc_final: 0.6797 (mtpt) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.1898 time to fit residues: 63.0026 Evaluate side-chains 213 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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: 8.9990 chunk 68 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 58 optimal weight: 0.0070 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 368 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8053 Z= 0.172 Angle : 0.586 10.573 10954 Z= 0.293 Chirality : 0.042 0.306 1209 Planarity : 0.004 0.069 1352 Dihedral : 6.661 132.844 1159 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.12 % Allowed : 1.81 % Favored : 98.07 % 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: -1.53 (0.26), residues: 978 helix: -1.25 (0.27), residues: 336 sheet: -0.14 (0.38), residues: 179 loop : -1.08 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 182 HIS 0.004 0.001 HIS V 240 PHE 0.018 0.002 PHE A 427 TYR 0.022 0.001 TYR H 120 ARG 0.002 0.000 ARG A 241 *********************** 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 241 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7414 (mp0) cc_final: 0.5682 (tt0) REVERT: A 90 LEU cc_start: 0.9411 (tp) cc_final: 0.9208 (tp) REVERT: A 103 TRP cc_start: 0.9217 (p-90) cc_final: 0.8972 (p-90) REVERT: A 104 ARG cc_start: 0.8980 (tpt170) cc_final: 0.8462 (ttm-80) REVERT: A 132 LEU cc_start: 0.9118 (tp) cc_final: 0.8898 (tp) REVERT: A 133 PHE cc_start: 0.7978 (m-80) cc_final: 0.7745 (m-80) REVERT: A 136 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8394 (tm-30) REVERT: A 166 CYS cc_start: 0.8676 (t) cc_final: 0.7797 (t) REVERT: A 237 LEU cc_start: 0.9248 (mm) cc_final: 0.8962 (mm) REVERT: A 260 MET cc_start: 0.3672 (ttt) cc_final: 0.3401 (ttt) REVERT: A 281 VAL cc_start: 0.8795 (t) cc_final: 0.8568 (t) REVERT: A 306 TRP cc_start: 0.8576 (p90) cc_final: 0.8177 (p90) REVERT: A 317 TRP cc_start: 0.7557 (p-90) cc_final: 0.6924 (m-10) REVERT: A 341 PHE cc_start: 0.8102 (t80) cc_final: 0.7643 (t80) REVERT: A 407 PHE cc_start: 0.9154 (m-80) cc_final: 0.8757 (m-10) REVERT: A 430 MET cc_start: 0.7903 (ttt) cc_final: 0.7150 (ttp) REVERT: A 444 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 447 ILE cc_start: 0.6569 (pt) cc_final: 0.6206 (tt) REVERT: A 473 CYS cc_start: 0.8278 (p) cc_final: 0.8015 (p) REVERT: A 596 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.7808 (mtt90) REVERT: V 45 THR cc_start: 0.7474 (p) cc_final: 0.6624 (t) REVERT: V 158 LYS cc_start: 0.8291 (ptmm) cc_final: 0.7938 (tmtt) REVERT: V 241 TYR cc_start: 0.8349 (t80) cc_final: 0.8015 (t80) REVERT: H 21 VAL cc_start: 0.7201 (t) cc_final: 0.6382 (t) REVERT: H 38 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7466 (ttt-90) REVERT: H 46 TYR cc_start: 0.8308 (p90) cc_final: 0.8055 (p90) REVERT: H 71 TYR cc_start: 0.8325 (t80) cc_final: 0.7941 (t80) REVERT: L 100 HIS cc_start: 0.6210 (m170) cc_final: 0.5730 (m-70) REVERT: L 127 LYS cc_start: 0.7189 (mttt) cc_final: 0.6752 (mtpt) outliers start: 1 outliers final: 1 residues processed: 240 average time/residue: 0.1896 time to fit residues: 62.0177 Evaluate side-chains 193 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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: 10.0000 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 85 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8053 Z= 0.290 Angle : 0.704 10.625 10954 Z= 0.360 Chirality : 0.045 0.285 1209 Planarity : 0.005 0.102 1352 Dihedral : 7.167 138.214 1159 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.12 % Allowed : 2.41 % Favored : 97.47 % 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: -1.40 (0.27), residues: 978 helix: -1.10 (0.28), residues: 323 sheet: -0.27 (0.37), residues: 190 loop : -0.97 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 541 HIS 0.011 0.002 HIS A 143 PHE 0.024 0.002 PHE A 133 TYR 0.026 0.002 TYR H 120 ARG 0.017 0.001 ARG A 241 *********************** 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 232 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 0.764 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: A 80 GLU cc_start: 0.7519 (mp0) cc_final: 0.5688 (tt0) REVERT: A 104 ARG cc_start: 0.8954 (tpt170) cc_final: 0.8525 (ttm-80) REVERT: A 166 CYS cc_start: 0.8820 (t) cc_final: 0.7952 (t) REVERT: A 229 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8691 (tm-30) REVERT: A 237 LEU cc_start: 0.9251 (mm) cc_final: 0.8999 (mm) REVERT: A 260 MET cc_start: 0.3701 (ttt) cc_final: 0.3447 (ttt) REVERT: A 287 PHE cc_start: 0.8008 (t80) cc_final: 0.7767 (t80) REVERT: A 306 TRP cc_start: 0.8511 (p90) cc_final: 0.8153 (p90) REVERT: A 317 TRP cc_start: 0.7571 (p-90) cc_final: 0.6994 (m-10) REVERT: A 326 TRP cc_start: 0.6681 (m100) cc_final: 0.6154 (m-10) REVERT: A 382 VAL cc_start: 0.9221 (t) cc_final: 0.9001 (t) REVERT: A 407 PHE cc_start: 0.9282 (m-80) cc_final: 0.9020 (m-80) REVERT: A 430 MET cc_start: 0.7875 (ttt) cc_final: 0.7098 (ttp) REVERT: A 444 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7953 (mt-10) REVERT: A 473 CYS cc_start: 0.8304 (p) cc_final: 0.8040 (p) REVERT: A 596 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.7846 (mtt90) REVERT: V 45 THR cc_start: 0.7430 (p) cc_final: 0.6581 (t) REVERT: V 241 TYR cc_start: 0.8284 (t80) cc_final: 0.8005 (t80) REVERT: H 21 VAL cc_start: 0.7314 (t) cc_final: 0.6894 (t) REVERT: H 38 ARG cc_start: 0.8319 (ttm170) cc_final: 0.7711 (ttt-90) REVERT: H 46 TYR cc_start: 0.8559 (p90) cc_final: 0.8201 (p90) REVERT: H 71 TYR cc_start: 0.8222 (t80) cc_final: 0.7880 (t80) REVERT: H 127 MET cc_start: 0.4801 (ptp) cc_final: 0.4547 (ptp) REVERT: L 100 HIS cc_start: 0.6652 (m170) cc_final: 0.6172 (m-70) REVERT: L 127 LYS cc_start: 0.7201 (mttt) cc_final: 0.6831 (mtpt) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.1847 time to fit residues: 58.0575 Evaluate side-chains 179 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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: 0.6980 chunk 89 optimal weight: 7.9990 chunk 52 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 368 ASN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8053 Z= 0.159 Angle : 0.614 10.176 10954 Z= 0.305 Chirality : 0.043 0.277 1209 Planarity : 0.004 0.069 1352 Dihedral : 6.777 131.346 1159 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % 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: -1.42 (0.27), residues: 978 helix: -1.15 (0.27), residues: 336 sheet: -0.07 (0.39), residues: 177 loop : -1.00 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.003 TRP A 541 HIS 0.005 0.001 HIS V 240 PHE 0.023 0.001 PHE A 231 TYR 0.020 0.001 TYR H 120 ARG 0.006 0.000 ARG V 113 *********************** 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 236 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TRP cc_start: 0.9289 (p-90) cc_final: 0.8977 (p-90) REVERT: A 104 ARG cc_start: 0.8982 (tpt170) cc_final: 0.8478 (ttm-80) REVERT: A 132 LEU cc_start: 0.9344 (tp) cc_final: 0.8871 (tp) REVERT: A 166 CYS cc_start: 0.8656 (t) cc_final: 0.8326 (p) REVERT: A 260 MET cc_start: 0.3618 (ttt) cc_final: 0.3395 (ttt) REVERT: A 306 TRP cc_start: 0.8506 (p90) cc_final: 0.7935 (p90) REVERT: A 317 TRP cc_start: 0.7521 (p-90) cc_final: 0.6965 (m-10) REVERT: A 326 TRP cc_start: 0.6670 (m100) cc_final: 0.6220 (m-10) REVERT: A 343 VAL cc_start: 0.8728 (t) cc_final: 0.8347 (t) REVERT: A 347 PHE cc_start: 0.8454 (m-80) cc_final: 0.8245 (m-80) REVERT: A 417 MET cc_start: 0.7773 (mmp) cc_final: 0.7518 (tpt) REVERT: A 430 MET cc_start: 0.7853 (ttt) cc_final: 0.7105 (ttp) REVERT: A 444 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 473 CYS cc_start: 0.8269 (p) cc_final: 0.8005 (p) REVERT: A 522 CYS cc_start: 0.8113 (m) cc_final: 0.7663 (p) REVERT: A 592 TYR cc_start: 0.7453 (m-10) cc_final: 0.7247 (m-10) REVERT: V 45 THR cc_start: 0.7412 (p) cc_final: 0.6543 (t) REVERT: V 241 TYR cc_start: 0.8118 (t80) cc_final: 0.7885 (t80) REVERT: H 38 ARG cc_start: 0.8199 (ttm170) cc_final: 0.7613 (ttt-90) REVERT: H 71 TYR cc_start: 0.8049 (t80) cc_final: 0.7743 (t80) REVERT: L 85 ARG cc_start: 0.8164 (ptm160) cc_final: 0.7923 (ptm160) REVERT: L 100 HIS cc_start: 0.6525 (m170) cc_final: 0.6063 (m-70) REVERT: L 127 LYS cc_start: 0.7080 (mttt) cc_final: 0.6676 (mtpt) outliers start: 2 outliers final: 1 residues processed: 235 average time/residue: 0.1882 time to fit residues: 60.0498 Evaluate side-chains 195 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 76 optimal weight: 0.0000 chunk 7 optimal weight: 0.3980 chunk 59 optimal weight: 0.0970 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8053 Z= 0.153 Angle : 0.618 10.210 10954 Z= 0.302 Chirality : 0.042 0.268 1209 Planarity : 0.004 0.065 1352 Dihedral : 6.564 127.162 1159 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -1.40 (0.27), residues: 978 helix: -1.25 (0.27), residues: 334 sheet: 0.03 (0.40), residues: 175 loop : -0.94 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 541 HIS 0.005 0.001 HIS V 240 PHE 0.029 0.002 PHE A 407 TYR 0.020 0.001 TYR H 120 ARG 0.006 0.000 ARG A 596 ********************** 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 228 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.9514 (p0) cc_final: 0.9291 (p0) REVERT: A 103 TRP cc_start: 0.9268 (p-90) cc_final: 0.9018 (p-90) REVERT: A 104 ARG cc_start: 0.8902 (tpt170) cc_final: 0.8319 (ttm-80) REVERT: A 111 GLN cc_start: 0.8121 (mm110) cc_final: 0.7913 (mm-40) REVERT: A 132 LEU cc_start: 0.9324 (tp) cc_final: 0.8842 (tp) REVERT: A 136 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 166 CYS cc_start: 0.8600 (t) cc_final: 0.8309 (p) REVERT: A 229 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8806 (tm-30) REVERT: A 260 MET cc_start: 0.3632 (ttt) cc_final: 0.3428 (ttt) REVERT: A 306 TRP cc_start: 0.8464 (p90) cc_final: 0.7927 (p90) REVERT: A 317 TRP cc_start: 0.7527 (p-90) cc_final: 0.7054 (m-10) REVERT: A 326 TRP cc_start: 0.6648 (m100) cc_final: 0.6150 (m-10) REVERT: A 341 PHE cc_start: 0.7975 (t80) cc_final: 0.7599 (t80) REVERT: A 343 VAL cc_start: 0.8724 (t) cc_final: 0.8374 (t) REVERT: A 417 MET cc_start: 0.7735 (mmp) cc_final: 0.7413 (tpt) REVERT: A 430 MET cc_start: 0.8067 (ttt) cc_final: 0.7285 (ttp) REVERT: A 444 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7793 (mt-10) REVERT: A 473 CYS cc_start: 0.8253 (p) cc_final: 0.7982 (p) REVERT: A 522 CYS cc_start: 0.7992 (m) cc_final: 0.7561 (p) REVERT: A 592 TYR cc_start: 0.7545 (m-10) cc_final: 0.7112 (m-10) REVERT: V 45 THR cc_start: 0.7310 (p) cc_final: 0.6351 (t) REVERT: V 241 TYR cc_start: 0.8104 (t80) cc_final: 0.7901 (t80) REVERT: H 38 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7569 (ttt-90) REVERT: H 71 TYR cc_start: 0.8116 (t80) cc_final: 0.7759 (t80) REVERT: L 57 LEU cc_start: 0.9437 (tp) cc_final: 0.9078 (tp) REVERT: L 85 ARG cc_start: 0.7460 (ptm160) cc_final: 0.6836 (ptt90) REVERT: L 100 HIS cc_start: 0.6428 (m170) cc_final: 0.5943 (m-70) REVERT: L 127 LYS cc_start: 0.7088 (mttt) cc_final: 0.6728 (mtpt) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1759 time to fit residues: 55.4686 Evaluate side-chains 198 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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: 0.9980 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.0470 chunk 67 optimal weight: 0.0970 chunk 4 optimal weight: 5.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 368 ASN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.179072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.143356 restraints weight = 16077.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.149188 restraints weight = 11334.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.153976 restraints weight = 8438.058| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8053 Z= 0.145 Angle : 0.607 12.876 10954 Z= 0.296 Chirality : 0.042 0.277 1209 Planarity : 0.004 0.067 1352 Dihedral : 6.383 123.800 1159 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.76 % 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: -1.32 (0.27), residues: 978 helix: -1.19 (0.27), residues: 326 sheet: 0.08 (0.40), residues: 175 loop : -0.90 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 541 HIS 0.005 0.001 HIS V 240 PHE 0.022 0.001 PHE A 133 TYR 0.019 0.001 TYR A 232 ARG 0.007 0.000 ARG A 596 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.08 seconds wall clock time: 39 minutes 28.21 seconds (2368.21 seconds total)