Starting phenix.real_space_refine on Fri Sep 11 05:50:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dzw_8941/09_2026/6dzw_8941.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzw_8941/09_2026/6dzw_8941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dzw_8941/09_2026/6dzw_8941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzw_8941/09_2026/6dzw_8941.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6dzw_8941/09_2026/6dzw_8941.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dzw_8941/09_2026/6dzw_8941.cif" model { file = "/net/cci-nas-00/data/ceres_data/6dzw_8941/09_2026/6dzw_8941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzw_8941/09_2026/6dzw_8941.cif" } 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-2.2.1-6174/lib/python3.11/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 chiralities: 2 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'8PR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.69, per 1000 atoms: 0.22 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: 0.60 Conformation dependent library (CDL) restraints added in 372.1 milliseconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 13 sheets defined 43.6% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 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: 1.27 Time building geometry restraints manager: 0.82 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 - 17.96: 4195 17.96 - 35.91: 312 35.91 - 53.86: 73 53.86 - 71.82: 10 71.82 - 89.77: 4 Dihedral angle restraints: 4594 sinusoidal: 1749 harmonic: 2845 Sorted by residual: dihedral pdb=" CA GLU L 47 " pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta harmonic sigma weight residual 0.00 32.90 -32.90 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA GLY A 249 " pdb=" C GLY A 249 " pdb=" N GLY A 250 " pdb=" CA GLY A 250 " ideal model delta harmonic sigma weight residual -180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA GLU V 254 " pdb=" C GLU V 254 " pdb=" N ILE V 255 " pdb=" CA ILE V 255 " ideal model delta harmonic sigma weight residual 0.00 20.71 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 4591 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.280 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5316 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 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 : 13.544 89.773 2775 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/Z covalent geometry : bond 0.00387 / 0.21 ( 8053) covalent geometry : angle 0.86962 / 0.47 (10954) SS BOND : bond 0.00094 / 0.06 ( 5) SS BOND : angle 0.31550 / 0.22 ( 10) hydrogen bonds : bond 0.35515 / 22.57 ( 219) hydrogen bonds : angle 11.21981 / 7.74 ( 630) link_BETA1-4 : bond 0.00064 / 0.03 ( 1) link_BETA1-4 : angle 0.83973 / 0.47 ( 3) link_NAG-ASN : bond 0.28881 / 13.77 ( 2) link_NAG-ASN : angle 13.19467 / 6.52 ( 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 : 0.280 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: 0.7906 (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: 0.8327 (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: 0.3789 (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: 0.8609 (m-80) cc_final: 0.8172 (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: 0.8577 (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: 0.7634 (mtt-85) REVERT: A 607 ARG cc_start: 0.7348 (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: 0.0913 time to fit residues: 35.8928 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 : 0.279 ------------------------------------------------------------------------------- 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... ** 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 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.217972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.175383 restraints weight = 13262.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.182898 restraints weight = 9195.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.189070 restraints weight = 6778.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.193828 restraints weight = 5171.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.197597 restraints weight = 4082.099| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5353 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8061 Z= 0.134 Angle : 0.652 12.328 10973 Z= 0.325 Chirality : 0.045 0.377 1209 Planarity : 0.005 0.039 1352 Dihedral : 4.415 28.577 1079 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.79 % 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: -3.74 (0.22), residues: 978 helix: -3.54 (0.18), residues: 332 sheet: -1.34 (0.37), residues: 157 loop : -2.00 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 607 TYR 0.017 0.001 TYR V 204 PHE 0.025 0.001 PHE A 191 TRP 0.035 0.002 TRP V 184 HIS 0.006 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8053) covalent geometry : angle 0.64680 / 0.32 (10954) SS BOND : bond 0.00232 / 0.12 ( 5) SS BOND : angle 0.54791 / 0.37 ( 10) hydrogen bonds : bond 0.06021 / 3.87 ( 219) hydrogen bonds : angle 6.27501 / 4.28 ( 630) link_BETA1-4 : bond 0.00129 / 0.07 ( 1) link_BETA1-4 : angle 2.44442 / 1.37 ( 3) link_NAG-ASN : bond 0.01244 / 0.65 ( 2) link_NAG-ASN : angle 3.00356 / 1.69 ( 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 261 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.284 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: 0.7029 (mp0) cc_final: 0.5767 (tt0) REVERT: A 90 LEU cc_start: 0.9539 (tp) cc_final: 0.9319 (tp) REVERT: A 104 ARG cc_start: 0.8409 (tpt170) cc_final: 0.7832 (tpp80) REVERT: A 136 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8552 (tm-30) REVERT: A 144 ARG cc_start: 0.5749 (ptm160) cc_final: 0.5522 (ptt180) REVERT: A 158 PHE cc_start: 0.8582 (m-80) cc_final: 0.8343 (m-80) REVERT: A 172 ILE cc_start: 0.9304 (mt) cc_final: 0.8678 (tt) REVERT: A 182 TRP cc_start: 0.8515 (m-10) cc_final: 0.7550 (m-10) REVERT: A 225 THR cc_start: 0.7276 (p) cc_final: 0.5020 (p) REVERT: A 229 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8439 (tm-30) REVERT: A 230 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8359 (mm-30) REVERT: A 237 LEU cc_start: 0.9273 (mm) cc_final: 0.8786 (mm) REVERT: A 238 GLN cc_start: 0.8166 (mt0) cc_final: 0.7696 (mt0) REVERT: A 253 TRP cc_start: 0.5752 (m100) cc_final: 0.5124 (p-90) REVERT: A 260 MET cc_start: 0.4184 (ttt) cc_final: 0.3970 (ttt) REVERT: A 313 LEU cc_start: 0.6027 (tt) cc_final: 0.5753 (tt) REVERT: A 317 TRP cc_start: 0.7525 (p-90) cc_final: 0.6926 (m-10) REVERT: A 332 GLN cc_start: 0.7697 (tp40) cc_final: 0.7372 (tp40) REVERT: A 343 VAL cc_start: 0.8990 (t) cc_final: 0.8771 (t) REVERT: A 344 LEU cc_start: 0.8477 (tt) cc_final: 0.7743 (tt) REVERT: A 358 TYR cc_start: 0.7618 (t80) cc_final: 0.6558 (t80) REVERT: A 407 PHE cc_start: 0.8938 (m-80) cc_final: 0.8461 (m-80) REVERT: A 430 MET cc_start: 0.7582 (ttt) cc_final: 0.6763 (ttp) REVERT: A 595 TYR cc_start: 0.6454 (t80) cc_final: 0.5652 (t80) REVERT: A 596 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.7775 (mpt180) REVERT: V 235 TYR cc_start: 0.7894 (m-80) cc_final: 0.7356 (m-80) REVERT: H 21 VAL cc_start: 0.7603 (t) cc_final: 0.5632 (t) REVERT: H 52 TRP cc_start: 0.7441 (m100) cc_final: 0.7231 (m100) REVERT: L 100 HIS cc_start: 0.6026 (m170) cc_final: 0.5622 (m-70) REVERT: L 110 TYR cc_start: 0.7915 (m-10) cc_final: 0.7386 (m-80) outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.0754 time to fit residues: 27.8913 Evaluate side-chains 201 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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: 5.9990 chunk 28 optimal weight: 0.0970 chunk 75 optimal weight: 6.9990 chunk 11 optimal weight: 0.0670 chunk 64 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 88 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.215790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.172835 restraints weight = 13164.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.180274 restraints weight = 9036.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.186062 restraints weight = 6629.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.190573 restraints weight = 5099.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.194180 restraints weight = 4057.893| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5439 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8061 Z= 0.112 Angle : 0.602 9.827 10973 Z= 0.297 Chirality : 0.044 0.335 1209 Planarity : 0.004 0.035 1352 Dihedral : 4.194 27.015 1079 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: -2.93 (0.24), residues: 978 helix: -2.66 (0.22), residues: 331 sheet: -0.69 (0.37), residues: 177 loop : -1.81 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 69 TYR 0.016 0.001 TYR H 120 PHE 0.019 0.001 PHE A 133 TRP 0.019 0.001 TRP V 184 HIS 0.002 0.001 HIS V 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 8053) covalent geometry : angle 0.59698 / 0.30 (10954) SS BOND : bond 0.00220 / 0.11 ( 5) SS BOND : angle 0.49042 / 0.33 ( 10) hydrogen bonds : bond 0.04960 / 3.16 ( 219) hydrogen bonds : angle 5.71325 / 3.89 ( 630) link_BETA1-4 : bond 0.00866 / 0.46 ( 1) link_BETA1-4 : angle 2.47870 / 1.39 ( 3) link_NAG-ASN : bond 0.00960 / 0.49 ( 2) link_NAG-ASN : angle 3.01350 / 1.65 ( 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 232 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.278 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: symmetry clash REVERT: A 80 GLU cc_start: 0.7130 (mp0) cc_final: 0.5851 (tt0) REVERT: A 98 ASP cc_start: 0.9547 (p0) cc_final: 0.9261 (p0) REVERT: A 104 ARG cc_start: 0.8542 (tpt170) cc_final: 0.8066 (ttm-80) REVERT: A 136 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8470 (tm-30) REVERT: A 158 PHE cc_start: 0.8573 (m-80) cc_final: 0.8370 (m-80) REVERT: A 166 CYS cc_start: 0.8562 (t) cc_final: 0.7714 (t) REVERT: A 172 ILE cc_start: 0.9336 (mt) cc_final: 0.8728 (tt) REVERT: A 238 GLN cc_start: 0.8205 (mt0) cc_final: 0.7705 (mt0) REVERT: A 253 TRP cc_start: 0.5491 (m100) cc_final: 0.4880 (p-90) REVERT: A 260 MET cc_start: 0.4361 (ttt) cc_final: 0.4120 (ttt) REVERT: A 317 TRP cc_start: 0.7565 (p-90) cc_final: 0.6942 (m-10) REVERT: A 343 VAL cc_start: 0.9077 (t) cc_final: 0.8821 (t) REVERT: A 358 TYR cc_start: 0.7713 (t80) cc_final: 0.6811 (t80) REVERT: A 407 PHE cc_start: 0.8966 (m-80) cc_final: 0.8711 (m-10) REVERT: A 430 MET cc_start: 0.7562 (ttt) cc_final: 0.6651 (ttp) REVERT: A 528 MET cc_start: 0.3758 (ppp) cc_final: 0.3350 (ppp) REVERT: A 595 TYR cc_start: 0.6432 (t80) cc_final: 0.5572 (t80) REVERT: V 43 THR cc_start: 0.8205 (m) cc_final: 0.7800 (m) REVERT: V 235 TYR cc_start: 0.7841 (m-80) cc_final: 0.7359 (m-80) REVERT: V 241 TYR cc_start: 0.8165 (t80) cc_final: 0.7925 (t80) REVERT: H 21 VAL cc_start: 0.7267 (t) cc_final: 0.5445 (t) REVERT: H 46 TYR cc_start: 0.8155 (p90) cc_final: 0.7892 (p90) REVERT: H 102 LEU cc_start: 0.8259 (mm) cc_final: 0.7936 (mm) REVERT: L 100 HIS cc_start: 0.6126 (m170) cc_final: 0.5709 (m-70) REVERT: L 102 MET cc_start: 0.4347 (ptt) cc_final: 0.4125 (ptt) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.0751 time to fit residues: 24.6531 Evaluate side-chains 193 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 69 ASN V 157 HIS ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.196818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.157319 restraints weight = 14315.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.164206 restraints weight = 9669.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.169707 restraints weight = 6994.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.173959 restraints weight = 5278.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.177343 restraints weight = 4143.510| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5802 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8061 Z= 0.164 Angle : 0.644 10.123 10973 Z= 0.328 Chirality : 0.045 0.309 1209 Planarity : 0.004 0.057 1352 Dihedral : 4.383 26.155 1079 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.12 % Allowed : 3.61 % Favored : 96.27 % 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: -2.22 (0.25), residues: 978 helix: -1.95 (0.24), residues: 335 sheet: -0.66 (0.38), residues: 182 loop : -1.31 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 69 TYR 0.019 0.002 TYR H 120 PHE 0.027 0.002 PHE A 170 TRP 0.014 0.002 TRP V 51 HIS 0.005 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 8053) covalent geometry : angle 0.63919 / 0.33 (10954) SS BOND : bond 0.00839 / 0.42 ( 5) SS BOND : angle 0.52860 / 0.40 ( 10) hydrogen bonds : bond 0.04135 / 2.71 ( 219) hydrogen bonds : angle 5.30752 / 3.64 ( 630) link_BETA1-4 : bond 0.01561 / 0.82 ( 1) link_BETA1-4 : angle 2.59064 / 1.49 ( 3) link_NAG-ASN : bond 0.00758 / 0.39 ( 2) link_NAG-ASN : angle 2.88268 / 1.55 ( 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 228 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.313 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 98 ASP cc_start: 0.9570 (p0) cc_final: 0.9325 (p0) REVERT: A 104 ARG cc_start: 0.8586 (tpt170) cc_final: 0.8192 (ttm-80) REVERT: A 111 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7628 (mm-40) REVERT: A 112 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7397 (m110) REVERT: A 136 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8535 (tm-30) REVERT: A 166 CYS cc_start: 0.8716 (t) cc_final: 0.8310 (p) REVERT: A 168 ILE cc_start: 0.9459 (mm) cc_final: 0.9224 (mm) REVERT: A 172 ILE cc_start: 0.9413 (mt) cc_final: 0.8803 (tt) REVERT: A 238 GLN cc_start: 0.8607 (mt0) cc_final: 0.8096 (mt0) REVERT: A 260 MET cc_start: 0.4384 (ttt) cc_final: 0.4115 (ttt) REVERT: A 292 LEU cc_start: 0.8339 (mt) cc_final: 0.8059 (mt) REVERT: A 302 LEU cc_start: 0.8295 (mt) cc_final: 0.7758 (mt) REVERT: A 317 TRP cc_start: 0.7558 (p-90) cc_final: 0.6989 (m-10) REVERT: A 358 TYR cc_start: 0.7676 (t80) cc_final: 0.6851 (t80) REVERT: A 430 MET cc_start: 0.7722 (ttt) cc_final: 0.6706 (ttp) REVERT: A 473 CYS cc_start: 0.7981 (p) cc_final: 0.7775 (p) REVERT: A 528 MET cc_start: 0.4476 (ppp) cc_final: 0.4245 (ppp) REVERT: A 595 TYR cc_start: 0.6802 (t80) cc_final: 0.5973 (t80) REVERT: V 45 THR cc_start: 0.7406 (p) cc_final: 0.6681 (t) REVERT: V 49 MET cc_start: 0.8329 (tpt) cc_final: 0.7998 (tpt) REVERT: V 63 ILE cc_start: 0.8637 (mt) cc_final: 0.8045 (mt) REVERT: V 109 TYR cc_start: 0.7975 (m-10) cc_final: 0.7458 (m-10) REVERT: V 159 PHE cc_start: 0.6519 (m-80) cc_final: 0.6219 (m-10) REVERT: H 46 TYR cc_start: 0.8344 (p90) cc_final: 0.7915 (p90) REVERT: L 33 VAL cc_start: 0.7111 (t) cc_final: 0.6754 (t) REVERT: L 97 LEU cc_start: 0.4295 (pt) cc_final: 0.3951 (pt) REVERT: L 100 HIS cc_start: 0.6297 (m170) cc_final: 0.5965 (m-70) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.0743 time to fit residues: 23.5865 Evaluate side-chains 189 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN A 177 ASN A 211 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 GLN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.195792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.156982 restraints weight = 14300.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.163902 restraints weight = 9685.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.169327 restraints weight = 6988.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.173611 restraints weight = 5261.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.176959 restraints weight = 4102.732| |-----------------------------------------------------------------------------| r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8061 Z= 0.130 Angle : 0.593 10.141 10973 Z= 0.299 Chirality : 0.044 0.294 1209 Planarity : 0.004 0.051 1352 Dihedral : 4.292 28.512 1079 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: -1.75 (0.26), residues: 978 helix: -1.39 (0.26), residues: 327 sheet: -0.30 (0.39), residues: 178 loop : -1.23 (0.28), residues: 473 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 0.024 0.001 PHE A 170 TRP 0.033 0.002 TRP V 62 HIS 0.005 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8053) covalent geometry : angle 0.58862 / 0.30 (10954) SS BOND : bond 0.00239 / 0.12 ( 5) SS BOND : angle 0.67627 / 0.39 ( 10) hydrogen bonds : bond 0.03789 / 2.44 ( 219) hydrogen bonds : angle 5.05969 / 3.52 ( 630) link_BETA1-4 : bond 0.00440 / 0.23 ( 1) link_BETA1-4 : angle 2.46241 / 1.37 ( 3) link_NAG-ASN : bond 0.00790 / 0.41 ( 2) link_NAG-ASN : angle 2.68733 / 1.44 ( 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 226 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7184 (mp0) cc_final: 0.5827 (tt0) REVERT: A 90 LEU cc_start: 0.9631 (tp) cc_final: 0.9430 (tp) REVERT: A 104 ARG cc_start: 0.8654 (tpt170) cc_final: 0.8191 (ttm-80) REVERT: A 133 PHE cc_start: 0.7790 (m-80) cc_final: 0.7340 (m-80) REVERT: A 136 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8704 (tm-30) REVERT: A 166 CYS cc_start: 0.8724 (t) cc_final: 0.8353 (p) REVERT: A 168 ILE cc_start: 0.9529 (mm) cc_final: 0.9299 (mm) REVERT: A 172 ILE cc_start: 0.9466 (mt) cc_final: 0.8973 (tt) REVERT: A 177 ASN cc_start: 0.8970 (m110) cc_final: 0.8669 (p0) REVERT: A 238 GLN cc_start: 0.8431 (mt0) cc_final: 0.7988 (mt0) REVERT: A 292 LEU cc_start: 0.8450 (mt) cc_final: 0.8218 (mt) REVERT: A 302 LEU cc_start: 0.8417 (mt) cc_final: 0.8008 (mt) REVERT: A 306 TRP cc_start: 0.8444 (p90) cc_final: 0.8155 (p90) REVERT: A 317 TRP cc_start: 0.7561 (p-90) cc_final: 0.6876 (m-10) REVERT: A 343 VAL cc_start: 0.9200 (t) cc_final: 0.8850 (t) REVERT: A 358 TYR cc_start: 0.7515 (t80) cc_final: 0.6993 (t80) REVERT: A 408 ILE cc_start: 0.9207 (mm) cc_final: 0.9002 (mm) REVERT: A 430 MET cc_start: 0.7508 (ttt) cc_final: 0.6621 (ttp) REVERT: A 528 MET cc_start: 0.4347 (ppp) cc_final: 0.4078 (ppp) REVERT: A 595 TYR cc_start: 0.7008 (t80) cc_final: 0.6161 (t80) REVERT: V 45 THR cc_start: 0.6994 (p) cc_final: 0.6293 (t) REVERT: V 63 ILE cc_start: 0.8330 (mt) cc_final: 0.7864 (mt) REVERT: V 109 TYR cc_start: 0.7870 (m-10) cc_final: 0.7383 (m-10) REVERT: V 159 PHE cc_start: 0.6438 (m-80) cc_final: 0.6177 (m-10) REVERT: V 241 TYR cc_start: 0.8163 (t80) cc_final: 0.7939 (t80) REVERT: H 46 TYR cc_start: 0.8277 (p90) cc_final: 0.7997 (p90) REVERT: L 85 ARG cc_start: 0.7714 (ptm160) cc_final: 0.7232 (ptm160) REVERT: L 97 LEU cc_start: 0.4575 (pt) cc_final: 0.4178 (pt) REVERT: L 100 HIS cc_start: 0.6381 (m170) cc_final: 0.6010 (m-70) REVERT: L 102 MET cc_start: 0.5709 (ptt) cc_final: 0.5093 (ptt) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.0782 time to fit residues: 24.9091 Evaluate side-chains 195 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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: 0.9990 chunk 88 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 GLN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 GLN ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.177020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.141343 restraints weight = 14815.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.147605 restraints weight = 9668.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.152542 restraints weight = 6878.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.156426 restraints weight = 5150.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.159435 restraints weight = 3997.950| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8061 Z= 0.228 Angle : 0.743 10.513 10973 Z= 0.386 Chirality : 0.048 0.333 1209 Planarity : 0.005 0.050 1352 Dihedral : 5.230 37.281 1079 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.79 (0.25), residues: 978 helix: -1.25 (0.26), residues: 326 sheet: -0.68 (0.37), residues: 182 loop : -1.24 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 69 TYR 0.021 0.002 TYR L 110 PHE 0.028 0.003 PHE A 170 TRP 0.032 0.003 TRP H 52 HIS 0.008 0.003 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 ( 8053) covalent geometry : angle 0.73840 / 0.39 (10954) SS BOND : bond 0.00742 / 0.41 ( 5) SS BOND : angle 1.04110 / 0.69 ( 10) hydrogen bonds : bond 0.04558 / 3.02 ( 219) hydrogen bonds : angle 5.73298 / 3.96 ( 630) link_BETA1-4 : bond 0.00972 / 0.51 ( 1) link_BETA1-4 : angle 2.70119 / 1.56 ( 3) link_NAG-ASN : bond 0.00370 / 0.19 ( 2) link_NAG-ASN : angle 2.81128 / 1.49 ( 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 235 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.311 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 90 LEU cc_start: 0.9595 (tp) cc_final: 0.9372 (tp) REVERT: A 104 ARG cc_start: 0.8710 (tpt170) cc_final: 0.8287 (ttm-80) REVERT: A 133 PHE cc_start: 0.7991 (m-80) cc_final: 0.7582 (m-80) REVERT: A 166 CYS cc_start: 0.8860 (t) cc_final: 0.8419 (p) REVERT: A 168 ILE cc_start: 0.9473 (mm) cc_final: 0.9215 (mm) REVERT: A 172 ILE cc_start: 0.9527 (mt) cc_final: 0.8962 (tt) REVERT: A 229 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8782 (tm-30) REVERT: A 238 GLN cc_start: 0.8887 (mt0) cc_final: 0.8360 (mt0) REVERT: A 260 MET cc_start: 0.4765 (ttt) cc_final: 0.4353 (ttt) REVERT: A 302 LEU cc_start: 0.8221 (mt) cc_final: 0.7736 (mt) REVERT: A 306 TRP cc_start: 0.8559 (p90) cc_final: 0.8091 (p90) REVERT: A 317 TRP cc_start: 0.7496 (p-90) cc_final: 0.7130 (m-10) REVERT: A 326 TRP cc_start: 0.7172 (m100) cc_final: 0.6407 (m-10) REVERT: A 358 TYR cc_start: 0.7680 (t80) cc_final: 0.7104 (t80) REVERT: A 430 MET cc_start: 0.7483 (ttt) cc_final: 0.6664 (ttp) REVERT: A 528 MET cc_start: 0.5886 (ppp) cc_final: 0.5528 (ppp) REVERT: V 45 THR cc_start: 0.7349 (p) cc_final: 0.7088 (p) REVERT: V 62 TRP cc_start: 0.8965 (t60) cc_final: 0.8700 (t60) REVERT: V 63 ILE cc_start: 0.8478 (mt) cc_final: 0.7853 (mt) REVERT: V 151 ILE cc_start: 0.7685 (mt) cc_final: 0.7421 (mt) REVERT: V 159 PHE cc_start: 0.6708 (m-80) cc_final: 0.6398 (m-80) REVERT: H 38 ARG cc_start: 0.8312 (ttm170) cc_final: 0.7793 (ttt-90) REVERT: H 52 TRP cc_start: 0.8275 (m100) cc_final: 0.7952 (m100) REVERT: H 102 LEU cc_start: 0.8879 (mm) cc_final: 0.8591 (mm) REVERT: L 95 PHE cc_start: 0.7075 (m-10) cc_final: 0.6507 (m-80) REVERT: L 97 LEU cc_start: 0.4619 (pt) cc_final: 0.4044 (pt) REVERT: L 100 HIS cc_start: 0.6398 (m170) cc_final: 0.5906 (m-70) REVERT: L 113 GLN cc_start: 0.7928 (tt0) cc_final: 0.7375 (tm-30) REVERT: L 127 LYS cc_start: 0.7346 (mttt) cc_final: 0.6722 (tttt) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.0797 time to fit residues: 26.1826 Evaluate side-chains 178 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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: 4.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 40 optimal weight: 0.3980 chunk 96 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 0.0970 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.180403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.144560 restraints weight = 14838.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.150877 restraints weight = 10173.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.155798 restraints weight = 7415.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.159737 restraints weight = 5658.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.162771 restraints weight = 4436.062| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8061 Z= 0.123 Angle : 0.625 10.238 10973 Z= 0.309 Chirality : 0.044 0.255 1209 Planarity : 0.004 0.045 1352 Dihedral : 4.716 34.329 1079 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.36 % Allowed : 1.68 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.50 (0.26), residues: 978 helix: -1.03 (0.27), residues: 326 sheet: -0.44 (0.37), residues: 183 loop : -1.09 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 44 TYR 0.017 0.001 TYR V 236 PHE 0.023 0.001 PHE A 170 TRP 0.037 0.002 TRP A 204 HIS 0.005 0.001 HIS V 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8053) covalent geometry : angle 0.62073 / 0.31 (10954) SS BOND : bond 0.00237 / 0.15 ( 5) SS BOND : angle 1.05061 / 0.69 ( 10) hydrogen bonds : bond 0.03661 / 2.35 ( 219) hydrogen bonds : angle 5.24890 / 3.65 ( 630) link_BETA1-4 : bond 0.00386 / 0.20 ( 1) link_BETA1-4 : angle 2.85129 / 1.59 ( 3) link_NAG-ASN : bond 0.00679 / 0.35 ( 2) link_NAG-ASN : angle 2.33980 / 1.24 ( 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 234 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 0.282 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: symmetry clash REVERT: A 80 GLU cc_start: 0.7338 (mp0) cc_final: 0.5988 (tt0) REVERT: A 98 ASP cc_start: 0.9460 (p0) cc_final: 0.9247 (p0) REVERT: A 104 ARG cc_start: 0.8762 (tpt170) cc_final: 0.8339 (ttm-80) REVERT: A 133 PHE cc_start: 0.7970 (m-80) cc_final: 0.7439 (m-80) REVERT: A 136 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8535 (tm-30) REVERT: A 166 CYS cc_start: 0.8662 (t) cc_final: 0.8399 (p) REVERT: A 168 ILE cc_start: 0.9517 (mm) cc_final: 0.9227 (mm) REVERT: A 172 ILE cc_start: 0.9496 (mt) cc_final: 0.8971 (tt) REVERT: A 185 TYR cc_start: 0.8107 (t80) cc_final: 0.7664 (t80) REVERT: A 229 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8763 (tm-30) REVERT: A 238 GLN cc_start: 0.8705 (mt0) cc_final: 0.8278 (mt0) REVERT: A 260 MET cc_start: 0.4730 (ttt) cc_final: 0.4284 (ttt) REVERT: A 302 LEU cc_start: 0.8263 (mt) cc_final: 0.7849 (mt) REVERT: A 317 TRP cc_start: 0.7488 (p-90) cc_final: 0.7111 (m-10) REVERT: A 407 PHE cc_start: 0.8900 (m-10) cc_final: 0.8626 (m-80) REVERT: A 430 MET cc_start: 0.7775 (ttt) cc_final: 0.7064 (ttp) REVERT: V 45 THR cc_start: 0.7369 (p) cc_final: 0.6571 (t) REVERT: V 63 ILE cc_start: 0.8430 (mt) cc_final: 0.7684 (mt) REVERT: H 21 VAL cc_start: 0.7230 (t) cc_final: 0.6249 (t) REVERT: H 38 ARG cc_start: 0.8238 (ttm170) cc_final: 0.7734 (ttt-90) REVERT: H 46 TYR cc_start: 0.8513 (p90) cc_final: 0.8258 (p90) REVERT: H 102 LEU cc_start: 0.8692 (mm) cc_final: 0.8475 (mm) REVERT: H 130 TRP cc_start: 0.8511 (m100) cc_final: 0.8191 (m-10) REVERT: L 95 PHE cc_start: 0.6987 (m-10) cc_final: 0.6310 (m-80) REVERT: L 100 HIS cc_start: 0.6337 (m170) cc_final: 0.5495 (m-70) REVERT: L 127 LYS cc_start: 0.7347 (mttt) cc_final: 0.6607 (tttt) outliers start: 3 outliers final: 2 residues processed: 232 average time/residue: 0.0771 time to fit residues: 25.0448 Evaluate side-chains 189 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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: 6.9990 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.175910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.139237 restraints weight = 14774.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.145559 restraints weight = 10036.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.150462 restraints weight = 7272.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.154297 restraints weight = 5531.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.157320 restraints weight = 4350.066| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.6183 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= 0.144 Angle : 0.635 10.072 10973 Z= 0.317 Chirality : 0.044 0.276 1209 Planarity : 0.004 0.044 1352 Dihedral : 4.773 33.718 1079 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.24 % Allowed : 0.84 % Favored : 98.92 % 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: -1.39 (0.26), residues: 978 helix: -0.87 (0.27), residues: 327 sheet: -0.54 (0.36), residues: 188 loop : -1.00 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 607 TYR 0.020 0.002 TYR V 236 PHE 0.026 0.002 PHE A 170 TRP 0.052 0.002 TRP V 62 HIS 0.005 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8053) covalent geometry : angle 0.63147 / 0.32 (10954) SS BOND : bond 0.00246 / 0.14 ( 5) SS BOND : angle 0.71914 / 0.54 ( 10) hydrogen bonds : bond 0.03558 / 2.32 ( 219) hydrogen bonds : angle 5.22368 / 3.62 ( 630) link_BETA1-4 : bond 0.00554 / 0.29 ( 1) link_BETA1-4 : angle 2.68349 / 1.51 ( 3) link_NAG-ASN : bond 0.00634 / 0.33 ( 2) link_NAG-ASN : angle 2.33307 / 1.25 ( 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 235 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7370 (mp0) cc_final: 0.6027 (tt0) REVERT: A 104 ARG cc_start: 0.8791 (tpt170) cc_final: 0.8320 (ttm-80) REVERT: A 132 LEU cc_start: 0.9066 (tp) cc_final: 0.8865 (tp) REVERT: A 133 PHE cc_start: 0.7987 (m-80) cc_final: 0.7429 (m-80) REVERT: A 136 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8422 (tm-30) REVERT: A 166 CYS cc_start: 0.8772 (t) cc_final: 0.8432 (p) REVERT: A 185 TYR cc_start: 0.8522 (t80) cc_final: 0.8027 (t80) REVERT: A 229 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8401 (tm-30) REVERT: A 230 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8150 (mm-30) REVERT: A 238 GLN cc_start: 0.8745 (mt0) cc_final: 0.8310 (mt0) REVERT: A 260 MET cc_start: 0.4734 (ttt) cc_final: 0.4305 (ttt) REVERT: A 302 LEU cc_start: 0.8243 (mt) cc_final: 0.7965 (mt) REVERT: A 317 TRP cc_start: 0.7541 (p-90) cc_final: 0.7336 (m-10) REVERT: A 343 VAL cc_start: 0.9118 (t) cc_final: 0.8702 (t) REVERT: A 347 PHE cc_start: 0.8488 (m-80) cc_final: 0.8245 (m-80) REVERT: A 408 ILE cc_start: 0.9235 (mm) cc_final: 0.8946 (mm) REVERT: A 417 MET cc_start: 0.7745 (mmp) cc_final: 0.7493 (tpp) REVERT: A 430 MET cc_start: 0.7756 (ttt) cc_final: 0.7054 (ttp) REVERT: A 444 GLU cc_start: 0.8617 (pt0) cc_final: 0.8371 (pt0) REVERT: V 45 THR cc_start: 0.7289 (p) cc_final: 0.6318 (t) REVERT: V 158 LYS cc_start: 0.7920 (ptmm) cc_final: 0.7611 (ttpp) REVERT: V 241 TYR cc_start: 0.8323 (t80) cc_final: 0.8123 (t80) REVERT: H 21 VAL cc_start: 0.7309 (t) cc_final: 0.6342 (t) REVERT: H 38 ARG cc_start: 0.8334 (ttm170) cc_final: 0.7826 (ttt-90) REVERT: H 46 TYR cc_start: 0.8498 (p90) cc_final: 0.8278 (p90) REVERT: H 130 TRP cc_start: 0.8561 (m100) cc_final: 0.8262 (m100) REVERT: L 95 PHE cc_start: 0.6966 (m-10) cc_final: 0.6272 (m-80) REVERT: L 127 LYS cc_start: 0.7309 (mttt) cc_final: 0.6992 (mtpt) outliers start: 2 outliers final: 0 residues processed: 233 average time/residue: 0.0793 time to fit residues: 25.8311 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 : 0.277 ------------------------------------------------------------------------------- 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: 0.6980 chunk 11 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 0.0040 chunk 47 optimal weight: 0.0370 chunk 91 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.4670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN V 155 GLN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.181612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.144843 restraints weight = 14337.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.151247 restraints weight = 9700.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.156194 restraints weight = 7041.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.160077 restraints weight = 5352.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.163185 restraints weight = 4213.504| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8061 Z= 0.113 Angle : 0.626 9.935 10973 Z= 0.308 Chirality : 0.044 0.232 1209 Planarity : 0.004 0.041 1352 Dihedral : 4.584 31.870 1079 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.36 % Allowed : 0.48 % 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: -1.33 (0.26), residues: 978 helix: -0.99 (0.27), residues: 321 sheet: -0.41 (0.38), residues: 181 loop : -0.87 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 38 TYR 0.025 0.001 TYR H 71 PHE 0.020 0.001 PHE A 170 TRP 0.058 0.003 TRP A 541 HIS 0.004 0.001 HIS V 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 8053) covalent geometry : angle 0.62214 / 0.31 (10954) SS BOND : bond 0.00141 / 0.07 ( 5) SS BOND : angle 0.67901 / 0.53 ( 10) hydrogen bonds : bond 0.03374 / 2.09 ( 219) hydrogen bonds : angle 4.96096 / 3.45 ( 630) link_BETA1-4 : bond 0.00425 / 0.22 ( 1) link_BETA1-4 : angle 2.83689 / 1.57 ( 3) link_NAG-ASN : bond 0.00680 / 0.35 ( 2) link_NAG-ASN : angle 2.12660 / 1.14 ( 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 234 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7237 (mp0) cc_final: 0.6016 (tt0) REVERT: A 90 LEU cc_start: 0.9510 (tp) cc_final: 0.9274 (tp) REVERT: A 104 ARG cc_start: 0.8823 (tpt170) cc_final: 0.8405 (ttm-80) REVERT: A 133 PHE cc_start: 0.8096 (m-80) cc_final: 0.7756 (m-80) REVERT: A 136 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 185 TYR cc_start: 0.8387 (t80) cc_final: 0.7952 (t80) REVERT: A 229 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8374 (tm-30) REVERT: A 230 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8088 (mm-30) REVERT: A 238 GLN cc_start: 0.8687 (mt0) cc_final: 0.8279 (mt0) REVERT: A 260 MET cc_start: 0.4659 (ttt) cc_final: 0.4298 (ttt) REVERT: A 302 LEU cc_start: 0.8214 (mt) cc_final: 0.7920 (mt) REVERT: A 317 TRP cc_start: 0.7507 (p-90) cc_final: 0.7294 (m-10) REVERT: A 343 VAL cc_start: 0.9078 (t) cc_final: 0.8684 (t) REVERT: A 417 MET cc_start: 0.7690 (mmp) cc_final: 0.7454 (tpp) REVERT: A 430 MET cc_start: 0.7772 (ttt) cc_final: 0.7063 (ttp) REVERT: A 444 GLU cc_start: 0.8490 (pt0) cc_final: 0.8270 (pt0) REVERT: A 607 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7721 (mtt-85) REVERT: V 45 THR cc_start: 0.7219 (p) cc_final: 0.6383 (t) REVERT: V 158 LYS cc_start: 0.7853 (ptmm) cc_final: 0.7586 (ttpp) REVERT: V 195 LEU cc_start: 0.8828 (tp) cc_final: 0.8602 (tp) REVERT: V 241 TYR cc_start: 0.8161 (t80) cc_final: 0.7857 (t80) REVERT: H 21 VAL cc_start: 0.7203 (t) cc_final: 0.6223 (t) REVERT: H 38 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7751 (ttt-90) REVERT: H 100 MET cc_start: 0.5734 (tmm) cc_final: 0.5465 (tmm) REVERT: H 114 PHE cc_start: 0.7713 (m-80) cc_final: 0.7365 (m-80) REVERT: H 130 TRP cc_start: 0.8419 (m100) cc_final: 0.8176 (m100) REVERT: L 85 ARG cc_start: 0.7067 (ptm160) cc_final: 0.5987 (ptp-170) REVERT: L 95 PHE cc_start: 0.6756 (m-10) cc_final: 0.6024 (m-80) REVERT: L 100 HIS cc_start: 0.6159 (m90) cc_final: 0.5544 (m90) REVERT: L 103 GLU cc_start: 0.7989 (mp0) cc_final: 0.7487 (mp0) REVERT: L 127 LYS cc_start: 0.7311 (mttt) cc_final: 0.6926 (mtpp) outliers start: 3 outliers final: 1 residues processed: 233 average time/residue: 0.0775 time to fit residues: 25.3282 Evaluate side-chains 199 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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: 1.9990 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 59 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 ASN A 235 HIS V 155 GLN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.186044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.147889 restraints weight = 14430.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.154323 restraints weight = 9929.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.159334 restraints weight = 7270.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.163250 restraints weight = 5578.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.166355 restraints weight = 4429.251| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8061 Z= 0.107 Angle : 0.616 9.899 10973 Z= 0.300 Chirality : 0.043 0.227 1209 Planarity : 0.004 0.041 1352 Dihedral : 4.431 28.506 1079 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.12 % Allowed : 0.36 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.27 (0.26), residues: 978 helix: -1.02 (0.27), residues: 329 sheet: -0.32 (0.38), residues: 181 loop : -0.78 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 607 TYR 0.019 0.001 TYR V 204 PHE 0.021 0.001 PHE A 170 TRP 0.057 0.002 TRP A 204 HIS 0.005 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8053) covalent geometry : angle 0.61263 / 0.30 (10954) SS BOND : bond 0.00156 / 0.08 ( 5) SS BOND : angle 0.57713 / 0.49 ( 10) hydrogen bonds : bond 0.03187 / 2.03 ( 219) hydrogen bonds : angle 4.83355 / 3.36 ( 630) link_BETA1-4 : bond 0.00419 / 0.22 ( 1) link_BETA1-4 : angle 2.73068 / 1.52 ( 3) link_NAG-ASN : bond 0.00700 / 0.36 ( 2) link_NAG-ASN : angle 2.09899 / 1.13 ( 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 225 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.346 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: 0.7259 (mp0) cc_final: 0.6045 (tt0) REVERT: A 90 LEU cc_start: 0.9529 (tp) cc_final: 0.9279 (tp) REVERT: A 104 ARG cc_start: 0.8791 (tpt170) cc_final: 0.8379 (ttm-80) REVERT: A 132 LEU cc_start: 0.9091 (tp) cc_final: 0.8812 (tp) REVERT: A 133 PHE cc_start: 0.8106 (m-80) cc_final: 0.7610 (m-80) REVERT: A 136 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 166 CYS cc_start: 0.8777 (p) cc_final: 0.8442 (p) REVERT: A 167 ILE cc_start: 0.8565 (pt) cc_final: 0.8279 (pt) REVERT: A 185 TYR cc_start: 0.8482 (t80) cc_final: 0.8020 (t80) REVERT: A 229 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 230 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8211 (mm-30) REVERT: A 238 GLN cc_start: 0.8555 (mt0) cc_final: 0.8148 (mt0) REVERT: A 260 MET cc_start: 0.4440 (ttt) cc_final: 0.4077 (ttt) REVERT: A 302 LEU cc_start: 0.8183 (mt) cc_final: 0.7870 (mt) REVERT: A 343 VAL cc_start: 0.9110 (t) cc_final: 0.8678 (t) REVERT: A 417 MET cc_start: 0.7693 (mmp) cc_final: 0.7426 (tpp) REVERT: A 430 MET cc_start: 0.7746 (ttt) cc_final: 0.7010 (ttp) REVERT: A 444 GLU cc_start: 0.8479 (pt0) cc_final: 0.8238 (pt0) REVERT: A 600 THR cc_start: 0.5062 (m) cc_final: 0.4851 (m) REVERT: A 607 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7391 (mpp80) REVERT: V 158 LYS cc_start: 0.7852 (ptmm) cc_final: 0.7539 (ttpp) REVERT: V 195 LEU cc_start: 0.8866 (tp) cc_final: 0.8651 (tp) REVERT: H 38 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7673 (ttt-90) REVERT: H 114 PHE cc_start: 0.7814 (m-80) cc_final: 0.7463 (m-80) REVERT: H 130 TRP cc_start: 0.8405 (m100) cc_final: 0.8194 (m100) REVERT: L 85 ARG cc_start: 0.7197 (ptm160) cc_final: 0.6082 (ptp-170) REVERT: L 95 PHE cc_start: 0.6740 (m-10) cc_final: 0.6068 (m-80) REVERT: L 100 HIS cc_start: 0.6228 (m90) cc_final: 0.5665 (m90) REVERT: L 103 GLU cc_start: 0.7834 (mp0) cc_final: 0.7393 (mp0) REVERT: L 127 LYS cc_start: 0.7280 (mttt) cc_final: 0.6934 (mtpt) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.0803 time to fit residues: 25.3449 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 : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 70 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 80 optimal weight: 0.0070 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 90 optimal weight: 0.0370 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.9478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN V 155 GLN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.183860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.146229 restraints weight = 14247.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.152608 restraints weight = 9753.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.157545 restraints weight = 7113.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.161475 restraints weight = 5435.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.164505 restraints weight = 4292.927| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8061 Z= 0.113 Angle : 0.607 9.868 10973 Z= 0.298 Chirality : 0.042 0.238 1209 Planarity : 0.004 0.041 1352 Dihedral : 4.458 27.957 1079 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.16 (0.27), residues: 978 helix: -0.98 (0.27), residues: 329 sheet: -0.27 (0.39), residues: 175 loop : -0.67 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 38 TYR 0.020 0.001 TYR V 204 PHE 0.022 0.001 PHE A 105 TRP 0.057 0.002 TRP A 204 HIS 0.004 0.001 HIS V 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 8053) covalent geometry : angle 0.60338 / 0.30 (10954) SS BOND : bond 0.00180 / 0.09 ( 5) SS BOND : angle 0.49668 / 0.40 ( 10) hydrogen bonds : bond 0.03249 / 2.04 ( 219) hydrogen bonds : angle 4.77665 / 3.29 ( 630) link_BETA1-4 : bond 0.00519 / 0.27 ( 1) link_BETA1-4 : angle 2.70467 / 1.50 ( 3) link_NAG-ASN : bond 0.00654 / 0.34 ( 2) link_NAG-ASN : angle 2.15406 / 1.16 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1510.89 seconds wall clock time: 26 minutes 48.15 seconds (1608.15 seconds total)