Starting phenix.real_space_refine on Sun May 11 08:54:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4f_41029/05_2025/8t4f_41029.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4f_41029/05_2025/8t4f_41029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4f_41029/05_2025/8t4f_41029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4f_41029/05_2025/8t4f_41029.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4f_41029/05_2025/8t4f_41029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4f_41029/05_2025/8t4f_41029.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4932 2.51 5 N 1372 2.21 5 O 1458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7793 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3508 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 191} Link IDs: {'PTRANS': 18, 'TRANS': 521} Chain breaks: 3 Unresolved non-hydrogen bonds: 686 Unresolved non-hydrogen angles: 885 Unresolved non-hydrogen dihedrals: 547 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 400 Chain: "B" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4202 Classifications: {'peptide': 548} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 527} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 83 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG A 529 " occ=0.62 ... (3 atoms not shown) pdb=" CB ARG A 529 " occ=0.62 Time building chain proxies: 5.37, per 1000 atoms: 0.69 Number of scatterers: 7793 At special positions: 0 Unit cell: (69.628, 100.048, 136.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1458 8.00 N 1372 7.00 C 4932 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=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 73.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 201 removed outlier: 3.518A pdb=" N SER A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.520A pdb=" N PHE A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 272 removed outlier: 3.631A pdb=" N HIS A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 324 removed outlier: 3.547A pdb=" N SER A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 340 through 372 removed outlier: 3.502A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 382 through 437 removed outlier: 3.587A pdb=" N GLU A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 484 removed outlier: 3.609A pdb=" N LEU A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) Proline residue: A 466 - end of helix removed outlier: 3.765A pdb=" N GLU A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.878A pdb=" N LEU A 519 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.844A pdb=" N GLY A 543 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS A 544 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.558A pdb=" N ALA A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.032A pdb=" N TYR A 572 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 644 through 658 Processing helix chain 'A' and resid 668 through 673 removed outlier: 3.587A pdb=" N ALA A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 687 Processing helix chain 'A' and resid 690 through 694 removed outlier: 3.930A pdb=" N ARG A 694 " --> pdb=" O ARG A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 removed outlier: 3.792A pdb=" N VAL A 706 " --> pdb=" O HIS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'B' and resid 132 through 145 removed outlier: 3.586A pdb=" N SER B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 168 removed outlier: 3.844A pdb=" N ALA B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.579A pdb=" N TYR B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 234 removed outlier: 3.754A pdb=" N GLY B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.879A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.621A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 266 through 289 removed outlier: 3.786A pdb=" N LEU B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 338 removed outlier: 4.306A pdb=" N LEU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.827A pdb=" N ALA B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 402 removed outlier: 3.831A pdb=" N CYS B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 448 removed outlier: 4.450A pdb=" N GLY B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 507 Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.528A pdb=" N VAL B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 516 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.817A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN B 545 " --> pdb=" O TYR B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 585 through 590 Processing helix chain 'B' and resid 594 through 598 removed outlier: 3.798A pdb=" N TYR B 597 " --> pdb=" O HIS B 594 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR B 598 " --> pdb=" O GLY B 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 594 through 598' Processing helix chain 'B' and resid 608 through 622 removed outlier: 3.731A pdb=" N ALA B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 636 Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 648 through 653 removed outlier: 4.598A pdb=" N ASP B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 668 removed outlier: 4.123A pdb=" N THR B 665 " --> pdb=" O ARG B 662 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 667 " --> pdb=" O GLN B 664 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 503 through 504 removed outlier: 3.833A pdb=" N VAL A 503 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 528 " --> pdb=" O VAL A 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 506 through 509 removed outlier: 3.694A pdb=" N GLN A 506 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 561 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 537 removed outlier: 6.787A pdb=" N VAL A 537 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AA5, first strand: chain 'B' and resid 486 through 493 removed outlier: 6.920A pdb=" N LYS B 487 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER B 474 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU B 489 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 468 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE B 470 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU B 528 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASP B 472 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLN B 526 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 546 through 548 removed outlier: 6.292A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2645 1.34 - 1.46: 1248 1.46 - 1.58: 3970 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 7916 Sorted by residual: bond pdb=" N VAL A 460 " pdb=" CA VAL A 460 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.72e+00 bond pdb=" N VAL A 366 " pdb=" CA VAL A 366 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.58e+00 bond pdb=" N VAL B 387 " pdb=" CA VAL B 387 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.46e+00 bond pdb=" N VAL B 276 " pdb=" CA VAL B 276 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.45e+00 bond pdb=" N LEU B 383 " pdb=" CA LEU B 383 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 7.09e+00 ... (remaining 7911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 10504 1.55 - 3.09: 229 3.09 - 4.64: 32 4.64 - 6.18: 9 6.18 - 7.73: 3 Bond angle restraints: 10777 Sorted by residual: angle pdb=" C GLN B 450 " pdb=" N PRO B 451 " pdb=" CA PRO B 451 " ideal model delta sigma weight residual 120.98 125.12 -4.14 1.07e+00 8.73e-01 1.50e+01 angle pdb=" CA LEU B 272 " pdb=" C LEU B 272 " pdb=" O LEU B 272 " ideal model delta sigma weight residual 121.00 117.81 3.19 1.05e+00 9.07e-01 9.22e+00 angle pdb=" CA VAL B 387 " pdb=" C VAL B 387 " pdb=" O VAL B 387 " ideal model delta sigma weight residual 121.17 118.03 3.14 1.06e+00 8.90e-01 8.79e+00 angle pdb=" CA HIS B 384 " pdb=" C HIS B 384 " pdb=" O HIS B 384 " ideal model delta sigma weight residual 120.82 117.80 3.02 1.05e+00 9.07e-01 8.30e+00 angle pdb=" CA VAL A 460 " pdb=" C VAL A 460 " pdb=" O VAL A 460 " ideal model delta sigma weight residual 121.17 118.14 3.03 1.06e+00 8.90e-01 8.15e+00 ... (remaining 10772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4204 17.63 - 35.26: 401 35.26 - 52.89: 98 52.89 - 70.52: 20 70.52 - 88.15: 8 Dihedral angle restraints: 4731 sinusoidal: 1588 harmonic: 3143 Sorted by residual: dihedral pdb=" CA THR B 167 " pdb=" C THR B 167 " pdb=" N LEU B 168 " pdb=" CA LEU B 168 " ideal model delta harmonic sigma weight residual -180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB GLU B 227 " pdb=" CG GLU B 227 " pdb=" CD GLU B 227 " pdb=" OE1 GLU B 227 " ideal model delta sinusoidal sigma weight residual 0.00 -88.15 88.15 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU C 8 " pdb=" CG GLU C 8 " pdb=" CD GLU C 8 " pdb=" OE1 GLU C 8 " ideal model delta sinusoidal sigma weight residual 0.00 87.63 -87.63 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 4728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 933 0.037 - 0.075: 264 0.075 - 0.112: 69 0.112 - 0.149: 14 0.149 - 0.186: 8 Chirality restraints: 1288 Sorted by residual: chirality pdb=" CA VAL B 276 " pdb=" N VAL B 276 " pdb=" C VAL B 276 " pdb=" CB VAL B 276 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CA VAL A 366 " pdb=" N VAL A 366 " pdb=" C VAL A 366 " pdb=" CB VAL A 366 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA VAL B 387 " pdb=" N VAL B 387 " pdb=" C VAL B 387 " pdb=" CB VAL B 387 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 1285 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 588 " 0.010 2.00e-02 2.50e+03 1.35e-02 3.20e+00 pdb=" CG PHE B 588 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 588 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 588 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 588 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 588 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 588 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 146 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO B 147 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 374 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 375 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.018 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1582 2.77 - 3.31: 7665 3.31 - 3.84: 12385 3.84 - 4.37: 12461 4.37 - 4.90: 23078 Nonbonded interactions: 57171 Sorted by model distance: nonbonded pdb=" OE1 GLN B 517 " pdb=" OG SER B 548 " model vdw 2.243 3.040 nonbonded pdb=" OD2 ASP B 256 " pdb=" NZ LYS B 442 " model vdw 2.265 3.120 nonbonded pdb=" O PHE B 284 " pdb=" OG SER B 287 " model vdw 2.348 3.040 nonbonded pdb=" OE2 GLU B 307 " pdb=" ND2 ASN B 311 " model vdw 2.351 3.120 nonbonded pdb=" NH1 ARG B 140 " pdb=" OD2 ASP B 448 " model vdw 2.354 3.120 ... (remaining 57166 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=0.62 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.170 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.490 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.003 0.034 7916 Z= 0.208 Angle : 0.571 7.728 10777 Z= 0.344 Chirality : 0.040 0.186 1288 Planarity : 0.003 0.036 1407 Dihedral : 15.367 88.146 2705 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.56 % Allowed : 19.41 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.27), residues: 1083 helix: 2.25 (0.20), residues: 707 sheet: -1.01 (0.66), residues: 64 loop : -0.31 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 348 HIS 0.002 0.001 HIS B 543 PHE 0.031 0.001 PHE B 588 TYR 0.012 0.001 TYR B 428 ARG 0.005 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.15909 ( 547) hydrogen bonds : angle 4.68124 ( 1590) covalent geometry : bond 0.00323 ( 7916) covalent geometry : angle 0.57094 (10777) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.868 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 113 average time/residue: 0.2590 time to fit residues: 37.4626 Evaluate side-chains 95 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.181035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138166 restraints weight = 9445.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137058 restraints weight = 9797.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139058 restraints weight = 7763.368| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7916 Z= 0.183 Angle : 0.550 6.957 10777 Z= 0.280 Chirality : 0.038 0.136 1288 Planarity : 0.004 0.040 1407 Dihedral : 3.366 17.275 1164 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.91 % Allowed : 19.83 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.27), residues: 1083 helix: 2.29 (0.20), residues: 720 sheet: -1.34 (0.64), residues: 64 loop : -0.53 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 348 HIS 0.004 0.001 HIS B 384 PHE 0.012 0.002 PHE A 207 TYR 0.012 0.001 TYR A 309 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.07716 ( 547) hydrogen bonds : angle 3.61863 ( 1590) covalent geometry : bond 0.00419 ( 7916) covalent geometry : angle 0.54965 (10777) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.767 Fit side-chains REVERT: A 432 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7595 (tt0) REVERT: B 135 LYS cc_start: 0.5143 (tptt) cc_final: 0.4668 (tptt) REVERT: B 166 GLU cc_start: 0.7556 (tp30) cc_final: 0.7186 (tp30) REVERT: B 536 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7947 (tm-30) outliers start: 28 outliers final: 20 residues processed: 117 average time/residue: 0.2326 time to fit residues: 35.3737 Evaluate side-chains 113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 536 GLN Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 30.0000 chunk 83 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.190763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148686 restraints weight = 9510.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149180 restraints weight = 8751.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150071 restraints weight = 5984.862| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7916 Z= 0.151 Angle : 0.503 7.665 10777 Z= 0.255 Chirality : 0.037 0.135 1288 Planarity : 0.003 0.040 1407 Dihedral : 3.242 17.549 1164 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.05 % Allowed : 19.55 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.27), residues: 1083 helix: 2.44 (0.20), residues: 720 sheet: -1.38 (0.64), residues: 64 loop : -0.49 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 348 HIS 0.003 0.001 HIS B 384 PHE 0.010 0.001 PHE A 207 TYR 0.015 0.001 TYR B 541 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.07171 ( 547) hydrogen bonds : angle 3.41636 ( 1590) covalent geometry : bond 0.00329 ( 7916) covalent geometry : angle 0.50274 (10777) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.890 Fit side-chains REVERT: B 135 LYS cc_start: 0.5058 (tptt) cc_final: 0.4527 (tptt) REVERT: B 166 GLU cc_start: 0.7546 (tp30) cc_final: 0.7038 (tp30) outliers start: 29 outliers final: 24 residues processed: 116 average time/residue: 0.2481 time to fit residues: 37.4838 Evaluate side-chains 118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.0270 chunk 102 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.191587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140444 restraints weight = 9400.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144422 restraints weight = 6215.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145641 restraints weight = 4250.780| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7916 Z= 0.118 Angle : 0.470 8.626 10777 Z= 0.234 Chirality : 0.036 0.124 1288 Planarity : 0.003 0.038 1407 Dihedral : 3.011 17.821 1164 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.49 % Allowed : 21.09 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.27), residues: 1083 helix: 2.69 (0.20), residues: 724 sheet: -1.28 (0.64), residues: 64 loop : -0.41 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 348 HIS 0.002 0.000 HIS B 543 PHE 0.010 0.001 PHE B 588 TYR 0.011 0.001 TYR A 309 ARG 0.005 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.06011 ( 547) hydrogen bonds : angle 3.15488 ( 1590) covalent geometry : bond 0.00227 ( 7916) covalent geometry : angle 0.47044 (10777) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.803 Fit side-chains REVERT: B 166 GLU cc_start: 0.7606 (tp30) cc_final: 0.7391 (tp30) REVERT: B 679 LYS cc_start: 0.8418 (tmtt) cc_final: 0.8045 (mttp) outliers start: 25 outliers final: 16 residues processed: 118 average time/residue: 0.2385 time to fit residues: 36.4746 Evaluate side-chains 107 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 584 HIS Chi-restraints excluded: chain B residue 592 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 93 optimal weight: 4.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.191120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139582 restraints weight = 9419.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143506 restraints weight = 6081.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144795 restraints weight = 4185.166| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7916 Z= 0.122 Angle : 0.482 9.190 10777 Z= 0.237 Chirality : 0.036 0.128 1288 Planarity : 0.003 0.036 1407 Dihedral : 2.950 17.063 1164 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.35 % Allowed : 22.35 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.27), residues: 1083 helix: 2.78 (0.20), residues: 721 sheet: -1.22 (0.64), residues: 64 loop : -0.33 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 348 HIS 0.002 0.000 HIS B 543 PHE 0.009 0.001 PHE A 447 TYR 0.014 0.001 TYR B 541 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.06064 ( 547) hydrogen bonds : angle 3.11055 ( 1590) covalent geometry : bond 0.00245 ( 7916) covalent geometry : angle 0.48213 (10777) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.830 Fit side-chains REVERT: B 166 GLU cc_start: 0.7594 (tp30) cc_final: 0.7374 (tp30) REVERT: B 679 LYS cc_start: 0.8450 (tmtt) cc_final: 0.8028 (mttp) outliers start: 24 outliers final: 22 residues processed: 110 average time/residue: 0.2432 time to fit residues: 34.7615 Evaluate side-chains 114 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 584 HIS Chi-restraints excluded: chain B residue 592 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 97 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.193396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142148 restraints weight = 9423.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145600 restraints weight = 5659.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147712 restraints weight = 4188.319| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7916 Z= 0.112 Angle : 0.483 10.050 10777 Z= 0.231 Chirality : 0.035 0.124 1288 Planarity : 0.003 0.035 1407 Dihedral : 2.882 19.674 1164 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.35 % Allowed : 22.77 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.27), residues: 1083 helix: 2.93 (0.20), residues: 720 sheet: -1.13 (0.64), residues: 64 loop : -0.26 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 348 HIS 0.003 0.001 HIS B 670 PHE 0.013 0.001 PHE B 588 TYR 0.012 0.001 TYR B 541 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.05498 ( 547) hydrogen bonds : angle 2.99456 ( 1590) covalent geometry : bond 0.00216 ( 7916) covalent geometry : angle 0.48251 (10777) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.815 Fit side-chains REVERT: B 166 GLU cc_start: 0.7556 (tp30) cc_final: 0.7342 (tp30) REVERT: B 679 LYS cc_start: 0.8533 (tmtt) cc_final: 0.8192 (mttp) outliers start: 24 outliers final: 20 residues processed: 113 average time/residue: 0.2341 time to fit residues: 34.5611 Evaluate side-chains 108 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 584 HIS Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 521 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.185671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.142293 restraints weight = 9462.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141159 restraints weight = 10759.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142730 restraints weight = 7940.146| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7916 Z= 0.169 Angle : 0.552 9.740 10777 Z= 0.269 Chirality : 0.038 0.129 1288 Planarity : 0.003 0.035 1407 Dihedral : 3.113 16.483 1164 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.05 % Allowed : 23.60 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.27), residues: 1083 helix: 2.66 (0.20), residues: 720 sheet: -1.27 (0.63), residues: 64 loop : -0.34 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 322 HIS 0.002 0.001 HIS B 543 PHE 0.011 0.001 PHE A 207 TYR 0.017 0.001 TYR B 541 ARG 0.004 0.000 ARG B 175 Details of bonding type rmsd hydrogen bonds : bond 0.07297 ( 547) hydrogen bonds : angle 3.28915 ( 1590) covalent geometry : bond 0.00387 ( 7916) covalent geometry : angle 0.55230 (10777) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.861 Fit side-chains REVERT: B 135 LYS cc_start: 0.5045 (tptt) cc_final: 0.4685 (tptt) REVERT: B 166 GLU cc_start: 0.7629 (tp30) cc_final: 0.7305 (tp30) REVERT: B 679 LYS cc_start: 0.8474 (tmtt) cc_final: 0.8072 (tptt) outliers start: 29 outliers final: 25 residues processed: 111 average time/residue: 0.2566 time to fit residues: 37.1667 Evaluate side-chains 112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 584 HIS Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.186219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142877 restraints weight = 9493.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141884 restraints weight = 10694.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143808 restraints weight = 7170.959| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7916 Z= 0.154 Angle : 0.537 10.150 10777 Z= 0.262 Chirality : 0.037 0.127 1288 Planarity : 0.003 0.037 1407 Dihedral : 3.119 17.204 1164 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.61 % Allowed : 22.77 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.27), residues: 1083 helix: 2.66 (0.20), residues: 720 sheet: -1.26 (0.63), residues: 64 loop : -0.33 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 322 HIS 0.002 0.001 HIS B 670 PHE 0.010 0.001 PHE A 207 TYR 0.017 0.001 TYR B 541 ARG 0.003 0.000 ARG B 175 Details of bonding type rmsd hydrogen bonds : bond 0.07027 ( 547) hydrogen bonds : angle 3.25278 ( 1590) covalent geometry : bond 0.00345 ( 7916) covalent geometry : angle 0.53695 (10777) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.760 Fit side-chains REVERT: A 215 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8474 (tt) REVERT: B 135 LYS cc_start: 0.5067 (tptt) cc_final: 0.4464 (tptt) REVERT: B 679 LYS cc_start: 0.8513 (tmtt) cc_final: 0.8248 (mttp) outliers start: 33 outliers final: 27 residues processed: 114 average time/residue: 0.2391 time to fit residues: 35.7975 Evaluate side-chains 115 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 584 HIS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 674 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.188963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147427 restraints weight = 9648.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146097 restraints weight = 11521.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147758 restraints weight = 9357.287| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7916 Z= 0.132 Angle : 0.525 10.326 10777 Z= 0.252 Chirality : 0.036 0.125 1288 Planarity : 0.003 0.036 1407 Dihedral : 3.024 17.576 1164 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.05 % Allowed : 23.46 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.27), residues: 1083 helix: 2.79 (0.20), residues: 720 sheet: -1.22 (0.63), residues: 64 loop : -0.23 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 322 HIS 0.004 0.001 HIS B 670 PHE 0.010 0.001 PHE B 588 TYR 0.015 0.001 TYR B 541 ARG 0.003 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.06466 ( 547) hydrogen bonds : angle 3.14039 ( 1590) covalent geometry : bond 0.00273 ( 7916) covalent geometry : angle 0.52510 (10777) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.782 Fit side-chains REVERT: A 215 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8482 (tt) REVERT: B 135 LYS cc_start: 0.5067 (tptt) cc_final: 0.4464 (tptt) REVERT: B 679 LYS cc_start: 0.8516 (tmtt) cc_final: 0.8289 (mttp) outliers start: 29 outliers final: 26 residues processed: 117 average time/residue: 0.2364 time to fit residues: 36.0348 Evaluate side-chains 120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 584 HIS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 674 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.189405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145011 restraints weight = 9476.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.143990 restraints weight = 10847.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145225 restraints weight = 6426.876| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7916 Z= 0.129 Angle : 0.517 10.521 10777 Z= 0.251 Chirality : 0.036 0.125 1288 Planarity : 0.003 0.036 1407 Dihedral : 2.979 17.428 1164 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.19 % Allowed : 23.74 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.27), residues: 1083 helix: 2.84 (0.20), residues: 720 sheet: -1.17 (0.63), residues: 64 loop : -0.19 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 322 HIS 0.004 0.001 HIS B 670 PHE 0.010 0.001 PHE B 588 TYR 0.014 0.001 TYR B 541 ARG 0.010 0.000 ARG C 1 Details of bonding type rmsd hydrogen bonds : bond 0.06276 ( 547) hydrogen bonds : angle 3.09481 ( 1590) covalent geometry : bond 0.00266 ( 7916) covalent geometry : angle 0.51738 (10777) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.802 Fit side-chains REVERT: A 215 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8477 (tt) REVERT: B 135 LYS cc_start: 0.4955 (tptt) cc_final: 0.4344 (tptt) REVERT: B 584 HIS cc_start: 0.5907 (OUTLIER) cc_final: 0.5542 (t-90) REVERT: B 679 LYS cc_start: 0.8585 (tmtt) cc_final: 0.8261 (mttp) outliers start: 30 outliers final: 25 residues processed: 115 average time/residue: 0.2386 time to fit residues: 35.7349 Evaluate side-chains 118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 584 HIS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 674 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.185807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143634 restraints weight = 9466.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142821 restraints weight = 10137.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144117 restraints weight = 8083.090| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7916 Z= 0.160 Angle : 0.567 10.384 10777 Z= 0.274 Chirality : 0.037 0.127 1288 Planarity : 0.003 0.036 1407 Dihedral : 3.119 17.321 1164 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.47 % Allowed : 23.88 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.27), residues: 1083 helix: 2.65 (0.20), residues: 720 sheet: -1.21 (0.63), residues: 64 loop : -0.26 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 322 HIS 0.005 0.001 HIS B 670 PHE 0.010 0.001 PHE A 207 TYR 0.017 0.001 TYR B 541 ARG 0.011 0.000 ARG C 1 Details of bonding type rmsd hydrogen bonds : bond 0.07157 ( 547) hydrogen bonds : angle 3.25819 ( 1590) covalent geometry : bond 0.00360 ( 7916) covalent geometry : angle 0.56669 (10777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2964.88 seconds wall clock time: 52 minutes 19.70 seconds (3139.70 seconds total)