Starting phenix.real_space_refine on Mon Nov 17 19:30:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dzw_8941/11_2025/6dzw_8941.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzw_8941/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/6dzw_8941/11_2025/6dzw_8941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzw_8941/11_2025/6dzw_8941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dzw_8941/11_2025/6dzw_8941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzw_8941/11_2025/6dzw_8941.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 1.92, per 1000 atoms: 0.25 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: 0.59 Conformation dependent library (CDL) restraints added in 328.4 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: 0.29 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: 1.19 Time building geometry restraints manager: 0.74 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.300 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG A 596 TYR 0.008 0.001 TYR V 48 PHE 0.012 0.001 PHE A 423 TRP 0.022 0.001 TRP A 151 HIS 0.001 0.000 HIS V 240 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8053) covalent geometry : angle 0.86962 (10954) SS BOND : bond 0.00094 ( 5) SS BOND : angle 0.31550 ( 10) hydrogen bonds : bond 0.35515 ( 219) hydrogen bonds : angle 11.21981 ( 630) link_BETA1-4 : bond 0.00064 ( 1) link_BETA1-4 : angle 0.83973 ( 3) link_NAG-ASN : bond 0.28881 ( 2) link_NAG-ASN : angle 13.19467 ( 6) *********************** 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 : 0.252 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: 0.0868 time to fit residues: 33.8003 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 : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.0010 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0670 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 0.3124 ------------------------------------------------------------------------------- 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 416 ASN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN H 58 GLN L 58 ASN L 62 GLN L 78 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.218171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.174640 restraints weight = 12737.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.182370 restraints weight = 8734.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.188638 restraints weight = 6359.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.193562 restraints weight = 4835.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.197340 restraints weight = 3792.733| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8061 Z= 0.139 Angle : 0.654 12.058 10973 Z= 0.328 Chirality : 0.045 0.396 1209 Planarity : 0.005 0.039 1352 Dihedral : 6.466 123.738 1159 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.22), residues: 978 helix: -3.52 (0.18), residues: 332 sheet: -1.28 (0.37), residues: 159 loop : -2.02 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 390 TYR 0.017 0.001 TYR H 50 PHE 0.030 0.001 PHE A 191 TRP 0.041 0.002 TRP V 184 HIS 0.007 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8053) covalent geometry : angle 0.64889 (10954) SS BOND : bond 0.00253 ( 5) SS BOND : angle 0.56063 ( 10) hydrogen bonds : bond 0.06257 ( 219) hydrogen bonds : angle 6.28461 ( 630) link_BETA1-4 : bond 0.00138 ( 1) link_BETA1-4 : angle 2.54003 ( 3) link_NAG-ASN : bond 0.01014 ( 2) link_NAG-ASN : angle 3.21331 ( 6) *********************** 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 262 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 0.231 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: 0.7029 (mp0) cc_final: 0.5763 (tt0) REVERT: A 90 LEU cc_start: 0.9521 (tp) cc_final: 0.9300 (tp) REVERT: A 104 ARG cc_start: 0.8417 (tpt170) cc_final: 0.7833 (tpp80) REVERT: A 136 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8533 (tm-30) REVERT: A 144 ARG cc_start: 0.5748 (ptm160) cc_final: 0.5520 (ptt180) REVERT: A 158 PHE cc_start: 0.8556 (m-80) cc_final: 0.8337 (m-80) REVERT: A 172 ILE cc_start: 0.9297 (mt) cc_final: 0.8673 (tt) REVERT: A 182 TRP cc_start: 0.8526 (m-10) cc_final: 0.7551 (m-10) REVERT: A 225 THR cc_start: 0.7268 (p) cc_final: 0.5097 (p) REVERT: A 229 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8468 (tm-30) REVERT: A 230 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8343 (mm-30) REVERT: A 237 LEU cc_start: 0.9300 (mm) cc_final: 0.8824 (mm) REVERT: A 238 GLN cc_start: 0.8205 (mt0) cc_final: 0.7688 (mt0) REVERT: A 253 TRP cc_start: 0.5756 (m100) cc_final: 0.5126 (p-90) REVERT: A 260 MET cc_start: 0.4238 (ttt) cc_final: 0.4005 (ttt) REVERT: A 313 LEU cc_start: 0.6037 (tt) cc_final: 0.5799 (tt) REVERT: A 317 TRP cc_start: 0.7547 (p-90) cc_final: 0.6975 (m-10) REVERT: A 332 GLN cc_start: 0.7721 (tp40) cc_final: 0.7401 (tp40) REVERT: A 344 LEU cc_start: 0.8470 (tt) cc_final: 0.7728 (tt) REVERT: A 358 TYR cc_start: 0.7598 (t80) cc_final: 0.6550 (t80) REVERT: A 407 PHE cc_start: 0.8910 (m-80) cc_final: 0.8440 (m-80) REVERT: A 423 PHE cc_start: 0.8760 (m-10) cc_final: 0.8541 (m-10) REVERT: A 430 MET cc_start: 0.7619 (ttt) cc_final: 0.6837 (ttp) REVERT: A 595 TYR cc_start: 0.6402 (t80) cc_final: 0.5610 (t80) REVERT: A 596 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.7764 (mpt180) REVERT: V 235 TYR cc_start: 0.7836 (m-80) cc_final: 0.7314 (m-80) REVERT: H 21 VAL cc_start: 0.7540 (t) cc_final: 0.5653 (t) REVERT: H 46 TYR cc_start: 0.8111 (p90) cc_final: 0.7887 (p90) REVERT: L 100 HIS cc_start: 0.6142 (m170) cc_final: 0.5725 (m-70) REVERT: L 110 TYR cc_start: 0.7841 (m-10) cc_final: 0.7269 (m-80) outliers start: 2 outliers final: 0 residues processed: 261 average time/residue: 0.0707 time to fit residues: 26.1621 Evaluate side-chains 204 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 58 optimal weight: 3.9990 chunk 28 optimal weight: 0.0370 chunk 75 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- 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 69 ASN V 157 HIS ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.205442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.164387 restraints weight = 14012.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.171755 restraints weight = 9562.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.177615 restraints weight = 6929.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.182034 restraints weight = 5242.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.185628 restraints weight = 4125.213| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8061 Z= 0.133 Angle : 0.620 10.034 10973 Z= 0.312 Chirality : 0.045 0.367 1209 Planarity : 0.004 0.033 1352 Dihedral : 6.241 122.117 1159 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.24), residues: 978 helix: -2.42 (0.23), residues: 336 sheet: -0.60 (0.38), residues: 181 loop : -1.63 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 69 TYR 0.018 0.001 TYR H 120 PHE 0.021 0.002 PHE A 170 TRP 0.027 0.002 TRP A 204 HIS 0.003 0.001 HIS V 240 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8053) covalent geometry : angle 0.61459 (10954) SS BOND : bond 0.00370 ( 5) SS BOND : angle 0.47929 ( 10) hydrogen bonds : bond 0.04731 ( 219) hydrogen bonds : angle 5.50238 ( 630) link_BETA1-4 : bond 0.00602 ( 1) link_BETA1-4 : angle 2.61701 ( 3) link_NAG-ASN : bond 0.00986 ( 2) link_NAG-ASN : angle 3.15013 ( 6) *********************** 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 238 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.281 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: 0.7222 (mp0) cc_final: 0.5793 (tt0) REVERT: A 98 ASP cc_start: 0.9568 (p0) cc_final: 0.9283 (p0) REVERT: A 104 ARG cc_start: 0.8543 (tpt170) cc_final: 0.8092 (ttm-80) REVERT: A 111 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7746 (mm-40) REVERT: A 166 CYS cc_start: 0.8660 (t) cc_final: 0.8217 (p) REVERT: A 168 ILE cc_start: 0.9436 (mm) cc_final: 0.9211 (mm) REVERT: A 172 ILE cc_start: 0.9335 (mt) cc_final: 0.8714 (tt) REVERT: A 191 PHE cc_start: 0.7034 (m-80) cc_final: 0.6704 (m-80) REVERT: A 238 GLN cc_start: 0.8253 (mt0) cc_final: 0.7725 (mt0) REVERT: A 253 TRP cc_start: 0.5484 (m100) cc_final: 0.4789 (p-90) REVERT: A 260 MET cc_start: 0.4272 (ttt) cc_final: 0.4000 (ttt) REVERT: A 317 TRP cc_start: 0.7564 (p-90) cc_final: 0.6954 (m-10) REVERT: A 332 GLN cc_start: 0.7651 (tp40) cc_final: 0.7438 (tp40) REVERT: A 343 VAL cc_start: 0.9123 (t) cc_final: 0.8861 (t) REVERT: A 358 TYR cc_start: 0.7829 (t80) cc_final: 0.6851 (t80) REVERT: A 407 PHE cc_start: 0.9031 (m-80) cc_final: 0.8737 (m-10) REVERT: A 423 PHE cc_start: 0.8764 (m-10) cc_final: 0.8474 (m-10) REVERT: A 430 MET cc_start: 0.7569 (ttt) cc_final: 0.6696 (ttp) REVERT: A 528 MET cc_start: 0.4096 (ppp) cc_final: 0.3774 (ppp) REVERT: A 595 TYR cc_start: 0.6669 (t80) cc_final: 0.5815 (t80) REVERT: V 43 THR cc_start: 0.8130 (m) cc_final: 0.7792 (m) REVERT: V 45 THR cc_start: 0.7464 (p) cc_final: 0.6689 (t) REVERT: V 65 ASN cc_start: 0.8802 (m110) cc_final: 0.8430 (m-40) REVERT: V 76 ASN cc_start: 0.8109 (p0) cc_final: 0.7828 (p0) REVERT: H 46 TYR cc_start: 0.8218 (p90) cc_final: 0.7980 (p90) REVERT: L 97 LEU cc_start: 0.4176 (pt) cc_final: 0.3920 (pt) REVERT: L 100 HIS cc_start: 0.6311 (m170) cc_final: 0.5954 (m-70) REVERT: L 102 MET cc_start: 0.4566 (ptt) cc_final: 0.4365 (ptt) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.0713 time to fit residues: 23.9432 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 : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4511 r_free = 0.4511 target = 0.199079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.159542 restraints weight = 14263.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.166601 restraints weight = 9680.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.172223 restraints weight = 7022.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.176631 restraints weight = 5308.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.179997 restraints weight = 4149.054| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.4230 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= 0.138 Angle : 0.611 10.138 10973 Z= 0.309 Chirality : 0.044 0.340 1209 Planarity : 0.004 0.065 1352 Dihedral : 6.297 126.060 1159 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.25), residues: 978 helix: -1.79 (0.25), residues: 338 sheet: -0.48 (0.38), residues: 184 loop : -1.38 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 596 TYR 0.017 0.001 TYR H 120 PHE 0.025 0.001 PHE A 170 TRP 0.023 0.002 TRP A 204 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8053) covalent geometry : angle 0.60586 (10954) SS BOND : bond 0.00317 ( 5) SS BOND : angle 0.51363 ( 10) hydrogen bonds : bond 0.04182 ( 219) hydrogen bonds : angle 5.33282 ( 630) link_BETA1-4 : bond 0.00520 ( 1) link_BETA1-4 : angle 2.79601 ( 3) link_NAG-ASN : bond 0.00785 ( 2) link_NAG-ASN : angle 2.87893 ( 6) *********************** 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 229 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.281 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 104 ARG cc_start: 0.8546 (tpt170) cc_final: 0.8079 (ttm-80) REVERT: A 133 PHE cc_start: 0.7957 (m-80) cc_final: 0.7500 (m-80) REVERT: A 136 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8603 (tm-30) REVERT: A 166 CYS cc_start: 0.8600 (t) cc_final: 0.8280 (p) REVERT: A 168 ILE cc_start: 0.9499 (mm) cc_final: 0.9210 (mm) REVERT: A 172 ILE cc_start: 0.9409 (mt) cc_final: 0.8872 (tt) REVERT: A 177 ASN cc_start: 0.8942 (m-40) cc_final: 0.8667 (p0) REVERT: A 238 GLN cc_start: 0.8232 (mt0) cc_final: 0.7822 (mt0) REVERT: A 260 MET cc_start: 0.3997 (ttt) cc_final: 0.3789 (ttt) REVERT: A 302 LEU cc_start: 0.8211 (mt) cc_final: 0.7806 (mt) REVERT: A 317 TRP cc_start: 0.7576 (p-90) cc_final: 0.6886 (m-10) REVERT: A 341 PHE cc_start: 0.8364 (t80) cc_final: 0.7832 (t80) REVERT: A 343 VAL cc_start: 0.9147 (t) cc_final: 0.8697 (t) REVERT: A 347 PHE cc_start: 0.8324 (m-80) cc_final: 0.8111 (m-80) REVERT: A 358 TYR cc_start: 0.7700 (t80) cc_final: 0.6897 (t80) REVERT: A 430 MET cc_start: 0.7558 (ttt) cc_final: 0.6712 (ttp) REVERT: A 528 MET cc_start: 0.4363 (ppp) cc_final: 0.4047 (ppp) REVERT: A 595 TYR cc_start: 0.6861 (t80) cc_final: 0.5970 (t80) REVERT: V 45 THR cc_start: 0.7062 (p) cc_final: 0.6334 (t) REVERT: V 109 TYR cc_start: 0.8124 (m-10) cc_final: 0.7705 (m-10) REVERT: V 176 GLN cc_start: 0.7004 (mt0) cc_final: 0.6643 (mt0) REVERT: H 21 VAL cc_start: 0.7338 (t) cc_final: 0.5796 (t) REVERT: H 46 TYR cc_start: 0.8163 (p90) cc_final: 0.7958 (p90) REVERT: L 97 LEU cc_start: 0.4489 (pt) cc_final: 0.4057 (pt) REVERT: L 100 HIS cc_start: 0.6344 (m170) cc_final: 0.6009 (m-70) REVERT: L 102 MET cc_start: 0.5603 (ptt) cc_final: 0.5037 (ptt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.0720 time to fit residues: 23.3285 Evaluate side-chains 194 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 211 ASN ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4534 r_free = 0.4534 target = 0.200951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.161666 restraints weight = 14335.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.168720 restraints weight = 9763.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.174223 restraints weight = 7107.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.178448 restraints weight = 5401.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.181974 restraints weight = 4259.787| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8061 Z= 0.123 Angle : 0.590 10.256 10973 Z= 0.293 Chirality : 0.043 0.323 1209 Planarity : 0.004 0.054 1352 Dihedral : 6.229 127.530 1159 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.12 % Allowed : 2.53 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.26), residues: 978 helix: -1.34 (0.26), residues: 331 sheet: -0.16 (0.39), residues: 176 loop : -1.23 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 113 TYR 0.019 0.001 TYR A 186 PHE 0.024 0.001 PHE A 170 TRP 0.024 0.002 TRP A 204 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8053) covalent geometry : angle 0.58481 (10954) SS BOND : bond 0.00725 ( 5) SS BOND : angle 0.48335 ( 10) hydrogen bonds : bond 0.03672 ( 219) hydrogen bonds : angle 4.99440 ( 630) link_BETA1-4 : bond 0.00571 ( 1) link_BETA1-4 : angle 2.83579 ( 3) link_NAG-ASN : bond 0.00880 ( 2) link_NAG-ASN : angle 2.75345 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.9626 (tp) cc_final: 0.9419 (tp) REVERT: A 104 ARG cc_start: 0.8595 (tpt170) cc_final: 0.8222 (ttm-80) REVERT: A 111 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7739 (mm-40) REVERT: A 133 PHE cc_start: 0.7927 (m-80) cc_final: 0.7423 (m-80) REVERT: A 136 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8412 (tm-30) REVERT: A 166 CYS cc_start: 0.8547 (t) cc_final: 0.8284 (p) REVERT: A 168 ILE cc_start: 0.9506 (mm) cc_final: 0.9194 (mm) REVERT: A 172 ILE cc_start: 0.9435 (mt) cc_final: 0.8890 (tt) REVERT: A 182 TRP cc_start: 0.8740 (m-10) cc_final: 0.7840 (m-90) REVERT: A 185 TYR cc_start: 0.7863 (t80) cc_final: 0.7544 (t80) REVERT: A 237 LEU cc_start: 0.9244 (mm) cc_final: 0.8819 (mm) REVERT: A 238 GLN cc_start: 0.8264 (mt0) cc_final: 0.7955 (mt0) REVERT: A 260 MET cc_start: 0.3849 (ttt) cc_final: 0.3648 (ttt) REVERT: A 302 LEU cc_start: 0.8172 (mt) cc_final: 0.7743 (mt) REVERT: A 306 TRP cc_start: 0.8404 (p90) cc_final: 0.8120 (p90) REVERT: A 317 TRP cc_start: 0.7592 (p-90) cc_final: 0.6960 (m-10) REVERT: A 341 PHE cc_start: 0.8208 (t80) cc_final: 0.7651 (t80) REVERT: A 343 VAL cc_start: 0.9093 (t) cc_final: 0.8626 (t) REVERT: A 347 PHE cc_start: 0.8313 (m-80) cc_final: 0.8005 (m-80) REVERT: A 358 TYR cc_start: 0.7536 (t80) cc_final: 0.7001 (t80) REVERT: A 430 MET cc_start: 0.7590 (ttt) cc_final: 0.6827 (ttp) REVERT: A 444 GLU cc_start: 0.8479 (pt0) cc_final: 0.8180 (pt0) REVERT: A 528 MET cc_start: 0.4392 (ppp) cc_final: 0.4154 (ppp) REVERT: A 595 TYR cc_start: 0.6770 (t80) cc_final: 0.5866 (t80) REVERT: V 20 GLN cc_start: 0.8207 (mp10) cc_final: 0.7996 (mp10) REVERT: V 45 THR cc_start: 0.7088 (p) cc_final: 0.6369 (t) REVERT: V 49 MET cc_start: 0.9222 (tpt) cc_final: 0.8782 (tpt) REVERT: V 109 TYR cc_start: 0.8185 (m-10) cc_final: 0.7654 (m-80) REVERT: H 21 VAL cc_start: 0.7499 (t) cc_final: 0.6102 (t) REVERT: L 85 ARG cc_start: 0.7381 (ptm160) cc_final: 0.7162 (ptm160) REVERT: L 97 LEU cc_start: 0.4469 (pt) cc_final: 0.4068 (pt) REVERT: L 100 HIS cc_start: 0.6320 (m170) cc_final: 0.5943 (m-70) REVERT: L 102 MET cc_start: 0.5556 (ptt) cc_final: 0.4996 (ptt) REVERT: L 113 GLN cc_start: 0.8222 (tt0) cc_final: 0.7816 (tm-30) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.0771 time to fit residues: 24.9890 Evaluate side-chains 192 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 GLN V 54 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 GLN ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.174802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.139160 restraints weight = 14998.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.145718 restraints weight = 9760.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.150928 restraints weight = 6899.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.154739 restraints weight = 5109.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.157864 restraints weight = 3948.036| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 8061 Z= 0.273 Angle : 0.807 10.500 10973 Z= 0.424 Chirality : 0.051 0.402 1209 Planarity : 0.005 0.057 1352 Dihedral : 7.483 146.990 1159 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.12 % Allowed : 3.37 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.25), residues: 978 helix: -1.27 (0.26), residues: 332 sheet: -0.61 (0.37), residues: 177 loop : -1.23 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 69 TYR 0.025 0.002 TYR H 120 PHE 0.030 0.003 PHE A 231 TRP 0.033 0.003 TRP H 52 HIS 0.009 0.003 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 8053) covalent geometry : angle 0.80193 (10954) SS BOND : bond 0.00622 ( 5) SS BOND : angle 1.29056 ( 10) hydrogen bonds : bond 0.04844 ( 219) hydrogen bonds : angle 5.77838 ( 630) link_BETA1-4 : bond 0.00162 ( 1) link_BETA1-4 : angle 2.76446 ( 3) link_NAG-ASN : bond 0.00466 ( 2) link_NAG-ASN : angle 3.22448 ( 6) *********************** 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 225 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.9597 (tp) cc_final: 0.9373 (tp) REVERT: A 104 ARG cc_start: 0.8854 (tpt170) cc_final: 0.8284 (ttm-80) REVERT: A 166 CYS cc_start: 0.8745 (t) cc_final: 0.8307 (p) REVERT: A 168 ILE cc_start: 0.9484 (mm) cc_final: 0.9267 (mm) REVERT: A 229 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8749 (tm-30) REVERT: A 238 GLN cc_start: 0.8823 (mt0) cc_final: 0.8264 (mt0) REVERT: A 260 MET cc_start: 0.3942 (ttt) cc_final: 0.3705 (ttt) REVERT: A 302 LEU cc_start: 0.7961 (mt) cc_final: 0.7667 (mt) REVERT: A 317 TRP cc_start: 0.7492 (p-90) cc_final: 0.7203 (m-10) REVERT: A 326 TRP cc_start: 0.7235 (m100) cc_final: 0.6269 (m-10) REVERT: A 358 TYR cc_start: 0.7866 (t80) cc_final: 0.7166 (t80) REVERT: A 430 MET cc_start: 0.7803 (ttt) cc_final: 0.7067 (ttp) REVERT: A 528 MET cc_start: 0.6210 (ppp) cc_final: 0.5816 (ppp) REVERT: A 595 TYR cc_start: 0.6916 (t80) cc_final: 0.6678 (t80) REVERT: V 176 GLN cc_start: 0.7486 (mt0) cc_final: 0.7219 (mt0) REVERT: H 38 ARG cc_start: 0.7912 (ttm170) cc_final: 0.7497 (ttt180) REVERT: H 71 TYR cc_start: 0.8254 (t80) cc_final: 0.8008 (t80) REVERT: H 100 MET cc_start: 0.4669 (tpt) cc_final: 0.4249 (tpp) REVERT: H 117 ARG cc_start: 0.8038 (tmt170) cc_final: 0.7598 (tmt170) REVERT: L 97 LEU cc_start: 0.4673 (pt) cc_final: 0.4129 (pt) REVERT: L 100 HIS cc_start: 0.6533 (m170) cc_final: 0.5717 (m-70) REVERT: L 127 LYS cc_start: 0.7460 (mttt) cc_final: 0.6777 (tttt) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.0803 time to fit residues: 24.8753 Evaluate side-chains 172 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 211 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.179528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.142492 restraints weight = 15740.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.149051 restraints weight = 10826.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.154147 restraints weight = 7889.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.158126 restraints weight = 5989.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.161185 restraints weight = 4710.291| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8061 Z= 0.125 Angle : 0.631 10.406 10973 Z= 0.314 Chirality : 0.044 0.290 1209 Planarity : 0.004 0.054 1352 Dihedral : 6.827 137.350 1159 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.24 % Allowed : 1.93 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.26), residues: 978 helix: -1.12 (0.27), residues: 327 sheet: -0.38 (0.35), residues: 186 loop : -1.07 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 596 TYR 0.025 0.002 TYR L 52 PHE 0.024 0.002 PHE A 170 TRP 0.036 0.002 TRP A 541 HIS 0.004 0.001 HIS V 240 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8053) covalent geometry : angle 0.62694 (10954) SS BOND : bond 0.00159 ( 5) SS BOND : angle 0.38196 ( 10) hydrogen bonds : bond 0.03486 ( 219) hydrogen bonds : angle 5.22284 ( 630) link_BETA1-4 : bond 0.00590 ( 1) link_BETA1-4 : angle 2.99490 ( 3) link_NAG-ASN : bond 0.00787 ( 2) link_NAG-ASN : angle 2.42311 ( 6) *********************** 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 228 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.8694 (tpt170) cc_final: 0.8285 (ttm-80) REVERT: A 136 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 166 CYS cc_start: 0.8641 (t) cc_final: 0.8324 (p) REVERT: A 168 ILE cc_start: 0.9529 (mm) cc_final: 0.9248 (mm) REVERT: A 172 ILE cc_start: 0.9499 (mt) cc_final: 0.8983 (tt) REVERT: A 229 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8321 (tm-30) REVERT: A 230 GLU cc_start: 0.8768 (mm-30) cc_final: 0.7933 (mm-30) REVERT: A 238 GLN cc_start: 0.8664 (mt0) cc_final: 0.8079 (mt0) REVERT: A 260 MET cc_start: 0.3886 (ttt) cc_final: 0.3676 (ttt) REVERT: A 302 LEU cc_start: 0.8314 (mt) cc_final: 0.8037 (mt) REVERT: A 317 TRP cc_start: 0.7515 (p-90) cc_final: 0.7128 (m-10) REVERT: A 326 TRP cc_start: 0.6913 (m100) cc_final: 0.6038 (m-10) REVERT: A 343 VAL cc_start: 0.9058 (t) cc_final: 0.8616 (t) REVERT: A 347 PHE cc_start: 0.8513 (m-80) cc_final: 0.8153 (m-80) REVERT: A 408 ILE cc_start: 0.9220 (mm) cc_final: 0.8985 (mm) REVERT: A 417 MET cc_start: 0.7911 (mmp) cc_final: 0.7601 (tpp) REVERT: A 423 PHE cc_start: 0.8879 (m-10) cc_final: 0.8657 (m-10) REVERT: A 430 MET cc_start: 0.7846 (ttt) cc_final: 0.7169 (ttp) REVERT: A 595 TYR cc_start: 0.6619 (t80) cc_final: 0.6378 (t80) REVERT: V 109 TYR cc_start: 0.7895 (m-10) cc_final: 0.7346 (m-80) REVERT: V 158 LYS cc_start: 0.8166 (ptmm) cc_final: 0.7758 (tmtt) REVERT: V 176 GLN cc_start: 0.7497 (mt0) cc_final: 0.7219 (mt0) REVERT: V 241 TYR cc_start: 0.8169 (t80) cc_final: 0.7824 (t80) REVERT: H 32 LYS cc_start: 0.7424 (pttt) cc_final: 0.7040 (pptt) REVERT: L 97 LEU cc_start: 0.4851 (pt) cc_final: 0.4622 (pt) REVERT: L 113 GLN cc_start: 0.8366 (tt0) cc_final: 0.7743 (tm-30) REVERT: L 127 LYS cc_start: 0.7279 (mttt) cc_final: 0.6619 (tttt) outliers start: 2 outliers final: 0 residues processed: 226 average time/residue: 0.0771 time to fit residues: 24.2528 Evaluate side-chains 188 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 92 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 75 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN ** L 62 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 = 0.4359 r_free = 0.4359 target = 0.178290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.142088 restraints weight = 14660.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.148511 restraints weight = 9760.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.153648 restraints weight = 6993.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.157663 restraints weight = 5236.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.160806 restraints weight = 4072.968| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8061 Z= 0.145 Angle : 0.644 10.116 10973 Z= 0.323 Chirality : 0.044 0.296 1209 Planarity : 0.004 0.047 1352 Dihedral : 6.853 138.241 1159 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.12 % Allowed : 0.72 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.26), residues: 978 helix: -1.11 (0.27), residues: 331 sheet: -0.38 (0.35), residues: 187 loop : -1.02 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 596 TYR 0.025 0.002 TYR L 52 PHE 0.025 0.002 PHE A 170 TRP 0.034 0.002 TRP A 204 HIS 0.007 0.002 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8053) covalent geometry : angle 0.64012 (10954) SS BOND : bond 0.00423 ( 5) SS BOND : angle 0.82765 ( 10) hydrogen bonds : bond 0.03543 ( 219) hydrogen bonds : angle 5.17535 ( 630) link_BETA1-4 : bond 0.00214 ( 1) link_BETA1-4 : angle 2.95291 ( 3) link_NAG-ASN : bond 0.00642 ( 2) link_NAG-ASN : angle 2.42995 ( 6) *********************** 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 228 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.8800 (tpt170) cc_final: 0.8397 (ttm-80) REVERT: A 133 PHE cc_start: 0.7949 (m-80) cc_final: 0.7708 (m-80) REVERT: A 135 MET cc_start: 0.8837 (ppp) cc_final: 0.8530 (ppp) REVERT: A 136 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8297 (tm-30) REVERT: A 166 CYS cc_start: 0.8660 (t) cc_final: 0.8362 (p) REVERT: A 238 GLN cc_start: 0.8775 (mt0) cc_final: 0.8117 (mt0) REVERT: A 260 MET cc_start: 0.3846 (ttt) cc_final: 0.3607 (ttt) REVERT: A 302 LEU cc_start: 0.8316 (mt) cc_final: 0.8019 (mt) REVERT: A 326 TRP cc_start: 0.7073 (m100) cc_final: 0.6068 (m-10) REVERT: A 343 VAL cc_start: 0.9095 (t) cc_final: 0.8687 (t) REVERT: A 347 PHE cc_start: 0.8483 (m-80) cc_final: 0.8199 (m-80) REVERT: A 417 MET cc_start: 0.7913 (mmp) cc_final: 0.7615 (tpp) REVERT: A 430 MET cc_start: 0.7806 (ttt) cc_final: 0.7117 (ttp) REVERT: A 444 GLU cc_start: 0.8783 (pt0) cc_final: 0.8548 (pt0) REVERT: A 541 TRP cc_start: 0.8520 (m-10) cc_final: 0.8300 (m100) REVERT: A 595 TYR cc_start: 0.6685 (t80) cc_final: 0.6468 (t80) REVERT: V 109 TYR cc_start: 0.8342 (m-10) cc_final: 0.8141 (m-80) REVERT: V 158 LYS cc_start: 0.8186 (ptmm) cc_final: 0.7714 (tmtt) REVERT: V 241 TYR cc_start: 0.8232 (t80) cc_final: 0.7785 (t80) REVERT: H 127 MET cc_start: 0.4585 (ptp) cc_final: 0.4382 (pmm) REVERT: H 129 TYR cc_start: 0.9182 (m-10) cc_final: 0.8956 (m-10) REVERT: L 97 LEU cc_start: 0.4820 (pt) cc_final: 0.4592 (pt) REVERT: L 100 HIS cc_start: 0.6245 (m90) cc_final: 0.5649 (m90) REVERT: L 113 GLN cc_start: 0.8085 (tt0) cc_final: 0.7768 (tm-30) REVERT: L 127 LYS cc_start: 0.7325 (mttt) cc_final: 0.7000 (mtpt) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.0807 time to fit residues: 25.8080 Evaluate side-chains 187 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 6 optimal weight: 0.0170 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- 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** ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN ** L 62 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 = 0.4370 r_free = 0.4370 target = 0.179184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.143020 restraints weight = 14636.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.149542 restraints weight = 9920.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.154560 restraints weight = 7139.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.158469 restraints weight = 5371.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.161572 restraints weight = 4188.646| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8061 Z= 0.126 Angle : 0.634 9.930 10973 Z= 0.313 Chirality : 0.044 0.320 1209 Planarity : 0.004 0.045 1352 Dihedral : 6.778 138.067 1159 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.26), residues: 978 helix: -1.15 (0.26), residues: 333 sheet: -0.28 (0.36), residues: 187 loop : -1.02 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG V 245 TYR 0.021 0.002 TYR V 204 PHE 0.021 0.002 PHE A 170 TRP 0.044 0.002 TRP H 130 HIS 0.007 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8053) covalent geometry : angle 0.62890 (10954) SS BOND : bond 0.00201 ( 5) SS BOND : angle 1.09876 ( 10) hydrogen bonds : bond 0.03359 ( 219) hydrogen bonds : angle 5.15461 ( 630) link_BETA1-4 : bond 0.00334 ( 1) link_BETA1-4 : angle 2.89585 ( 3) link_NAG-ASN : bond 0.00713 ( 2) link_NAG-ASN : angle 2.47106 ( 6) *********************** 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 226 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.9587 (tp) cc_final: 0.9352 (tp) REVERT: A 104 ARG cc_start: 0.8803 (tpt170) cc_final: 0.8423 (ttm-80) REVERT: A 135 MET cc_start: 0.8866 (ppp) cc_final: 0.8577 (ppp) REVERT: A 136 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8180 (tm-30) REVERT: A 238 GLN cc_start: 0.8753 (mt0) cc_final: 0.8059 (mt0) REVERT: A 260 MET cc_start: 0.3853 (ttt) cc_final: 0.3624 (ttt) REVERT: A 302 LEU cc_start: 0.8268 (mt) cc_final: 0.7944 (mt) REVERT: A 326 TRP cc_start: 0.7019 (m100) cc_final: 0.6392 (m-10) REVERT: A 343 VAL cc_start: 0.9094 (t) cc_final: 0.8714 (t) REVERT: A 347 PHE cc_start: 0.8484 (m-80) cc_final: 0.8178 (m-80) REVERT: A 408 ILE cc_start: 0.9245 (mm) cc_final: 0.8987 (mm) REVERT: A 417 MET cc_start: 0.7922 (mmp) cc_final: 0.7629 (tpp) REVERT: A 430 MET cc_start: 0.7812 (ttt) cc_final: 0.7107 (ttp) REVERT: A 444 GLU cc_start: 0.8788 (pt0) cc_final: 0.8509 (pt0) REVERT: A 490 LYS cc_start: 0.8904 (tttt) cc_final: 0.8605 (tttt) REVERT: V 109 TYR cc_start: 0.8302 (m-10) cc_final: 0.8032 (m-80) REVERT: V 158 LYS cc_start: 0.8164 (ptmm) cc_final: 0.7663 (tmtt) REVERT: V 241 TYR cc_start: 0.8209 (t80) cc_final: 0.7730 (t80) REVERT: H 21 VAL cc_start: 0.7242 (t) cc_final: 0.6145 (t) REVERT: H 38 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7570 (ttt180) REVERT: H 129 TYR cc_start: 0.9137 (m-10) cc_final: 0.8891 (m-10) REVERT: L 58 ASN cc_start: 0.8418 (m110) cc_final: 0.8117 (m110) REVERT: L 85 ARG cc_start: 0.7198 (ptm160) cc_final: 0.6217 (ptp-170) REVERT: L 100 HIS cc_start: 0.6250 (m90) cc_final: 0.5620 (m90) REVERT: L 103 GLU cc_start: 0.8024 (mp0) cc_final: 0.7578 (mp0) REVERT: L 127 LYS cc_start: 0.7384 (mttt) cc_final: 0.7051 (mtpt) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.0841 time to fit residues: 26.1928 Evaluate side-chains 190 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 50 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN L 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.175687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.139978 restraints weight = 14680.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.146307 restraints weight = 9893.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.151291 restraints weight = 7113.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.155180 restraints weight = 5334.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.158252 restraints weight = 4137.917| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8061 Z= 0.141 Angle : 0.645 9.839 10973 Z= 0.324 Chirality : 0.044 0.301 1209 Planarity : 0.004 0.070 1352 Dihedral : 6.847 137.796 1159 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.26), residues: 978 helix: -1.16 (0.27), residues: 333 sheet: -0.28 (0.36), residues: 187 loop : -1.00 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 117 TYR 0.022 0.002 TYR L 52 PHE 0.024 0.002 PHE A 170 TRP 0.043 0.002 TRP A 541 HIS 0.007 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8053) covalent geometry : angle 0.64088 (10954) SS BOND : bond 0.00323 ( 5) SS BOND : angle 0.76839 ( 10) hydrogen bonds : bond 0.03383 ( 219) hydrogen bonds : angle 5.16472 ( 630) link_BETA1-4 : bond 0.00471 ( 1) link_BETA1-4 : angle 2.83551 ( 3) link_NAG-ASN : bond 0.00678 ( 2) link_NAG-ASN : angle 2.48423 ( 6) ********************** 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 224 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.9577 (tp) cc_final: 0.9344 (tp) REVERT: A 104 ARG cc_start: 0.8834 (tpt170) cc_final: 0.8444 (ttm-80) REVERT: A 136 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 166 CYS cc_start: 0.8900 (p) cc_final: 0.8546 (p) REVERT: A 182 TRP cc_start: 0.8892 (m-10) cc_final: 0.7775 (m-90) REVERT: A 237 LEU cc_start: 0.9184 (mm) cc_final: 0.8837 (mm) REVERT: A 260 MET cc_start: 0.3891 (ttt) cc_final: 0.3675 (ttt) REVERT: A 302 LEU cc_start: 0.8252 (mt) cc_final: 0.7912 (mt) REVERT: A 326 TRP cc_start: 0.7050 (m100) cc_final: 0.6429 (m-10) REVERT: A 343 VAL cc_start: 0.9092 (t) cc_final: 0.8697 (t) REVERT: A 347 PHE cc_start: 0.8485 (m-80) cc_final: 0.8184 (m-80) REVERT: A 408 ILE cc_start: 0.9266 (mm) cc_final: 0.8992 (mm) REVERT: A 417 MET cc_start: 0.7946 (mmp) cc_final: 0.7621 (tpp) REVERT: A 423 PHE cc_start: 0.8771 (m-10) cc_final: 0.8568 (m-10) REVERT: A 430 MET cc_start: 0.7858 (ttt) cc_final: 0.7188 (ttp) REVERT: A 444 GLU cc_start: 0.8773 (pt0) cc_final: 0.8482 (pt0) REVERT: A 490 LYS cc_start: 0.8890 (tttt) cc_final: 0.8645 (tttt) REVERT: V 96 MET cc_start: 0.4253 (ppp) cc_final: 0.3560 (ppp) REVERT: V 241 TYR cc_start: 0.8229 (t80) cc_final: 0.7761 (t80) REVERT: H 38 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7733 (ttt180) REVERT: L 58 ASN cc_start: 0.8207 (m-40) cc_final: 0.7935 (m110) REVERT: L 85 ARG cc_start: 0.7460 (ptm160) cc_final: 0.6452 (ptp-170) REVERT: L 100 HIS cc_start: 0.6400 (m90) cc_final: 0.5764 (m90) REVERT: L 103 GLU cc_start: 0.8195 (mp0) cc_final: 0.7891 (mp0) REVERT: L 127 LYS cc_start: 0.7486 (mttt) cc_final: 0.7098 (mtpt) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.0807 time to fit residues: 25.2743 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 : 0.240 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN ** L 62 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 = 0.4342 r_free = 0.4342 target = 0.175987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.140368 restraints weight = 14511.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.146914 restraints weight = 9763.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.151892 restraints weight = 6974.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.155733 restraints weight = 5208.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.158665 restraints weight = 4036.830| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8061 Z= 0.127 Angle : 0.624 9.860 10973 Z= 0.312 Chirality : 0.043 0.321 1209 Planarity : 0.004 0.070 1352 Dihedral : 6.774 138.711 1159 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.24 % Allowed : 0.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.26), residues: 978 helix: -0.96 (0.27), residues: 325 sheet: -0.30 (0.35), residues: 197 loop : -0.94 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG V 245 TYR 0.018 0.001 TYR V 236 PHE 0.020 0.001 PHE A 170 TRP 0.047 0.002 TRP A 204 HIS 0.006 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8053) covalent geometry : angle 0.61984 (10954) SS BOND : bond 0.00176 ( 5) SS BOND : angle 0.63328 ( 10) hydrogen bonds : bond 0.03237 ( 219) hydrogen bonds : angle 5.07802 ( 630) link_BETA1-4 : bond 0.00462 ( 1) link_BETA1-4 : angle 2.82028 ( 3) link_NAG-ASN : bond 0.00668 ( 2) link_NAG-ASN : angle 2.47523 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1499.11 seconds wall clock time: 26 minutes 35.23 seconds (1595.23 seconds total)