Starting phenix.real_space_refine on Sat Sep 12 19:16:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bvg_30219/09_2026/7bvg_30219.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bvg_30219/09_2026/7bvg_30219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7bvg_30219/09_2026/7bvg_30219.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bvg_30219/09_2026/7bvg_30219.cif" model { file = "/net/cci-nas-00/data/ceres_data/7bvg_30219/09_2026/7bvg_30219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bvg_30219/09_2026/7bvg_30219.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bvg_30219/09_2026/7bvg_30219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bvg_30219/09_2026/7bvg_30219.map" } resolution = 3.1 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= 0.060 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 7 5.49 5 S 60 5.16 5 C 11116 2.51 5 N 2919 2.21 5 O 3127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.18s 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: 17231 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8147 Classifications: {'peptide': 1078} Link IDs: {'PCIS': 1, 'PTRANS': 78, 'TRANS': 998} Chain: "B" Number of atoms: 8105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8105 Classifications: {'peptide': 1063} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 985} Chain: "P" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 706 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'BXY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {' CA': 1, 'CDL': 1, 'F8L': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'F8L:plan-1': 1, 'F8L:plan-2': 1, 'F8L:plan-3': 1, 'F8L:plan-4': 1, 'F8L:plan-10': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 128 Unusual residues: {' CA': 1, 'CDL': 1, 'PNS': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.07, per 1000 atoms: 0.24 Number of scatterers: 17231 At special positions: 0 Unit cell: (123, 133.66, 122.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 60 16.00 P 7 15.00 O 3127 8.00 N 2919 7.00 C 11116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Links applied ALPHA1-5 " BXY C 1 " - " BXY C 2 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 807.0 milliseconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4066 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 21 sheets defined 40.6% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 removed outlier: 3.739A pdb=" N VAL A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 25 Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.777A pdb=" N ASN A 98 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 195 through 220 removed outlier: 3.731A pdb=" N VAL A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 235 through 251 removed outlier: 3.600A pdb=" N TRP A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 271 Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.697A pdb=" N GLY A 286 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 4.082A pdb=" N HIS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.665A pdb=" N ARG A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 removed outlier: 3.660A pdb=" N ALA A 319 " --> pdb=" O PRO A 315 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A 320 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.842A pdb=" N ALA A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 341' Processing helix chain 'A' and resid 342 through 358 removed outlier: 4.122A pdb=" N LEU A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 348 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 386 removed outlier: 4.017A pdb=" N PHE A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 405 removed outlier: 4.040A pdb=" N ILE A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 405 " --> pdb=" O MET A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 removed outlier: 3.942A pdb=" N LEU A 411 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 412 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 420 through 429 removed outlier: 3.785A pdb=" N ILE A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 460 through 474 removed outlier: 3.553A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 482 removed outlier: 3.624A pdb=" N GLN A 482 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 483 through 491 removed outlier: 4.246A pdb=" N TYR A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 523 removed outlier: 3.757A pdb=" N ALA A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 506 " --> pdb=" O ARG A 502 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 548 removed outlier: 3.730A pdb=" N LEU A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 561 removed outlier: 3.772A pdb=" N GLN A 558 " --> pdb=" O TRP A 555 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 559 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 560 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 561 " --> pdb=" O GLN A 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 555 through 561' Processing helix chain 'A' and resid 562 through 583 removed outlier: 3.921A pdb=" N GLY A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 568 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 574 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 579 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.086A pdb=" N LEU A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 652 removed outlier: 3.638A pdb=" N ILE A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 652 " --> pdb=" O TRP A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 removed outlier: 3.663A pdb=" N ALA A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 696 removed outlier: 4.533A pdb=" N MET A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 removed outlier: 3.962A pdb=" N ASN A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 removed outlier: 3.760A pdb=" N THR A 823 " --> pdb=" O PRO A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1008 removed outlier: 3.558A pdb=" N VAL A1002 " --> pdb=" O LYS A 998 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASN A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLN A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.799A pdb=" N TRP B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.703A pdb=" N ASN B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 230 through 245 removed outlier: 4.474A pdb=" N ALA B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.829A pdb=" N GLY B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.650A pdb=" N ILE B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.712A pdb=" N GLY B 310 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 327 removed outlier: 3.517A pdb=" N LEU B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 removed outlier: 3.519A pdb=" N CYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.683A pdb=" N GLY B 360 " --> pdb=" O PRO B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 382 removed outlier: 3.665A pdb=" N MET B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 412 removed outlier: 3.651A pdb=" N ILE B 394 " --> pdb=" O PRO B 390 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 429 removed outlier: 3.850A pdb=" N LEU B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA B 420 " --> pdb=" O PRO B 416 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 444 removed outlier: 3.626A pdb=" N LEU B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 460 removed outlier: 3.605A pdb=" N ILE B 451 " --> pdb=" O PRO B 447 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ARG B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 473 Proline residue: B 467 - end of helix removed outlier: 3.561A pdb=" N GLY B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'B' and resid 484 through 499 Processing helix chain 'B' and resid 503 through 507 removed outlier: 3.505A pdb=" N GLU B 507 " --> pdb=" O TRP B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.944A pdb=" N LEU B 514 " --> pdb=" O ARG B 510 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 546 removed outlier: 4.059A pdb=" N THR B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Proline residue: B 538 - end of helix removed outlier: 3.533A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 570 removed outlier: 3.538A pdb=" N MET B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 584 through 600 removed outlier: 4.511A pdb=" N VAL B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET B 592 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 626 Processing helix chain 'B' and resid 654 through 675 Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 689 through 713 removed outlier: 4.145A pdb=" N VAL B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET B 698 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY B 709 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL B 710 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 727 removed outlier: 3.673A pdb=" N ILE B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE B 727 " --> pdb=" O ASN B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 962 Processing helix chain 'B' and resid 1001 through 1006 Processing helix chain 'B' and resid 1014 through 1018 removed outlier: 3.878A pdb=" N GLY B1018 " --> pdb=" O GLY B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1023 removed outlier: 3.780A pdb=" N GLY B1022 " --> pdb=" O GLY B1019 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B1023 " --> pdb=" O LEU B1020 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1019 through 1023' Processing helix chain 'P' and resid 4 through 20 removed outlier: 3.748A pdb=" N ALA P 10 " --> pdb=" O GLU P 6 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU P 14 " --> pdb=" O ALA P 10 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE P 15 " --> pdb=" O GLY P 11 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU P 18 " --> pdb=" O GLU P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 55 removed outlier: 3.856A pdb=" N GLU P 46 " --> pdb=" O LEU P 42 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU P 52 " --> pdb=" O ALA P 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP P 53 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR P 55 " --> pdb=" O THR P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 65 removed outlier: 3.935A pdb=" N ALA P 65 " --> pdb=" O ASP P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 83 removed outlier: 3.519A pdb=" N GLU P 83 " --> pdb=" O LYS P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 removed outlier: 3.740A pdb=" N LEU P 91 " --> pdb=" O ALA P 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 39 removed outlier: 3.696A pdb=" N ALA A 64 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 951 through 952 Processing sheet with id=AA4, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.694A pdb=" N MET A 826 " --> pdb=" O PHE A 942 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 839 Processing sheet with id=AA6, first strand: chain 'A' and resid 837 through 839 removed outlier: 3.500A pdb=" N VAL A 928 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 879 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 877 " --> pdb=" O ASP A 930 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP A 882 " --> pdb=" O SER A 895 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER A 895 " --> pdb=" O TRP A 882 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL A 884 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA A 893 " --> pdb=" O VAL A 884 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 855 through 858 Processing sheet with id=AA8, first strand: chain 'A' and resid 977 through 978 removed outlier: 8.434A pdb=" N ILE A 993 " --> pdb=" O PRO A 962 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 964 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A1043 " --> pdb=" O ILE A1028 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AB2, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AB3, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AB4, first strand: chain 'B' and resid 82 through 84 Processing sheet with id=AB5, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.149A pdb=" N PHE B 99 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B 124 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 125 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA B 133 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 127 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.802A pdb=" N THR B 178 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AB8, first strand: chain 'B' and resid 826 through 828 removed outlier: 3.957A pdb=" N ILE B 945 " --> pdb=" O THR B 828 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 865 " --> pdb=" O ALA B 946 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 838 through 840 Processing sheet with id=AC1, first strand: chain 'B' and resid 838 through 840 removed outlier: 3.794A pdb=" N ALA B 929 " --> pdb=" O ALA B 888 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 889 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 968 through 970 Processing sheet with id=AC3, first strand: chain 'B' and resid 986 through 987 572 hydrogen bonds defined for protein. 1614 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: 3.22 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2755 1.29 - 1.42: 4467 1.42 - 1.55: 10316 1.55 - 1.69: 19 1.69 - 1.82: 102 Bond restraints: 17659 Sorted by residual: bond pdb=" C2 BXY C 2 " pdb=" C3 BXY C 2 " ideal model delta sigma weight residual 1.518 1.220 0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C1 BXY C 1 " pdb=" C2 BXY C 1 " ideal model delta sigma weight residual 1.525 1.254 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C1 BXY C 1 " pdb=" O4 BXY C 1 " ideal model delta sigma weight residual 1.412 1.653 -0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C55 F8L A1101 " pdb=" C57 F8L A1101 " ideal model delta sigma weight residual 1.545 1.315 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" CB7 CDL A1102 " pdb=" OB8 CDL A1102 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 ... (remaining 17654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 23838 3.48 - 6.96: 233 6.96 - 10.44: 58 10.44 - 13.92: 11 13.92 - 17.41: 6 Bond angle restraints: 24146 Sorted by residual: angle pdb=" N TYR B 305 " pdb=" CA TYR B 305 " pdb=" C TYR B 305 " ideal model delta sigma weight residual 111.71 123.61 -11.90 1.15e+00 7.56e-01 1.07e+02 angle pdb=" C11 CDL B1203 " pdb=" CA5 CDL B1203 " pdb=" OA6 CDL B1203 " ideal model delta sigma weight residual 111.33 123.60 -12.27 1.32e+00 5.72e-01 8.62e+01 angle pdb=" C71 CDL B1203 " pdb=" CB7 CDL B1203 " pdb=" OB8 CDL B1203 " ideal model delta sigma weight residual 111.64 125.88 -14.24 1.65e+00 3.69e-01 7.49e+01 angle pdb=" C51 CDL A1102 " pdb=" CB5 CDL A1102 " pdb=" OB6 CDL A1102 " ideal model delta sigma weight residual 111.33 122.40 -11.07 1.32e+00 5.72e-01 7.02e+01 angle pdb=" N TYR A 281 " pdb=" CA TYR A 281 " pdb=" C TYR A 281 " ideal model delta sigma weight residual 112.87 122.68 -9.81 1.20e+00 6.94e-01 6.69e+01 ... (remaining 24141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.53: 9823 23.53 - 47.06: 504 47.06 - 70.58: 69 70.58 - 94.11: 19 94.11 - 117.64: 4 Dihedral angle restraints: 10419 sinusoidal: 4061 harmonic: 6358 Sorted by residual: dihedral pdb=" CA TRP A 40 " pdb=" C TRP A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta harmonic sigma weight residual -180.00 -62.36 -117.64 0 5.00e+00 4.00e-02 5.54e+02 dihedral pdb=" CA TRP B 58 " pdb=" C TRP B 58 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta harmonic sigma weight residual 180.00 82.70 97.30 0 5.00e+00 4.00e-02 3.79e+02 dihedral pdb=" N THR B 716 " pdb=" C THR B 716 " pdb=" CA THR B 716 " pdb=" CB THR B 716 " ideal model delta harmonic sigma weight residual 123.40 142.08 -18.68 0 2.50e+00 1.60e-01 5.58e+01 ... (remaining 10416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2747 0.146 - 0.291: 17 0.291 - 0.437: 3 0.437 - 0.583: 1 0.583 - 0.728: 1 Chirality restraints: 2769 Sorted by residual: chirality pdb=" CA THR B 716 " pdb=" N THR B 716 " pdb=" C THR B 716 " pdb=" CB THR B 716 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 BXY C 2 " pdb=" O5 BXY C 1 " pdb=" C2 BXY C 2 " pdb=" O4 BXY C 2 " both_signs ideal model delta sigma weight residual False 2.60 2.54 0.06 2.00e-02 2.50e+03 7.88e+00 chirality pdb=" CA PRO A 41 " pdb=" N PRO A 41 " pdb=" C PRO A 41 " pdb=" CB PRO A 41 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.12e+00 ... (remaining 2766 not shown) Planarity restraints: 3086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1079 " 0.065 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO A1080 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A1080 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1080 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 58 " -0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C TRP B 58 " 0.068 2.00e-02 2.50e+03 pdb=" O TRP B 58 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO B 59 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 910 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.92e+00 pdb=" N PRO B 911 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 911 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 911 " 0.043 5.00e-02 4.00e+02 ... (remaining 3083 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 68 2.43 - 3.05: 10780 3.05 - 3.67: 24826 3.67 - 4.28: 37896 4.28 - 4.90: 65232 Nonbonded interactions: 138802 Sorted by model distance: nonbonded pdb=" OG SER P 41 " pdb=" O25 PNS B1202 " model vdw 1.815 3.040 nonbonded pdb=" OG SER P 41 " pdb=" O23 PNS B1202 " model vdw 1.937 3.040 nonbonded pdb=" CB SER P 41 " pdb=" O25 PNS B1202 " model vdw 1.961 3.440 nonbonded pdb=" O PRO A 699 " pdb=" N TYR A 701 " model vdw 2.143 3.120 nonbonded pdb=" N ASN B 57 " pdb=" OD1 ASN B 57 " model vdw 2.166 3.120 ... (remaining 138797 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 individual isotropic 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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.440 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 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 : 0.008 0.303 17661 Z= 0.486 Angle : 0.955 17.406 24149 Z= 0.529 Chirality : 0.051 0.728 2769 Planarity : 0.006 0.099 3086 Dihedral : 14.454 117.638 6353 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.57 % Favored : 91.16 % Rotamer: Outliers : 0.17 % Allowed : 4.15 % Favored : 95.67 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -4.51 (0.15), residues: 2228 helix: -2.53 (0.15), residues: 839 sheet: -2.69 (0.32), residues: 218 loop : -3.50 (0.15), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 914 TYR 0.039 0.002 TYR B 714 PHE 0.012 0.001 PHE A 942 TRP 0.012 0.001 TRP A 324 HIS 0.002 0.001 HIS B 857 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.42 (17659) covalent geometry : angle 0.95287 / 0.53 (24146) hydrogen bonds : bond 0.14482 / 9.88 ( 564) hydrogen bonds : angle 6.30456 / 4.30 ( 1614) glycosidic custom : bond 0.16851 / 8.87 ( 1) glycosidic custom : angle 5.54657 / 2.91 ( 3) Misc. bond : bond 0.30323 / 15.96 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 248 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 PRO cc_start: 0.8529 (OUTLIER) cc_final: 0.8312 (Cg_exo) REVERT: B 21 LYS cc_start: 0.7286 (tptt) cc_final: 0.7074 (ttpp) REVERT: B 273 MET cc_start: 0.7330 (tpt) cc_final: 0.6968 (tpp) REVERT: P 63 ASP cc_start: 0.8051 (t70) cc_final: 0.7766 (t0) outliers start: 3 outliers final: 2 residues processed: 251 average time/residue: 0.1659 time to fit residues: 59.6078 Evaluate side-chains 180 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 177 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PRO Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain B residue 57 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS A 177 GLN A 361 ASN A 482 GLN A 650 HIS A 667 ASN A 741 GLN B 291 GLN B 393 GLN B 431 GLN B 502 GLN B 653 GLN B 673 HIS B 719 ASN ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.096218 restraints weight = 25581.249| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.17 r_work: 0.3065 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 17661 Z= 0.328 Angle : 0.763 9.959 24149 Z= 0.384 Chirality : 0.050 0.169 2769 Planarity : 0.007 0.115 3086 Dihedral : 10.626 96.164 2630 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.13 % Favored : 88.64 % Rotamer: Outliers : 1.42 % Allowed : 11.90 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -3.90 (0.16), residues: 2228 helix: -2.03 (0.16), residues: 859 sheet: -2.54 (0.32), residues: 235 loop : -3.10 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 338 TYR 0.028 0.002 TYR A 281 PHE 0.021 0.002 PHE B 99 TRP 0.014 0.002 TRP A 137 HIS 0.008 0.002 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00802 / 0.33 (17659) covalent geometry : angle 0.76304 / 0.38 (24146) hydrogen bonds : bond 0.04402 / 3.01 ( 564) hydrogen bonds : angle 5.03395 / 3.50 ( 1614) glycosidic custom : bond 0.00860 / 0.45 ( 1) glycosidic custom : angle 1.18859 / 0.61 ( 3) Misc. bond : bond 0.01001 / 0.53 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 494 ASP cc_start: 0.8444 (t0) cc_final: 0.8183 (t0) REVERT: A 957 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8932 (pp) REVERT: B 21 LYS cc_start: 0.7577 (tptt) cc_final: 0.6973 (ttpt) REVERT: B 367 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7457 (ptm-80) REVERT: B 681 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7691 (ttp-110) REVERT: B 793 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: P 63 ASP cc_start: 0.8393 (t70) cc_final: 0.7944 (t0) outliers start: 25 outliers final: 18 residues processed: 193 average time/residue: 0.1502 time to fit residues: 42.6709 Evaluate side-chains 178 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 775 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 1016 ILE Chi-restraints excluded: chain P residue 4 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 67 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 153 optimal weight: 0.2980 chunk 146 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 215 optimal weight: 0.0000 chunk 43 optimal weight: 0.4980 chunk 206 optimal weight: 0.5980 chunk 98 optimal weight: 0.1980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 623 GLN A 741 GLN B 580 HIS B 767 GLN B1013 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102924 restraints weight = 25271.510| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.12 r_work: 0.3171 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 17661 Z= 0.106 Angle : 0.591 9.103 24149 Z= 0.296 Chirality : 0.043 0.179 2769 Planarity : 0.006 0.130 3086 Dihedral : 9.567 95.559 2622 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.76 % Favored : 92.15 % Rotamer: Outliers : 1.54 % Allowed : 13.38 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -3.20 (0.17), residues: 2228 helix: -1.38 (0.17), residues: 867 sheet: -2.11 (0.33), residues: 225 loop : -2.77 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1081 TYR 0.019 0.001 TYR A 891 PHE 0.014 0.001 PHE A 979 TRP 0.014 0.001 TRP B 843 HIS 0.003 0.001 HIS B 857 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (17659) covalent geometry : angle 0.59085 / 0.30 (24146) hydrogen bonds : bond 0.02910 / 1.99 ( 564) hydrogen bonds : angle 4.47705 / 3.11 ( 1614) glycosidic custom : bond 0.00313 / 0.16 ( 1) glycosidic custom : angle 1.48146 / 0.79 ( 3) Misc. bond : bond 0.00465 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.604 Fit side-chains REVERT: A 494 ASP cc_start: 0.8312 (t0) cc_final: 0.8038 (t0) REVERT: A 579 ARG cc_start: 0.7351 (ttp80) cc_final: 0.7150 (ttp80) REVERT: A 947 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8772 (p) REVERT: B 367 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7339 (ptm-80) REVERT: B 681 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7635 (ttp-110) REVERT: B 801 LYS cc_start: 0.8091 (tptt) cc_final: 0.7644 (ttmt) REVERT: B 854 ARG cc_start: 0.6203 (ttm-80) cc_final: 0.5965 (tpt90) REVERT: P 63 ASP cc_start: 0.8389 (t70) cc_final: 0.7975 (t0) outliers start: 27 outliers final: 13 residues processed: 206 average time/residue: 0.1500 time to fit residues: 45.6412 Evaluate side-chains 178 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1047 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 34 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 chunk 54 optimal weight: 0.0670 chunk 44 optimal weight: 7.9990 chunk 204 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 144 optimal weight: 0.0770 chunk 145 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 741 GLN B 719 ASN B 881 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104686 restraints weight = 25020.210| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.14 r_work: 0.3204 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 17661 Z= 0.099 Angle : 0.572 9.653 24149 Z= 0.283 Chirality : 0.042 0.211 2769 Planarity : 0.006 0.140 3086 Dihedral : 8.738 94.691 2622 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.72 % Favored : 92.19 % Rotamer: Outliers : 1.99 % Allowed : 14.29 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -2.72 (0.17), residues: 2228 helix: -0.89 (0.18), residues: 853 sheet: -1.88 (0.33), residues: 228 loop : -2.57 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 122 TYR 0.015 0.001 TYR A 746 PHE 0.012 0.001 PHE A 979 TRP 0.013 0.001 TRP B 843 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (17659) covalent geometry : angle 0.57133 / 0.28 (24146) hydrogen bonds : bond 0.02565 / 1.75 ( 564) hydrogen bonds : angle 4.18333 / 2.92 ( 1614) glycosidic custom : bond 0.00589 / 0.31 ( 1) glycosidic custom : angle 1.58790 / 0.87 ( 3) Misc. bond : bond 0.00336 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.507 Fit side-chains REVERT: A 494 ASP cc_start: 0.8319 (t0) cc_final: 0.8038 (t0) REVERT: B 21 LYS cc_start: 0.7381 (tptt) cc_final: 0.6904 (ttpt) REVERT: B 367 ARG cc_start: 0.7748 (tpp80) cc_final: 0.7272 (ptm-80) REVERT: B 681 ARG cc_start: 0.7867 (ttm110) cc_final: 0.7626 (ttp-110) REVERT: B 821 LYS cc_start: 0.8608 (mptt) cc_final: 0.8407 (mmtm) REVERT: P 63 ASP cc_start: 0.8435 (t70) cc_final: 0.7992 (t0) outliers start: 35 outliers final: 17 residues processed: 214 average time/residue: 0.1318 time to fit residues: 42.5970 Evaluate side-chains 189 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 719 ASN Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain P residue 4 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 9 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.098182 restraints weight = 25315.772| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.15 r_work: 0.3103 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17661 Z= 0.254 Angle : 0.680 9.756 24149 Z= 0.339 Chirality : 0.047 0.176 2769 Planarity : 0.006 0.145 3086 Dihedral : 8.906 95.254 2622 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.23 % Favored : 89.68 % Rotamer: Outliers : 2.33 % Allowed : 15.42 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -2.89 (0.17), residues: 2228 helix: -1.11 (0.18), residues: 862 sheet: -2.00 (0.32), residues: 245 loop : -2.59 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 668 TYR 0.023 0.002 TYR A 281 PHE 0.018 0.002 PHE B 99 TRP 0.014 0.001 TRP B 843 HIS 0.004 0.001 HIS B 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.25 (17659) covalent geometry : angle 0.67994 / 0.34 (24146) hydrogen bonds : bond 0.03637 / 2.49 ( 564) hydrogen bonds : angle 4.49807 / 3.14 ( 1614) glycosidic custom : bond 0.00586 / 0.31 ( 1) glycosidic custom : angle 1.38006 / 0.75 ( 3) Misc. bond : bond 0.00656 / 0.35 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.552 Fit side-chains REVERT: A 494 ASP cc_start: 0.8438 (t0) cc_final: 0.8153 (t0) REVERT: A 579 ARG cc_start: 0.7300 (ttp80) cc_final: 0.6978 (ttp80) REVERT: A 767 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7856 (tm-30) REVERT: B 21 LYS cc_start: 0.7517 (tptt) cc_final: 0.6993 (ttpt) REVERT: B 367 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7359 (ptm-80) REVERT: B 543 MET cc_start: 0.9045 (mmm) cc_final: 0.8562 (mtp) REVERT: B 681 ARG cc_start: 0.7939 (ttm110) cc_final: 0.7642 (ttp-110) REVERT: P 63 ASP cc_start: 0.8425 (t70) cc_final: 0.7970 (t0) outliers start: 41 outliers final: 24 residues processed: 209 average time/residue: 0.1428 time to fit residues: 44.1840 Evaluate side-chains 194 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain B residue 1068 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 667 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101416 restraints weight = 25032.953| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.04 r_work: 0.3155 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17661 Z= 0.133 Angle : 0.600 10.130 24149 Z= 0.298 Chirality : 0.044 0.186 2769 Planarity : 0.006 0.148 3086 Dihedral : 8.427 95.665 2622 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.35 % Favored : 91.56 % Rotamer: Outliers : 1.76 % Allowed : 16.28 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -2.65 (0.17), residues: 2228 helix: -0.87 (0.18), residues: 853 sheet: -1.85 (0.33), residues: 226 loop : -2.49 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 668 TYR 0.016 0.001 TYR A 746 PHE 0.013 0.001 PHE A 979 TRP 0.012 0.001 TRP B 843 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (17659) covalent geometry : angle 0.59977 / 0.30 (24146) hydrogen bonds : bond 0.02937 / 2.02 ( 564) hydrogen bonds : angle 4.33123 / 3.02 ( 1614) glycosidic custom : bond 0.00714 / 0.38 ( 1) glycosidic custom : angle 1.51824 / 0.83 ( 3) Misc. bond : bond 0.00524 / 0.28 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7059 (tpp80) cc_final: 0.6825 (tpp80) REVERT: A 494 ASP cc_start: 0.8316 (t0) cc_final: 0.8042 (t0) REVERT: A 579 ARG cc_start: 0.7327 (ttp80) cc_final: 0.7045 (ttp80) REVERT: A 767 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 21 LYS cc_start: 0.7414 (tptt) cc_final: 0.6976 (ttpt) REVERT: B 367 ARG cc_start: 0.7815 (tpp80) cc_final: 0.7401 (ptm-80) REVERT: B 543 MET cc_start: 0.8980 (mmm) cc_final: 0.8533 (mtp) REVERT: B 681 ARG cc_start: 0.7948 (ttm110) cc_final: 0.7693 (ttp-110) REVERT: B 821 LYS cc_start: 0.8646 (mptt) cc_final: 0.8419 (mmtp) REVERT: P 63 ASP cc_start: 0.8384 (t70) cc_final: 0.7953 (t0) outliers start: 31 outliers final: 24 residues processed: 202 average time/residue: 0.1477 time to fit residues: 44.5685 Evaluate side-chains 195 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1016 ILE Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain P residue 4 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 16 optimal weight: 1.9990 chunk 132 optimal weight: 0.0270 chunk 48 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 137 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 64.8162 > 50:) chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102479 restraints weight = 24901.697| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.14 r_work: 0.3170 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17661 Z= 0.113 Angle : 0.582 10.110 24149 Z= 0.288 Chirality : 0.043 0.162 2769 Planarity : 0.006 0.149 3086 Dihedral : 7.985 96.022 2622 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.48 % Favored : 91.43 % Rotamer: Outliers : 1.88 % Allowed : 16.79 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -2.42 (0.17), residues: 2228 helix: -0.64 (0.18), residues: 851 sheet: -1.68 (0.33), residues: 234 loop : -2.39 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 668 TYR 0.017 0.001 TYR A 611 PHE 0.012 0.001 PHE A 979 TRP 0.010 0.001 TRP B 843 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 (17659) covalent geometry : angle 0.58183 / 0.29 (24146) hydrogen bonds : bond 0.02690 / 1.85 ( 564) hydrogen bonds : angle 4.18608 / 2.93 ( 1614) glycosidic custom : bond 0.00586 / 0.31 ( 1) glycosidic custom : angle 1.49482 / 0.82 ( 3) Misc. bond : bond 0.00437 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.385 Fit side-chains REVERT: A 97 ARG cc_start: 0.7082 (tpp80) cc_final: 0.6803 (tpp80) REVERT: A 494 ASP cc_start: 0.8332 (t0) cc_final: 0.8049 (t0) REVERT: A 579 ARG cc_start: 0.7336 (ttp80) cc_final: 0.7072 (ttp80) REVERT: B 89 ARG cc_start: 0.8575 (ttp-110) cc_final: 0.8296 (ptp90) REVERT: B 367 ARG cc_start: 0.7781 (tpp80) cc_final: 0.7301 (ptm-80) REVERT: B 543 MET cc_start: 0.9000 (mmm) cc_final: 0.8546 (mtp) REVERT: B 821 LYS cc_start: 0.8575 (mptt) cc_final: 0.8347 (mmtp) REVERT: P 63 ASP cc_start: 0.8404 (t70) cc_final: 0.7956 (t0) outliers start: 33 outliers final: 24 residues processed: 200 average time/residue: 0.1374 time to fit residues: 41.5061 Evaluate side-chains 194 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain P residue 4 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 26 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 25 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104399 restraints weight = 25063.703| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.12 r_work: 0.3219 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 17661 Z= 0.103 Angle : 0.576 11.458 24149 Z= 0.285 Chirality : 0.042 0.200 2769 Planarity : 0.005 0.149 3086 Dihedral : 7.691 96.728 2622 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.18 % Favored : 92.73 % Rotamer: Outliers : 1.65 % Allowed : 17.36 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -2.15 (0.18), residues: 2228 helix: -0.40 (0.19), residues: 844 sheet: -1.56 (0.33), residues: 235 loop : -2.23 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 668 TYR 0.016 0.001 TYR A 611 PHE 0.012 0.001 PHE A 979 TRP 0.015 0.001 TRP B 843 HIS 0.002 0.001 HIS B 857 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 (17659) covalent geometry : angle 0.57577 / 0.29 (24146) hydrogen bonds : bond 0.02512 / 1.73 ( 564) hydrogen bonds : angle 4.07175 / 2.85 ( 1614) glycosidic custom : bond 0.00584 / 0.31 ( 1) glycosidic custom : angle 1.54998 / 0.85 ( 3) Misc. bond : bond 0.00378 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.639 Fit side-chains REVERT: A 494 ASP cc_start: 0.8296 (t0) cc_final: 0.8007 (t0) REVERT: A 579 ARG cc_start: 0.7287 (ttp80) cc_final: 0.7031 (ttp80) REVERT: B 89 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8321 (ptp90) REVERT: B 367 ARG cc_start: 0.7755 (tpp80) cc_final: 0.7321 (ptm-80) REVERT: B 543 MET cc_start: 0.8999 (mmm) cc_final: 0.8555 (mtp) REVERT: B 821 LYS cc_start: 0.8489 (mptt) cc_final: 0.8275 (mmtp) REVERT: B 1008 SER cc_start: 0.8909 (m) cc_final: 0.8555 (p) REVERT: P 63 ASP cc_start: 0.8424 (t70) cc_final: 0.7975 (t0) outliers start: 29 outliers final: 23 residues processed: 198 average time/residue: 0.1516 time to fit residues: 44.6584 Evaluate side-chains 197 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain P residue 4 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 53 optimal weight: 0.0470 chunk 126 optimal weight: 0.6980 chunk 7 optimal weight: 0.0070 chunk 37 optimal weight: 0.5980 chunk 66 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 0.0040 overall best weight: 0.2708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106815 restraints weight = 24760.556| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.12 r_work: 0.3231 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 17661 Z= 0.095 Angle : 0.565 10.760 24149 Z= 0.278 Chirality : 0.042 0.203 2769 Planarity : 0.005 0.149 3086 Dihedral : 7.394 96.688 2622 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.14 % Favored : 92.77 % Rotamer: Outliers : 1.42 % Allowed : 17.59 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -1.89 (0.18), residues: 2228 helix: -0.15 (0.19), residues: 839 sheet: -1.37 (0.34), residues: 233 loop : -2.12 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 668 TYR 0.014 0.001 TYR A 746 PHE 0.011 0.001 PHE A 979 TRP 0.014 0.001 TRP B 843 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (17659) covalent geometry : angle 0.56475 / 0.28 (24146) hydrogen bonds : bond 0.02342 / 1.62 ( 564) hydrogen bonds : angle 3.94024 / 2.76 ( 1614) glycosidic custom : bond 0.00629 / 0.33 ( 1) glycosidic custom : angle 1.62316 / 0.89 ( 3) Misc. bond : bond 0.00349 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 494 ASP cc_start: 0.8296 (t0) cc_final: 0.8045 (t0) REVERT: B 89 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8330 (ptp90) REVERT: B 543 MET cc_start: 0.8952 (mmm) cc_final: 0.8492 (mtp) REVERT: B 821 LYS cc_start: 0.8444 (mptt) cc_final: 0.8236 (mmtp) REVERT: B 1008 SER cc_start: 0.8916 (m) cc_final: 0.8596 (p) REVERT: P 63 ASP cc_start: 0.8431 (t70) cc_final: 0.7965 (t0) outliers start: 25 outliers final: 22 residues processed: 202 average time/residue: 0.1309 time to fit residues: 39.5159 Evaluate side-chains 192 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain P residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 140 optimal weight: 0.7980 chunk 212 optimal weight: 0.0370 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 146 optimal weight: 0.0570 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106542 restraints weight = 24609.261| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.01 r_work: 0.3216 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17661 Z= 0.114 Angle : 0.581 10.572 24149 Z= 0.284 Chirality : 0.043 0.207 2769 Planarity : 0.005 0.148 3086 Dihedral : 7.372 96.494 2622 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.63 % Favored : 92.28 % Rotamer: Outliers : 1.31 % Allowed : 18.04 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -1.87 (0.18), residues: 2228 helix: -0.17 (0.19), residues: 846 sheet: -1.46 (0.33), residues: 239 loop : -2.07 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 668 TYR 0.015 0.001 TYR A 746 PHE 0.012 0.001 PHE B 99 TRP 0.013 0.001 TRP B 843 HIS 0.002 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.11 (17659) covalent geometry : angle 0.58037 / 0.28 (24146) hydrogen bonds : bond 0.02545 / 1.75 ( 564) hydrogen bonds : angle 3.98230 / 2.78 ( 1614) glycosidic custom : bond 0.00609 / 0.32 ( 1) glycosidic custom : angle 1.58371 / 0.87 ( 3) Misc. bond : bond 0.00360 / 0.19 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 ASP cc_start: 0.8339 (t0) cc_final: 0.8092 (t0) REVERT: B 89 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8308 (ptp90) REVERT: B 543 MET cc_start: 0.8936 (mmm) cc_final: 0.8482 (mtp) REVERT: B 821 LYS cc_start: 0.8519 (mptt) cc_final: 0.8305 (mmtp) REVERT: B 1008 SER cc_start: 0.8914 (m) cc_final: 0.8587 (p) REVERT: B 1073 TYR cc_start: 0.8609 (t80) cc_final: 0.8139 (t80) REVERT: P 63 ASP cc_start: 0.8422 (t70) cc_final: 0.8000 (t0) outliers start: 23 outliers final: 23 residues processed: 189 average time/residue: 0.1481 time to fit residues: 41.8905 Evaluate side-chains 192 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain P residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 104 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.0060 chunk 4 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104649 restraints weight = 24836.586| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.02 r_work: 0.3192 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17661 Z= 0.136 Angle : 0.594 10.092 24149 Z= 0.293 Chirality : 0.043 0.196 2769 Planarity : 0.005 0.148 3086 Dihedral : 7.476 97.126 2622 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.30 % Favored : 91.61 % Rotamer: Outliers : 1.54 % Allowed : 17.87 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: -1.92 (0.18), residues: 2228 helix: -0.25 (0.19), residues: 851 sheet: -1.51 (0.33), residues: 239 loop : -2.05 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 668 TYR 0.016 0.001 TYR A 611 PHE 0.014 0.001 PHE B 99 TRP 0.012 0.001 TRP B 843 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (17659) covalent geometry : angle 0.59390 / 0.29 (24146) hydrogen bonds : bond 0.02767 / 1.89 ( 564) hydrogen bonds : angle 4.07915 / 2.85 ( 1614) glycosidic custom : bond 0.00684 / 0.36 ( 1) glycosidic custom : angle 1.58651 / 0.87 ( 3) Misc. bond : bond 0.00448 / 0.24 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4475.53 seconds wall clock time: 77 minutes 5.67 seconds (4625.67 seconds total)