Starting phenix.real_space_refine on Mon Apr 28 21:17:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dzw_8941/04_2025/6dzw_8941.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzw_8941/04_2025/6dzw_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/cci-nas-00/data/ceres_data/6dzw_8941/04_2025/6dzw_8941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzw_8941/04_2025/6dzw_8941.map" model { file = "/net/cci-nas-00/data/ceres_data/6dzw_8941/04_2025/6dzw_8941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzw_8941/04_2025/6dzw_8941.cif" } 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. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 4.96, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 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: 1.84 Conformation dependent library (CDL) restraints added in 850.1 milliseconds 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... Secondary structure from input PDB file: 38 helices and 13 sheets defined 43.6% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 4.450A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) 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 98 through 102 removed outlier: 3.657A pdb=" N ASN A 101 " --> pdb=" O ASP A 98 " (cutoff:3.500A) 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 98 through 102' Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.542A pdb=" N TYR A 107 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.676A pdb=" N TYR A 121 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 125 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.869A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) 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 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 158 through 190 removed outlier: 4.454A pdb=" N GLY A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 271 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) removed outlier: 3.932A pdb=" N TRP A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 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 286 through 301 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) removed outlier: 3.635A pdb=" N THR A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.538A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 3.793A pdb=" N ILE A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) 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 344 through 350 removed outlier: 3.732A pdb=" N ALA A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 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 376 through 390 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 393 through 398 Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.542A pdb=" N PHE A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 removed outlier: 3.851A pdb=" N GLU A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) 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) removed outlier: 3.872A pdb=" N ASN A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 408 through 416' Processing helix chain 'A' and resid 419 through 454 removed outlier: 3.809A pdb=" N PHE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) 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) removed outlier: 3.918A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.941A pdb=" N VAL A 466 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 477 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) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.795A pdb=" N VAL A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) 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 496 through 514 removed outlier: 3.780A pdb=" N ALA A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) 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 517 through 530 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 534 through 541 removed outlier: 3.635A pdb=" N ARG A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 539 " --> pdb=" O TRP A 535 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 557 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) removed outlier: 3.563A pdb=" N LEU A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 587 removed outlier: 4.748A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.562A pdb=" N THR A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'V' and resid 77 through 80 removed outlier: 3.617A pdb=" N LYS V 80 " --> pdb=" O GLN V 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 77 through 80' Processing helix chain 'V' and resid 102 through 105 Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.646A pdb=" N TYR H 50 " --> pdb=" O ARG H 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 47 through 51' Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.623A pdb=" N ASP L 106 " --> pdb=" O GLU L 103 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR L 107 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 103 through 107' Processing sheet with id=AA1, first strand: chain 'V' and resid 18 through 19 removed outlier: 3.795A pdb=" N GLN V 18 " --> pdb=" O SER V 40 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER V 40 " --> pdb=" O GLN V 18 " (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=AA2, first strand: chain 'V' and resid 73 through 75 removed outlier: 3.521A pdb=" N ILE V 63 " --> pdb=" O TRP V 51 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TRP V 51 " --> pdb=" O ILE V 63 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN V 65 " --> pdb=" O MET V 49 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET V 49 " --> pdb=" O ASN V 65 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA V 107 " --> pdb=" O LEU V 130 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, first strand: chain 'V' and resid 159 through 160 removed outlier: 7.380A pdb=" N LYS V 252 " --> pdb=" O MET V 160 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR V 236 " --> pdb=" O TYR V 185 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR V 185 " --> pdb=" O TYR V 236 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'V' and resid 197 through 198 Processing sheet with id=AA6, 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=AA7, first strand: chain 'H' and resid 29 through 30 removed outlier: 3.897A pdb=" N GLU H 29 " --> pdb=" O SER H 135 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR H 137 " --> pdb=" O GLU H 29 " (cutoff:3.500A) 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: 6.174A pdb=" N MET H 53 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (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) Processing sheet with id=AA8, first strand: chain 'H' and resid 29 through 30 removed outlier: 3.897A pdb=" N GLU H 29 " --> pdb=" O SER H 135 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR H 137 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR H 113 " --> pdb=" O THR H 134 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N CYS H 115 " --> pdb=" O TRP H 130 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TRP H 130 " --> pdb=" O CYS H 115 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG H 117 " --> pdb=" O ASP H 128 " (cutoff:3.500A) Processing sheet with id=AA9, 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=AB1, first strand: chain 'L' and resid 30 through 32 removed outlier: 3.735A pdb=" N THR L 126 " --> pdb=" O TYR L 110 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR L 110 " --> pdb=" O THR L 126 " (cutoff:3.500A) 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) Processing sheet with id=AB2, first strand: chain 'L' and resid 30 through 32 removed outlier: 3.735A pdb=" N THR L 126 " --> pdb=" O TYR L 110 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR L 110 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN L 114 " --> pdb=" O THR L 121 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 72 through 73 Processing sheet with id=AB4, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.670A pdb=" N SER L 89 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER L 91 " --> pdb=" O TYR L 94 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR L 94 " --> pdb=" O SER L 91 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 2.20 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: 0.00 - 2.56: 10750 2.56 - 5.11: 149 5.11 - 7.67: 41 7.67 - 10.23: 12 10.23 - 12.78: 2 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: 51 2.62 - 3.19: 6155 3.19 - 3.76: 11748 3.76 - 4.33: 16047 4.33 - 4.90: 25697 Nonbonded interactions: 59698 Sorted by model distance: nonbonded pdb=" O3 NAG B 2 " pdb=" O7 NAG B 2 " model vdw 2.052 3.040 nonbonded pdb=" OH TYR A 495 " pdb=" O PRO A 561 " model vdw 2.317 3.040 nonbonded pdb=" OG SER V 59 " pdb=" O GLY V 248 " model vdw 2.337 3.040 nonbonded pdb=" OG1 THR V 112 " pdb=" O TYR V 123 " model vdw 2.339 3.040 nonbonded pdb=" O SER H 96 " pdb=" OG SER H 96 " model vdw 2.340 3.040 ... (remaining 59693 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.260 Find NCS groups from input model: 0.080 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- 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 : 0.006 0.406 8061 Z= 0.306 Angle : 0.922 25.588 10973 Z= 0.479 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 Details of bonding type rmsd link_NAG-ASN : bond 0.28881 ( 2) link_NAG-ASN : angle 13.19467 ( 6) link_BETA1-4 : bond 0.00064 ( 1) link_BETA1-4 : angle 0.83973 ( 3) hydrogen bonds : bond 0.35515 ( 219) hydrogen bonds : angle 11.21981 ( 630) SS BOND : bond 0.00094 ( 5) SS BOND : angle 0.31550 ( 10) covalent geometry : bond 0.00387 ( 8053) covalent geometry : angle 0.86962 (10954) *********************** 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 to be fit. rotamer outliers: 3 poor density : 293 time to evaluate : 0.873 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: 0.2115 time to fit residues: 81.3415 Evaluate side-chains 215 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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: 0.7980 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 223 HIS ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 416 ASN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN H 58 GLN L 58 ASN L 78 GLN L 114 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.211539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.169682 restraints weight = 13221.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.177202 restraints weight = 8891.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.183377 restraints weight = 6426.968| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5599 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8061 Z= 0.160 Angle : 0.678 10.477 10973 Z= 0.345 Chirality : 0.045 0.379 1209 Planarity : 0.005 0.037 1352 Dihedral : 6.624 129.283 1159 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.36 % Allowed : 6.02 % Favored : 93.62 % 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: -3.42 (0.23), residues: 978 helix: -3.24 (0.20), residues: 322 sheet: -1.11 (0.36), residues: 181 loop : -1.92 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP V 184 HIS 0.005 0.001 HIS V 240 PHE 0.026 0.002 PHE A 191 TYR 0.020 0.001 TYR H 120 ARG 0.004 0.001 ARG H 69 Details of bonding type rmsd link_NAG-ASN : bond 0.01007 ( 2) link_NAG-ASN : angle 3.16975 ( 6) link_BETA1-4 : bond 0.00072 ( 1) link_BETA1-4 : angle 2.77497 ( 3) hydrogen bonds : bond 0.05479 ( 219) hydrogen bonds : angle 6.17742 ( 630) SS BOND : bond 0.00226 ( 5) SS BOND : angle 0.45196 ( 10) covalent geometry : bond 0.00349 ( 8053) covalent geometry : angle 0.67238 (10954) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 254 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7169 (mp0) cc_final: 0.5816 (tt0) REVERT: A 90 LEU cc_start: 0.9584 (tp) cc_final: 0.9347 (tp) REVERT: A 104 ARG cc_start: 0.8396 (tpt170) cc_final: 0.7873 (tpp80) REVERT: A 136 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8698 (tm-30) REVERT: A 144 ARG cc_start: 0.5843 (ptm160) cc_final: 0.5589 (ptt180) REVERT: A 158 PHE cc_start: 0.8812 (m-80) cc_final: 0.8597 (m-80) REVERT: A 166 CYS cc_start: 0.8536 (t) cc_final: 0.7651 (t) REVERT: A 172 ILE cc_start: 0.9334 (mt) cc_final: 0.8752 (tt) REVERT: A 182 TRP cc_start: 0.8572 (m-10) cc_final: 0.7576 (m-10) REVERT: A 205 ASN cc_start: 0.8825 (t0) cc_final: 0.8568 (t0) REVERT: A 223 HIS cc_start: 0.7591 (m170) cc_final: 0.7346 (m-70) REVERT: A 237 LEU cc_start: 0.9228 (mm) cc_final: 0.8739 (mm) REVERT: A 238 GLN cc_start: 0.8256 (mt0) cc_final: 0.7792 (mt0) REVERT: A 253 TRP cc_start: 0.5445 (m100) cc_final: 0.4717 (p-90) REVERT: A 302 LEU cc_start: 0.7798 (tt) cc_final: 0.7034 (mt) REVERT: A 312 TYR cc_start: 0.8242 (t80) cc_final: 0.7928 (t80) REVERT: A 317 TRP cc_start: 0.7567 (p-90) cc_final: 0.6886 (m-10) REVERT: A 332 GLN cc_start: 0.7773 (tp40) cc_final: 0.7445 (tp40) REVERT: A 343 VAL cc_start: 0.9189 (t) cc_final: 0.8818 (t) REVERT: A 358 TYR cc_start: 0.7780 (t80) cc_final: 0.6757 (t80) REVERT: A 407 PHE cc_start: 0.8980 (m-80) cc_final: 0.8482 (m-10) REVERT: A 430 MET cc_start: 0.7556 (ttt) cc_final: 0.6713 (ttp) REVERT: A 595 TYR cc_start: 0.6753 (t80) cc_final: 0.5912 (t80) REVERT: A 596 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8088 (mpt180) REVERT: V 45 THR cc_start: 0.7284 (p) cc_final: 0.6315 (t) REVERT: V 63 ILE cc_start: 0.8513 (mt) cc_final: 0.7886 (mt) REVERT: V 76 ASN cc_start: 0.8128 (t0) cc_final: 0.7841 (p0) REVERT: V 85 LEU cc_start: 0.6701 (mt) cc_final: 0.6403 (mt) REVERT: H 21 VAL cc_start: 0.7587 (t) cc_final: 0.5219 (t) REVERT: L 33 VAL cc_start: 0.7314 (t) cc_final: 0.7022 (t) REVERT: L 100 HIS cc_start: 0.6209 (m170) cc_final: 0.5813 (m-70) REVERT: L 102 MET cc_start: 0.5245 (ptt) cc_final: 0.4924 (ptt) REVERT: L 110 TYR cc_start: 0.8196 (m-10) cc_final: 0.7714 (m-80) outliers start: 3 outliers final: 0 residues processed: 255 average time/residue: 0.1980 time to fit residues: 70.0469 Evaluate side-chains 203 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 26 optimal weight: 0.0670 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** V 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 157 HIS ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.200959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.160510 restraints weight = 14215.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.167852 restraints weight = 9610.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.173539 restraints weight = 6930.257| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8061 Z= 0.143 Angle : 0.625 9.973 10973 Z= 0.313 Chirality : 0.044 0.331 1209 Planarity : 0.004 0.057 1352 Dihedral : 6.388 129.685 1159 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: -2.66 (0.25), residues: 978 helix: -2.32 (0.23), residues: 342 sheet: -0.77 (0.38), residues: 182 loop : -1.60 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP V 62 HIS 0.003 0.001 HIS V 240 PHE 0.020 0.001 PHE A 170 TYR 0.017 0.001 TYR H 120 ARG 0.003 0.000 ARG H 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00928 ( 2) link_NAG-ASN : angle 2.93073 ( 6) link_BETA1-4 : bond 0.00653 ( 1) link_BETA1-4 : angle 2.75542 ( 3) hydrogen bonds : bond 0.04783 ( 219) hydrogen bonds : angle 5.61013 ( 630) SS BOND : bond 0.00128 ( 5) SS BOND : angle 0.39810 ( 10) covalent geometry : bond 0.00325 ( 8053) covalent geometry : angle 0.62044 (10954) *********************** 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 236 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.739 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: 0.7253 (mp0) cc_final: 0.5827 (tt0) REVERT: A 90 LEU cc_start: 0.9440 (tp) cc_final: 0.9236 (tp) REVERT: A 98 ASP cc_start: 0.9578 (p0) cc_final: 0.9342 (p0) REVERT: A 104 ARG cc_start: 0.8583 (tpt170) cc_final: 0.8115 (ttm-80) REVERT: A 111 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7658 (mm-40) REVERT: A 166 CYS cc_start: 0.8658 (t) cc_final: 0.8291 (p) REVERT: A 172 ILE cc_start: 0.9391 (mt) cc_final: 0.8775 (tt) REVERT: A 205 ASN cc_start: 0.8753 (t0) cc_final: 0.8550 (t0) REVERT: A 223 HIS cc_start: 0.7656 (m170) cc_final: 0.7422 (m-70) REVERT: A 238 GLN cc_start: 0.8357 (mt0) cc_final: 0.7849 (mt0) REVERT: A 253 TRP cc_start: 0.5503 (m100) cc_final: 0.4594 (p-90) REVERT: A 317 TRP cc_start: 0.7594 (p-90) cc_final: 0.6961 (m-10) REVERT: A 343 VAL cc_start: 0.9036 (t) cc_final: 0.8791 (t) REVERT: A 407 PHE cc_start: 0.9051 (m-80) cc_final: 0.8802 (m-10) REVERT: A 430 MET cc_start: 0.7678 (ttt) cc_final: 0.6778 (ttp) REVERT: A 595 TYR cc_start: 0.6636 (t80) cc_final: 0.5705 (t80) REVERT: V 45 THR cc_start: 0.7449 (p) cc_final: 0.6460 (t) REVERT: V 63 ILE cc_start: 0.8383 (mt) cc_final: 0.7771 (mt) REVERT: V 76 ASN cc_start: 0.7878 (t0) cc_final: 0.7542 (p0) REVERT: V 85 LEU cc_start: 0.6551 (mt) cc_final: 0.6341 (mt) REVERT: H 21 VAL cc_start: 0.7293 (t) cc_final: 0.5629 (t) REVERT: H 46 TYR cc_start: 0.8376 (p90) cc_final: 0.8011 (p90) REVERT: L 33 VAL cc_start: 0.6849 (t) cc_final: 0.6450 (t) REVERT: L 97 LEU cc_start: 0.4553 (pt) cc_final: 0.4297 (pt) REVERT: L 100 HIS cc_start: 0.6289 (m170) cc_final: 0.5915 (m-70) REVERT: L 102 MET cc_start: 0.5554 (ptt) cc_final: 0.5191 (ptt) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1885 time to fit residues: 61.2947 Evaluate side-chains 195 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 59 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 211 ASN A 223 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN V 54 GLN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 GLN L 114 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.184038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.146088 restraints weight = 14700.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.152750 restraints weight = 9691.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.157989 restraints weight = 6915.103| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8061 Z= 0.227 Angle : 0.735 10.291 10973 Z= 0.385 Chirality : 0.047 0.353 1209 Planarity : 0.005 0.054 1352 Dihedral : 6.972 137.809 1159 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.24 % Allowed : 4.33 % Favored : 95.43 % 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: -2.16 (0.25), residues: 978 helix: -1.72 (0.25), residues: 330 sheet: -0.70 (0.37), residues: 183 loop : -1.40 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 204 HIS 0.010 0.003 HIS A 235 PHE 0.028 0.002 PHE A 170 TYR 0.022 0.002 TYR H 120 ARG 0.005 0.001 ARG H 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 2) link_NAG-ASN : angle 2.92279 ( 6) link_BETA1-4 : bond 0.00372 ( 1) link_BETA1-4 : angle 3.13160 ( 3) hydrogen bonds : bond 0.04732 ( 219) hydrogen bonds : angle 5.73436 ( 630) SS BOND : bond 0.00498 ( 5) SS BOND : angle 1.42681 ( 10) covalent geometry : bond 0.00485 ( 8053) covalent geometry : angle 0.72957 (10954) *********************** 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 237 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 235 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7389 (mp0) cc_final: 0.5653 (tt0) REVERT: A 104 ARG cc_start: 0.8582 (tpt170) cc_final: 0.8103 (ttm-80) REVERT: A 112 ASN cc_start: 0.7903 (m110) cc_final: 0.7602 (m110) REVERT: A 133 PHE cc_start: 0.7908 (m-80) cc_final: 0.7541 (m-80) REVERT: A 136 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8641 (tm-30) REVERT: A 166 CYS cc_start: 0.8665 (t) cc_final: 0.7716 (t) REVERT: A 168 ILE cc_start: 0.9475 (mm) cc_final: 0.9261 (mm) REVERT: A 172 ILE cc_start: 0.9492 (mt) cc_final: 0.8942 (tt) REVERT: A 229 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8398 (tm-30) REVERT: A 230 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 238 GLN cc_start: 0.8644 (mt0) cc_final: 0.8048 (mt0) REVERT: A 306 TRP cc_start: 0.8540 (p90) cc_final: 0.8274 (p90) REVERT: A 317 TRP cc_start: 0.7531 (p-90) cc_final: 0.7004 (m-10) REVERT: A 326 TRP cc_start: 0.6996 (m100) cc_final: 0.6089 (m-10) REVERT: A 343 VAL cc_start: 0.9229 (t) cc_final: 0.8848 (t) REVERT: A 358 TYR cc_start: 0.7938 (t80) cc_final: 0.6648 (t80) REVERT: A 430 MET cc_start: 0.7893 (ttt) cc_final: 0.7119 (ttp) REVERT: A 444 GLU cc_start: 0.8944 (pt0) cc_final: 0.8438 (pt0) REVERT: A 528 MET cc_start: 0.5819 (ppp) cc_final: 0.5607 (ppp) REVERT: V 62 TRP cc_start: 0.9071 (t60) cc_final: 0.8851 (t60) REVERT: V 63 ILE cc_start: 0.8711 (mt) cc_final: 0.7793 (mt) REVERT: V 76 ASN cc_start: 0.7744 (t0) cc_final: 0.7160 (t0) REVERT: V 176 GLN cc_start: 0.7266 (mt0) cc_final: 0.7046 (mt0) REVERT: H 21 VAL cc_start: 0.7630 (t) cc_final: 0.5972 (t) REVERT: H 38 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7398 (ttt-90) REVERT: H 46 TYR cc_start: 0.8576 (p90) cc_final: 0.8244 (p90) REVERT: H 71 TYR cc_start: 0.8338 (t80) cc_final: 0.8133 (t80) REVERT: H 100 MET cc_start: 0.5712 (tpp) cc_final: 0.5495 (tpp) REVERT: H 117 ARG cc_start: 0.7605 (ttt-90) cc_final: 0.7390 (tmt170) REVERT: L 97 LEU cc_start: 0.4825 (pt) cc_final: 0.4385 (pt) REVERT: L 100 HIS cc_start: 0.6573 (m170) cc_final: 0.6158 (m-70) REVERT: L 127 LYS cc_start: 0.7212 (mttt) cc_final: 0.6481 (tttt) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.1917 time to fit residues: 61.3599 Evaluate side-chains 183 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 22 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 70 optimal weight: 0.0000 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 0.2980 chunk 90 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 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 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.193616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.155419 restraints weight = 14479.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.162106 restraints weight = 9705.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.167354 restraints weight = 7002.404| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8061 Z= 0.121 Angle : 0.620 10.256 10973 Z= 0.305 Chirality : 0.045 0.323 1209 Planarity : 0.004 0.047 1352 Dihedral : 6.564 131.574 1159 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.12 % Allowed : 2.89 % Favored : 96.99 % 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: -1.82 (0.26), residues: 978 helix: -1.37 (0.26), residues: 329 sheet: -0.58 (0.37), residues: 183 loop : -1.22 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 204 HIS 0.005 0.001 HIS A 235 PHE 0.024 0.001 PHE A 170 TYR 0.018 0.001 TYR H 120 ARG 0.006 0.000 ARG H 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00791 ( 2) link_NAG-ASN : angle 2.65496 ( 6) link_BETA1-4 : bond 0.00217 ( 1) link_BETA1-4 : angle 2.94077 ( 3) hydrogen bonds : bond 0.03866 ( 219) hydrogen bonds : angle 5.28014 ( 630) SS BOND : bond 0.00346 ( 5) SS BOND : angle 0.56506 ( 10) covalent geometry : bond 0.00261 ( 8053) covalent geometry : angle 0.61510 (10954) *********************** 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 235 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7389 (mp0) cc_final: 0.5961 (tt0) REVERT: A 104 ARG cc_start: 0.8634 (tpt170) cc_final: 0.8150 (ttm-80) REVERT: A 133 PHE cc_start: 0.7833 (m-80) cc_final: 0.7561 (m-80) REVERT: A 136 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8309 (tm-30) REVERT: A 166 CYS cc_start: 0.8691 (t) cc_final: 0.8373 (p) REVERT: A 168 ILE cc_start: 0.9508 (mm) cc_final: 0.9212 (mm) REVERT: A 172 ILE cc_start: 0.9447 (mt) cc_final: 0.8901 (tt) REVERT: A 185 TYR cc_start: 0.7849 (t80) cc_final: 0.7524 (t80) REVERT: A 229 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 230 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8160 (mm-30) REVERT: A 238 GLN cc_start: 0.8570 (mt0) cc_final: 0.8076 (mt0) REVERT: A 306 TRP cc_start: 0.8531 (p90) cc_final: 0.8175 (p90) REVERT: A 317 TRP cc_start: 0.7485 (p-90) cc_final: 0.6925 (m-10) REVERT: A 341 PHE cc_start: 0.8033 (t80) cc_final: 0.7508 (t80) REVERT: A 344 LEU cc_start: 0.8269 (tt) cc_final: 0.7768 (tt) REVERT: A 347 PHE cc_start: 0.8219 (m-80) cc_final: 0.8005 (m-80) REVERT: A 358 TYR cc_start: 0.7643 (t80) cc_final: 0.6722 (t80) REVERT: A 407 PHE cc_start: 0.8715 (m-80) cc_final: 0.8405 (m-10) REVERT: A 430 MET cc_start: 0.7981 (ttt) cc_final: 0.7241 (ttp) REVERT: A 444 GLU cc_start: 0.8824 (pt0) cc_final: 0.8422 (pt0) REVERT: V 45 THR cc_start: 0.7398 (p) cc_final: 0.6502 (t) REVERT: V 63 ILE cc_start: 0.8313 (mt) cc_final: 0.7517 (mt) REVERT: V 151 ILE cc_start: 0.7954 (mt) cc_final: 0.7619 (mt) REVERT: H 21 VAL cc_start: 0.7490 (t) cc_final: 0.6806 (t) REVERT: H 38 ARG cc_start: 0.7646 (ttm170) cc_final: 0.7268 (ttt-90) REVERT: H 100 MET cc_start: 0.4882 (tpp) cc_final: 0.4115 (tpp) REVERT: H 102 LEU cc_start: 0.8575 (mm) cc_final: 0.8345 (mm) REVERT: H 127 MET cc_start: 0.5983 (mpp) cc_final: 0.4814 (ptp) REVERT: L 85 ARG cc_start: 0.7454 (ptm160) cc_final: 0.6702 (ptm160) REVERT: L 97 LEU cc_start: 0.4613 (pt) cc_final: 0.4248 (pt) REVERT: L 100 HIS cc_start: 0.6412 (m170) cc_final: 0.5980 (m-70) REVERT: L 113 GLN cc_start: 0.8091 (tt0) cc_final: 0.7532 (tm-30) REVERT: L 127 LYS cc_start: 0.7159 (mttt) cc_final: 0.6433 (tttt) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.1889 time to fit residues: 60.6874 Evaluate side-chains 196 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 34 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 70 optimal weight: 0.0070 chunk 93 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 67 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.196201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.157119 restraints weight = 13932.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.163990 restraints weight = 9276.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.169466 restraints weight = 6678.138| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5726 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8061 Z= 0.108 Angle : 0.600 10.420 10973 Z= 0.295 Chirality : 0.044 0.285 1209 Planarity : 0.004 0.043 1352 Dihedral : 6.429 129.252 1159 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.24 % Allowed : 2.29 % 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: -1.62 (0.26), residues: 978 helix: -1.25 (0.26), residues: 330 sheet: -0.38 (0.37), residues: 183 loop : -1.11 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP V 62 HIS 0.004 0.001 HIS V 240 PHE 0.023 0.001 PHE A 170 TYR 0.023 0.001 TYR A 186 ARG 0.003 0.000 ARG H 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00760 ( 2) link_NAG-ASN : angle 2.47767 ( 6) link_BETA1-4 : bond 0.00455 ( 1) link_BETA1-4 : angle 2.93472 ( 3) hydrogen bonds : bond 0.03602 ( 219) hydrogen bonds : angle 5.10823 ( 630) SS BOND : bond 0.00158 ( 5) SS BOND : angle 0.57316 ( 10) covalent geometry : bond 0.00245 ( 8053) covalent geometry : angle 0.59514 (10954) *********************** 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 228 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7175 (mp0) cc_final: 0.5902 (tt0) REVERT: A 90 LEU cc_start: 0.9599 (tp) cc_final: 0.9393 (tp) REVERT: A 104 ARG cc_start: 0.8538 (tpt170) cc_final: 0.8103 (ttm-80) REVERT: A 135 MET cc_start: 0.9095 (ppp) cc_final: 0.8644 (ppp) REVERT: A 136 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8587 (tm-30) REVERT: A 166 CYS cc_start: 0.8605 (t) cc_final: 0.8391 (p) REVERT: A 168 ILE cc_start: 0.9509 (mm) cc_final: 0.9186 (mm) REVERT: A 172 ILE cc_start: 0.9381 (mt) cc_final: 0.8856 (tt) REVERT: A 185 TYR cc_start: 0.7745 (t80) cc_final: 0.7323 (t80) REVERT: A 229 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8596 (tm-30) REVERT: A 230 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8276 (mm-30) REVERT: A 238 GLN cc_start: 0.8275 (mt0) cc_final: 0.7855 (mt0) REVERT: A 306 TRP cc_start: 0.8375 (p90) cc_final: 0.8018 (p90) REVERT: A 317 TRP cc_start: 0.7438 (p-90) cc_final: 0.6891 (m-10) REVERT: A 341 PHE cc_start: 0.8098 (t80) cc_final: 0.7524 (t80) REVERT: A 343 VAL cc_start: 0.9275 (t) cc_final: 0.8885 (t) REVERT: A 344 LEU cc_start: 0.8458 (tt) cc_final: 0.8052 (tt) REVERT: A 347 PHE cc_start: 0.8340 (m-80) cc_final: 0.8114 (m-80) REVERT: A 358 TYR cc_start: 0.7088 (t80) cc_final: 0.6540 (t80) REVERT: A 408 ILE cc_start: 0.8936 (mm) cc_final: 0.8724 (mm) REVERT: A 430 MET cc_start: 0.7872 (ttt) cc_final: 0.7160 (ttp) REVERT: A 444 GLU cc_start: 0.8864 (pt0) cc_final: 0.8472 (pt0) REVERT: A 541 TRP cc_start: 0.8695 (m-10) cc_final: 0.8447 (m100) REVERT: V 45 THR cc_start: 0.6870 (p) cc_final: 0.6066 (t) REVERT: V 130 LEU cc_start: 0.8258 (mt) cc_final: 0.7797 (mt) REVERT: V 151 ILE cc_start: 0.6974 (mt) cc_final: 0.6593 (mt) REVERT: V 153 MET cc_start: 0.7625 (mmp) cc_final: 0.7199 (mmm) REVERT: V 158 LYS cc_start: 0.8197 (ptmm) cc_final: 0.7595 (tmtt) REVERT: H 21 VAL cc_start: 0.7313 (t) cc_final: 0.5506 (t) REVERT: H 100 MET cc_start: 0.4715 (tpp) cc_final: 0.4024 (tpp) REVERT: H 127 MET cc_start: 0.4808 (mpp) cc_final: 0.3772 (ptp) REVERT: L 97 LEU cc_start: 0.4991 (pt) cc_final: 0.4493 (pt) REVERT: L 100 HIS cc_start: 0.6472 (m170) cc_final: 0.6015 (m-70) REVERT: L 113 GLN cc_start: 0.8420 (tt0) cc_final: 0.7684 (tm-30) REVERT: L 127 LYS cc_start: 0.6765 (mttt) cc_final: 0.6163 (tttt) outliers start: 2 outliers final: 2 residues processed: 227 average time/residue: 0.2491 time to fit residues: 77.8672 Evaluate side-chains 192 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.1980 chunk 6 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 81 optimal weight: 0.0470 chunk 70 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN A 368 ASN V 155 GLN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.193597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.155521 restraints weight = 14381.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.162019 restraints weight = 9764.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.167212 restraints weight = 7097.733| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8061 Z= 0.103 Angle : 0.584 10.510 10973 Z= 0.288 Chirality : 0.043 0.279 1209 Planarity : 0.004 0.041 1352 Dihedral : 6.265 126.873 1159 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: -1.51 (0.26), residues: 978 helix: -1.19 (0.26), residues: 334 sheet: -0.20 (0.38), residues: 183 loop : -1.07 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP V 62 HIS 0.003 0.001 HIS V 240 PHE 0.022 0.001 PHE A 170 TYR 0.015 0.001 TYR H 71 ARG 0.003 0.000 ARG A 607 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 2) link_NAG-ASN : angle 2.36092 ( 6) link_BETA1-4 : bond 0.00375 ( 1) link_BETA1-4 : angle 2.91144 ( 3) hydrogen bonds : bond 0.03421 ( 219) hydrogen bonds : angle 4.85392 ( 630) SS BOND : bond 0.00196 ( 5) SS BOND : angle 0.52611 ( 10) covalent geometry : bond 0.00230 ( 8053) covalent geometry : angle 0.57954 (10954) *********************** 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 231 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7265 (mp0) cc_final: 0.5954 (tt0) REVERT: A 90 LEU cc_start: 0.9446 (tp) cc_final: 0.9233 (tp) REVERT: A 104 ARG cc_start: 0.8704 (tpt170) cc_final: 0.8264 (ttm-80) REVERT: A 135 MET cc_start: 0.8781 (ppp) cc_final: 0.8470 (ppp) REVERT: A 136 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8088 (tm-30) REVERT: A 166 CYS cc_start: 0.8714 (t) cc_final: 0.8403 (p) REVERT: A 168 ILE cc_start: 0.9492 (mm) cc_final: 0.9177 (mm) REVERT: A 172 ILE cc_start: 0.9421 (mt) cc_final: 0.8863 (tt) REVERT: A 229 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 230 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8158 (mm-30) REVERT: A 238 GLN cc_start: 0.8547 (mt0) cc_final: 0.8055 (mt0) REVERT: A 260 MET cc_start: 0.5361 (ttt) cc_final: 0.5138 (ttt) REVERT: A 317 TRP cc_start: 0.7504 (p-90) cc_final: 0.7081 (m-10) REVERT: A 341 PHE cc_start: 0.8025 (t80) cc_final: 0.7520 (t80) REVERT: A 343 VAL cc_start: 0.9194 (t) cc_final: 0.8970 (t) REVERT: A 344 LEU cc_start: 0.8296 (tt) cc_final: 0.7744 (tt) REVERT: A 408 ILE cc_start: 0.9181 (mm) cc_final: 0.8929 (mm) REVERT: A 430 MET cc_start: 0.8148 (ttt) cc_final: 0.7394 (ttp) REVERT: A 444 GLU cc_start: 0.8744 (pt0) cc_final: 0.8352 (pt0) REVERT: A 541 TRP cc_start: 0.8626 (m-10) cc_final: 0.8391 (m100) REVERT: V 45 THR cc_start: 0.7399 (p) cc_final: 0.6562 (t) REVERT: V 65 ASN cc_start: 0.8357 (m110) cc_final: 0.8089 (m-40) REVERT: V 158 LYS cc_start: 0.8256 (ptmm) cc_final: 0.7801 (tmtt) REVERT: H 21 VAL cc_start: 0.6748 (t) cc_final: 0.6487 (t) REVERT: H 38 ARG cc_start: 0.7611 (ttm170) cc_final: 0.7254 (ttt180) REVERT: H 100 MET cc_start: 0.4691 (tpp) cc_final: 0.3800 (tpp) REVERT: H 127 MET cc_start: 0.5945 (mpp) cc_final: 0.5223 (mpp) REVERT: L 85 ARG cc_start: 0.7814 (ptm160) cc_final: 0.7397 (ptm160) REVERT: L 95 PHE cc_start: 0.6574 (m-10) cc_final: 0.6099 (m-80) REVERT: L 97 LEU cc_start: 0.4431 (pt) cc_final: 0.4132 (pt) REVERT: L 100 HIS cc_start: 0.6369 (m170) cc_final: 0.5897 (m-70) REVERT: L 113 GLN cc_start: 0.8213 (tt0) cc_final: 0.7778 (tm-30) REVERT: L 127 LYS cc_start: 0.7298 (mttt) cc_final: 0.6628 (tttt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2129 time to fit residues: 66.4710 Evaluate side-chains 199 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 17 optimal weight: 0.0470 chunk 44 optimal weight: 0.0470 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.197951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.158633 restraints weight = 14091.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.165469 restraints weight = 9555.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.170908 restraints weight = 6916.487| |-----------------------------------------------------------------------------| r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8061 Z= 0.105 Angle : 0.594 10.447 10973 Z= 0.290 Chirality : 0.043 0.276 1209 Planarity : 0.004 0.040 1352 Dihedral : 6.143 123.079 1159 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.12 % Allowed : 0.84 % Favored : 99.04 % 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: -1.37 (0.26), residues: 978 helix: -1.09 (0.26), residues: 336 sheet: -0.11 (0.39), residues: 180 loop : -0.98 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP V 62 HIS 0.003 0.001 HIS V 240 PHE 0.021 0.001 PHE A 170 TYR 0.015 0.001 TYR H 71 ARG 0.004 0.000 ARG H 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 2) link_NAG-ASN : angle 2.35695 ( 6) link_BETA1-4 : bond 0.00492 ( 1) link_BETA1-4 : angle 2.81601 ( 3) hydrogen bonds : bond 0.03276 ( 219) hydrogen bonds : angle 4.76946 ( 630) SS BOND : bond 0.00153 ( 5) SS BOND : angle 0.55251 ( 10) covalent geometry : bond 0.00233 ( 8053) covalent geometry : angle 0.58964 (10954) *********************** 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 233 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.801 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: 0.7219 (mp0) cc_final: 0.5974 (tt0) REVERT: A 90 LEU cc_start: 0.9537 (tp) cc_final: 0.9276 (tp) REVERT: A 104 ARG cc_start: 0.8637 (tpt170) cc_final: 0.8245 (ttm-80) REVERT: A 135 MET cc_start: 0.8980 (ppp) cc_final: 0.8536 (ppp) REVERT: A 136 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8235 (tm-30) REVERT: A 166 CYS cc_start: 0.8627 (t) cc_final: 0.8423 (p) REVERT: A 168 ILE cc_start: 0.9502 (mm) cc_final: 0.9180 (mm) REVERT: A 172 ILE cc_start: 0.9385 (mt) cc_final: 0.8828 (tt) REVERT: A 229 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8527 (tm-30) REVERT: A 230 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8243 (mm-30) REVERT: A 238 GLN cc_start: 0.8392 (mt0) cc_final: 0.7969 (mt0) REVERT: A 260 MET cc_start: 0.5061 (ttt) cc_final: 0.4855 (ttt) REVERT: A 317 TRP cc_start: 0.7548 (p-90) cc_final: 0.7050 (m-10) REVERT: A 341 PHE cc_start: 0.8047 (t80) cc_final: 0.7444 (t80) REVERT: A 343 VAL cc_start: 0.9268 (t) cc_final: 0.8991 (t) REVERT: A 358 TYR cc_start: 0.6372 (t80) cc_final: 0.6135 (t80) REVERT: A 408 ILE cc_start: 0.9066 (mm) cc_final: 0.8846 (mm) REVERT: A 417 MET cc_start: 0.7611 (mmp) cc_final: 0.7231 (tpp) REVERT: A 423 PHE cc_start: 0.8859 (m-10) cc_final: 0.8645 (m-10) REVERT: A 430 MET cc_start: 0.8116 (ttt) cc_final: 0.7346 (ttp) REVERT: A 444 GLU cc_start: 0.8849 (pt0) cc_final: 0.8231 (pt0) REVERT: A 541 TRP cc_start: 0.8617 (m-10) cc_final: 0.8320 (m100) REVERT: V 20 GLN cc_start: 0.8220 (mp10) cc_final: 0.7995 (mp10) REVERT: V 45 THR cc_start: 0.7254 (p) cc_final: 0.6471 (t) REVERT: V 63 ILE cc_start: 0.8313 (mt) cc_final: 0.8012 (mt) REVERT: V 65 ASN cc_start: 0.8582 (m110) cc_final: 0.8364 (m-40) REVERT: V 96 MET cc_start: 0.4105 (tmm) cc_final: 0.3297 (tmm) REVERT: V 241 TYR cc_start: 0.8078 (t80) cc_final: 0.7847 (t80) REVERT: H 21 VAL cc_start: 0.7290 (t) cc_final: 0.6999 (t) REVERT: H 100 MET cc_start: 0.4335 (tpp) cc_final: 0.3552 (tpp) REVERT: H 127 MET cc_start: 0.5214 (mpp) cc_final: 0.4685 (mpp) REVERT: L 95 PHE cc_start: 0.6605 (m-10) cc_final: 0.6109 (m-80) REVERT: L 97 LEU cc_start: 0.4545 (pt) cc_final: 0.4176 (pt) REVERT: L 113 GLN cc_start: 0.8407 (tt0) cc_final: 0.7703 (tm-30) REVERT: L 127 LYS cc_start: 0.7004 (mttt) cc_final: 0.6334 (tttt) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.2170 time to fit residues: 69.5792 Evaluate side-chains 203 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 28 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.186878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.148516 restraints weight = 14522.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.155105 restraints weight = 9843.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.160323 restraints weight = 7154.053| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8061 Z= 0.109 Angle : 0.596 10.381 10973 Z= 0.292 Chirality : 0.043 0.289 1209 Planarity : 0.004 0.040 1352 Dihedral : 6.143 120.842 1159 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -1.21 (0.27), residues: 978 helix: -0.98 (0.27), residues: 327 sheet: -0.10 (0.39), residues: 180 loop : -0.83 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 130 HIS 0.004 0.001 HIS A 143 PHE 0.020 0.001 PHE A 170 TYR 0.019 0.001 TYR V 236 ARG 0.007 0.000 ARG L 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 2) link_NAG-ASN : angle 2.44282 ( 6) link_BETA1-4 : bond 0.00400 ( 1) link_BETA1-4 : angle 2.70548 ( 3) hydrogen bonds : bond 0.03171 ( 219) hydrogen bonds : angle 4.75466 ( 630) SS BOND : bond 0.00149 ( 5) SS BOND : angle 0.55595 ( 10) covalent geometry : bond 0.00248 ( 8053) covalent geometry : angle 0.59168 (10954) *********************** 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 223 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 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: A 80 GLU cc_start: 0.7248 (mp0) cc_final: 0.5983 (tt0) REVERT: A 90 LEU cc_start: 0.9405 (tp) cc_final: 0.9154 (tp) REVERT: A 104 ARG cc_start: 0.8635 (tpt170) cc_final: 0.8303 (ttm-80) REVERT: A 135 MET cc_start: 0.8857 (ppp) cc_final: 0.8525 (ppp) REVERT: A 136 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8081 (tm-30) REVERT: A 166 CYS cc_start: 0.8648 (t) cc_final: 0.8422 (p) REVERT: A 168 ILE cc_start: 0.9454 (mm) cc_final: 0.9130 (mm) REVERT: A 172 ILE cc_start: 0.9371 (mt) cc_final: 0.8792 (tt) REVERT: A 238 GLN cc_start: 0.8596 (mt0) cc_final: 0.8046 (mt0) REVERT: A 260 MET cc_start: 0.5187 (ttt) cc_final: 0.4959 (ttt) REVERT: A 317 TRP cc_start: 0.7496 (p-90) cc_final: 0.7065 (m-10) REVERT: A 341 PHE cc_start: 0.8122 (t80) cc_final: 0.7682 (t80) REVERT: A 343 VAL cc_start: 0.9227 (t) cc_final: 0.8940 (t) REVERT: A 358 TYR cc_start: 0.6412 (t80) cc_final: 0.6147 (t80) REVERT: A 408 ILE cc_start: 0.9196 (mm) cc_final: 0.8958 (mm) REVERT: A 417 MET cc_start: 0.7596 (mmp) cc_final: 0.7327 (tpp) REVERT: A 430 MET cc_start: 0.8362 (ttp) cc_final: 0.7670 (ttp) REVERT: A 444 GLU cc_start: 0.8813 (pt0) cc_final: 0.8353 (pt0) REVERT: A 541 TRP cc_start: 0.8549 (m-10) cc_final: 0.8309 (m100) REVERT: V 45 THR cc_start: 0.7374 (p) cc_final: 0.6568 (t) REVERT: V 63 ILE cc_start: 0.8685 (mt) cc_final: 0.8007 (mt) REVERT: V 65 ASN cc_start: 0.8715 (m110) cc_final: 0.8464 (m-40) REVERT: V 96 MET cc_start: 0.3981 (tmm) cc_final: 0.3266 (tmm) REVERT: V 158 LYS cc_start: 0.8419 (ptmm) cc_final: 0.8027 (tmtt) REVERT: H 21 VAL cc_start: 0.7383 (t) cc_final: 0.7124 (t) REVERT: H 38 ARG cc_start: 0.7542 (ttm170) cc_final: 0.7090 (ttt-90) REVERT: H 70 ILE cc_start: 0.8969 (tp) cc_final: 0.8687 (tp) REVERT: H 100 MET cc_start: 0.4482 (tpp) cc_final: 0.3523 (tpp) REVERT: H 127 MET cc_start: 0.5595 (mpp) cc_final: 0.5286 (mpp) REVERT: L 85 ARG cc_start: 0.7088 (ptm160) cc_final: 0.6674 (ptm160) REVERT: L 95 PHE cc_start: 0.6635 (m-10) cc_final: 0.6102 (m-80) REVERT: L 100 HIS cc_start: 0.6323 (m90) cc_final: 0.5770 (m90) REVERT: L 113 GLN cc_start: 0.8249 (tt0) cc_final: 0.7459 (tm-30) REVERT: L 127 LYS cc_start: 0.7293 (mttt) cc_final: 0.6627 (tttt) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1787 time to fit residues: 55.3968 Evaluate side-chains 185 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 70 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.0070 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.187800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.149968 restraints weight = 14811.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.156482 restraints weight = 10385.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.161765 restraints weight = 7662.261| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8061 Z= 0.105 Angle : 0.594 10.297 10973 Z= 0.291 Chirality : 0.043 0.289 1209 Planarity : 0.004 0.040 1352 Dihedral : 6.050 117.319 1159 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % 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: -1.20 (0.26), residues: 978 helix: -0.96 (0.26), residues: 327 sheet: -0.23 (0.39), residues: 173 loop : -0.75 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP V 62 HIS 0.003 0.001 HIS V 240 PHE 0.021 0.001 PHE A 170 TYR 0.016 0.001 TYR V 236 ARG 0.005 0.000 ARG L 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 2) link_NAG-ASN : angle 2.46595 ( 6) link_BETA1-4 : bond 0.00409 ( 1) link_BETA1-4 : angle 2.64726 ( 3) hydrogen bonds : bond 0.03099 ( 219) hydrogen bonds : angle 4.66750 ( 630) SS BOND : bond 0.00191 ( 5) SS BOND : angle 0.58164 ( 10) covalent geometry : bond 0.00237 ( 8053) covalent geometry : angle 0.58944 (10954) ********************** 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 226 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7180 (mp0) cc_final: 0.5964 (tt0) REVERT: A 90 LEU cc_start: 0.9298 (tp) cc_final: 0.9052 (tp) REVERT: A 104 ARG cc_start: 0.8684 (tpt170) cc_final: 0.8368 (ttm-80) REVERT: A 135 MET cc_start: 0.8780 (ppp) cc_final: 0.8512 (ppp) REVERT: A 136 GLU cc_start: 0.8514 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 166 CYS cc_start: 0.8697 (t) cc_final: 0.8430 (p) REVERT: A 168 ILE cc_start: 0.9444 (mm) cc_final: 0.9076 (mm) REVERT: A 172 ILE cc_start: 0.9419 (mt) cc_final: 0.8688 (tt) REVERT: A 182 TRP cc_start: 0.8895 (m-10) cc_final: 0.7909 (m-90) REVERT: A 237 LEU cc_start: 0.9129 (mm) cc_final: 0.8839 (mm) REVERT: A 238 GLN cc_start: 0.8567 (mt0) cc_final: 0.8031 (mt0) REVERT: A 260 MET cc_start: 0.5140 (ttt) cc_final: 0.4913 (ttt) REVERT: A 317 TRP cc_start: 0.7558 (p-90) cc_final: 0.7199 (m-10) REVERT: A 341 PHE cc_start: 0.8077 (t80) cc_final: 0.7646 (t80) REVERT: A 343 VAL cc_start: 0.9176 (t) cc_final: 0.8968 (t) REVERT: A 358 TYR cc_start: 0.6369 (t80) cc_final: 0.6097 (t80) REVERT: A 408 ILE cc_start: 0.9243 (mm) cc_final: 0.8982 (mm) REVERT: A 417 MET cc_start: 0.7581 (mmp) cc_final: 0.7378 (tpp) REVERT: A 430 MET cc_start: 0.8432 (ttp) cc_final: 0.7713 (ttp) REVERT: A 444 GLU cc_start: 0.8740 (pt0) cc_final: 0.7977 (pt0) REVERT: A 541 TRP cc_start: 0.8444 (m-10) cc_final: 0.8200 (m100) REVERT: V 45 THR cc_start: 0.7465 (p) cc_final: 0.6648 (t) REVERT: V 65 ASN cc_start: 0.8481 (m110) cc_final: 0.8267 (m-40) REVERT: V 96 MET cc_start: 0.4327 (tmm) cc_final: 0.3897 (tmm) REVERT: V 151 ILE cc_start: 0.7938 (mt) cc_final: 0.7345 (tt) REVERT: V 158 LYS cc_start: 0.8420 (ptmm) cc_final: 0.7938 (tmtt) REVERT: H 21 VAL cc_start: 0.7462 (t) cc_final: 0.6970 (t) REVERT: H 38 ARG cc_start: 0.7466 (ttm170) cc_final: 0.7091 (ttt-90) REVERT: H 70 ILE cc_start: 0.8919 (tp) cc_final: 0.8638 (tp) REVERT: H 100 MET cc_start: 0.4378 (tpp) cc_final: 0.3422 (tpp) REVERT: L 85 ARG cc_start: 0.6920 (ptm160) cc_final: 0.6366 (ptm160) REVERT: L 95 PHE cc_start: 0.6498 (m-10) cc_final: 0.5958 (m-80) REVERT: L 97 LEU cc_start: 0.4054 (pt) cc_final: 0.3810 (pt) REVERT: L 100 HIS cc_start: 0.6187 (m90) cc_final: 0.5643 (m90) REVERT: L 113 GLN cc_start: 0.8129 (tt0) cc_final: 0.7470 (tm-30) REVERT: L 127 LYS cc_start: 0.7445 (mttt) cc_final: 0.6766 (tttt) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1812 time to fit residues: 56.7611 Evaluate side-chains 195 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 79 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 overall best weight: 0.9008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 368 ASN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.185470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.148698 restraints weight = 14084.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.155262 restraints weight = 9555.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.160363 restraints weight = 6916.294| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8061 Z= 0.108 Angle : 0.590 10.279 10973 Z= 0.290 Chirality : 0.043 0.297 1209 Planarity : 0.004 0.040 1352 Dihedral : 6.049 115.705 1159 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % 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: -1.11 (0.27), residues: 978 helix: -0.87 (0.27), residues: 325 sheet: -0.21 (0.40), residues: 173 loop : -0.71 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP V 62 HIS 0.004 0.001 HIS A 143 PHE 0.021 0.001 PHE A 170 TYR 0.021 0.001 TYR V 204 ARG 0.006 0.000 ARG H 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00740 ( 2) link_NAG-ASN : angle 2.51216 ( 6) link_BETA1-4 : bond 0.00555 ( 1) link_BETA1-4 : angle 2.54156 ( 3) hydrogen bonds : bond 0.03130 ( 219) hydrogen bonds : angle 4.66034 ( 630) SS BOND : bond 0.00252 ( 5) SS BOND : angle 0.58621 ( 10) covalent geometry : bond 0.00246 ( 8053) covalent geometry : angle 0.58554 (10954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3065.65 seconds wall clock time: 55 minutes 5.53 seconds (3305.53 seconds total)