Starting phenix.real_space_refine on Thu Nov 14 23:57:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4f_41029/11_2024/8t4f_41029.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4f_41029/11_2024/8t4f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4f_41029/11_2024/8t4f_41029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4f_41029/11_2024/8t4f_41029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4f_41029/11_2024/8t4f_41029.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4f_41029/11_2024/8t4f_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-5513/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: 0.00, per 1000 atoms: 0.00 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: 2.40 Conformation dependent library (CDL) restraints added in 1.4 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: 0.95 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: 2.41 Time building geometry restraints manager: 2.31 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: 30.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 13.210 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.580 ------------------------------------------------------------------------------- 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= 0.216 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 *********************** 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 : 0.871 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 113 average time/residue: 0.2783 time to fit residues: 40.5017 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 : 0.909 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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= 0.280 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 *********************** 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 : 0.989 Fit side-chains REVERT: A 432 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7601 (tt0) REVERT: B 135 LYS cc_start: 0.5155 (tptt) cc_final: 0.4684 (tptt) REVERT: B 166 GLU cc_start: 0.7530 (tp30) cc_final: 0.7161 (tp30) REVERT: B 536 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7973 (tm-30) outliers start: 28 outliers final: 20 residues processed: 117 average time/residue: 0.2421 time to fit residues: 37.0974 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 : 0.873 ------------------------------------------------------------------------------- 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 54 optimal weight: 1.9990 chunk 30 optimal weight: 30.0000 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7916 Z= 0.261 Angle : 0.527 7.850 10777 Z= 0.268 Chirality : 0.038 0.136 1288 Planarity : 0.004 0.041 1407 Dihedral : 3.332 17.398 1164 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.47 % Allowed : 19.41 % Favored : 76.12 % 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: 2.01 (0.27), residues: 1083 helix: 2.34 (0.20), residues: 720 sheet: -1.42 (0.63), residues: 64 loop : -0.55 (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 B 157 TYR 0.017 0.001 TYR B 541 ARG 0.004 0.000 ARG A 270 *********************** 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 129 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.873 Fit side-chains REVERT: B 135 LYS cc_start: 0.5121 (tptt) cc_final: 0.4599 (tptt) REVERT: B 166 GLU cc_start: 0.7585 (tp30) cc_final: 0.7083 (tp30) outliers start: 32 outliers final: 26 residues processed: 117 average time/residue: 0.2640 time to fit residues: 39.9643 Evaluate side-chains 120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 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 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 97 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 51 optimal weight: 0.0170 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7916 Z= 0.272 Angle : 0.544 9.135 10777 Z= 0.274 Chirality : 0.038 0.134 1288 Planarity : 0.003 0.041 1407 Dihedral : 3.326 17.315 1164 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.89 % Allowed : 20.25 % Favored : 74.86 % 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: 2.00 (0.27), residues: 1083 helix: 2.34 (0.20), residues: 720 sheet: -1.43 (0.64), residues: 64 loop : -0.58 (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 0.011 0.002 PHE B 588 TYR 0.015 0.001 TYR B 541 ARG 0.004 0.000 ARG A 270 *********************** 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 132 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.849 Fit side-chains REVERT: B 166 GLU cc_start: 0.7586 (tp30) cc_final: 0.7194 (tp30) REVERT: B 536 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.8020 (tm-30) outliers start: 35 outliers final: 29 residues processed: 121 average time/residue: 0.2454 time to fit residues: 38.4825 Evaluate side-chains 123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 304 SER 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 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 163 VAL 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 429 ILE Chi-restraints excluded: chain B residue 433 MET 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 536 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 50.0000 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7916 Z= 0.200 Angle : 0.504 9.835 10777 Z= 0.253 Chirality : 0.037 0.133 1288 Planarity : 0.003 0.041 1407 Dihedral : 3.175 17.714 1164 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.91 % Allowed : 21.93 % Favored : 74.16 % 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: 2.23 (0.27), residues: 1083 helix: 2.55 (0.20), residues: 720 sheet: -1.40 (0.64), residues: 64 loop : -0.55 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 322 HIS 0.002 0.001 HIS B 384 PHE 0.009 0.001 PHE A 447 TYR 0.014 0.001 TYR B 428 ARG 0.005 0.000 ARG B 333 *********************** 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 125 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.925 Fit side-chains outliers start: 28 outliers final: 25 residues processed: 114 average time/residue: 0.2423 time to fit residues: 36.4717 Evaluate side-chains 120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 304 SER 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 433 MET 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 592 MET Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 30.0000 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 521 GLN ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1680 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= 0.255 Angle : 0.538 10.026 10777 Z= 0.269 Chirality : 0.038 0.133 1288 Planarity : 0.003 0.040 1407 Dihedral : 3.227 17.298 1164 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.75 % Allowed : 22.21 % Favored : 73.04 % 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: 2.15 (0.27), residues: 1083 helix: 2.46 (0.20), residues: 720 sheet: -1.38 (0.64), residues: 64 loop : -0.54 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 322 HIS 0.003 0.001 HIS B 384 PHE 0.013 0.001 PHE B 588 TYR 0.013 0.001 TYR B 541 ARG 0.004 0.000 ARG B 333 *********************** 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 131 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.955 Fit side-chains REVERT: A 215 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8555 (tt) outliers start: 34 outliers final: 28 residues processed: 120 average time/residue: 0.2429 time to fit residues: 38.0764 Evaluate side-chains 125 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 304 SER 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 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 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 429 ILE Chi-restraints excluded: chain B residue 433 MET 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 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 100 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 65 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7916 Z= 0.188 Angle : 0.493 10.212 10777 Z= 0.246 Chirality : 0.036 0.121 1288 Planarity : 0.003 0.040 1407 Dihedral : 3.083 17.755 1164 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.91 % Allowed : 23.04 % Favored : 73.04 % 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: 2.42 (0.27), residues: 1083 helix: 2.68 (0.20), residues: 720 sheet: -1.32 (0.64), residues: 64 loop : -0.44 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 322 HIS 0.002 0.001 HIS B 543 PHE 0.010 0.001 PHE B 588 TYR 0.014 0.001 TYR B 541 ARG 0.006 0.000 ARG A 270 *********************** 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 121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.978 Fit side-chains REVERT: A 215 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8477 (tt) outliers start: 28 outliers final: 23 residues processed: 110 average time/residue: 0.2495 time to fit residues: 35.8499 Evaluate side-chains 111 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 368 ILE 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 387 VAL Chi-restraints excluded: chain B residue 389 MET 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 546 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 674 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.0570 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 0.0670 chunk 99 optimal weight: 0.0570 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7916 Z= 0.139 Angle : 0.482 10.027 10777 Z= 0.235 Chirality : 0.035 0.121 1288 Planarity : 0.003 0.037 1407 Dihedral : 2.843 18.499 1164 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.79 % Allowed : 24.16 % Favored : 73.04 % 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: 2.78 (0.27), residues: 1083 helix: 2.95 (0.20), residues: 721 sheet: -1.19 (0.64), residues: 64 loop : -0.29 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 322 HIS 0.002 0.000 HIS B 670 PHE 0.009 0.001 PHE B 491 TYR 0.010 0.001 TYR A 309 ARG 0.006 0.000 ARG A 270 *********************** 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 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.846 Fit side-chains REVERT: A 461 LEU cc_start: 0.8467 (mt) cc_final: 0.8240 (tt) outliers start: 20 outliers final: 14 residues processed: 111 average time/residue: 0.2859 time to fit residues: 41.1102 Evaluate side-chains 105 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 421 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 380 ARG 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 546 VAL 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 90 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7916 Z= 0.308 Angle : 0.586 10.031 10777 Z= 0.290 Chirality : 0.039 0.134 1288 Planarity : 0.004 0.051 1407 Dihedral : 3.227 16.912 1164 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.91 % Allowed : 23.74 % 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: 2.30 (0.27), residues: 1083 helix: 2.55 (0.20), residues: 720 sheet: -1.27 (0.64), residues: 64 loop : -0.41 (0.37), 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 0.012 0.002 PHE A 207 TYR 0.022 0.002 TYR B 541 ARG 0.004 0.000 ARG A 270 *********************** 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 122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.781 Fit side-chains REVERT: B 135 LYS cc_start: 0.5133 (tptt) cc_final: 0.4831 (tptt) outliers start: 28 outliers final: 23 residues processed: 113 average time/residue: 0.2687 time to fit residues: 38.8911 Evaluate side-chains 116 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 417 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 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 312 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL 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 546 VAL 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 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7916 Z= 0.202 Angle : 0.534 10.218 10777 Z= 0.260 Chirality : 0.036 0.126 1288 Planarity : 0.003 0.039 1407 Dihedral : 3.098 18.069 1164 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.65 % Allowed : 25.14 % Favored : 72.21 % 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: 2.69 (0.20), residues: 720 sheet: -1.19 (0.64), residues: 64 loop : -0.39 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 322 HIS 0.004 0.001 HIS B 670 PHE 0.019 0.001 PHE B 588 TYR 0.018 0.001 TYR B 541 ARG 0.006 0.000 ARG A 270 ********************** 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 112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.888 Fit side-chains outliers start: 19 outliers final: 19 residues processed: 108 average time/residue: 0.2597 time to fit residues: 36.0821 Evaluate side-chains 109 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 THR 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 421 LEU Chi-restraints excluded: chain A residue 479 PHE 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 312 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 387 VAL 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 546 VAL 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 91 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.189043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.148087 restraints weight = 9390.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.146724 restraints weight = 10209.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149146 restraints weight = 8409.592| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7916 Z= 0.189 Angle : 0.538 10.241 10777 Z= 0.261 Chirality : 0.036 0.124 1288 Planarity : 0.003 0.037 1407 Dihedral : 3.021 17.669 1164 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.65 % Allowed : 25.70 % 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: 2.60 (0.27), residues: 1083 helix: 2.82 (0.20), residues: 716 sheet: -1.15 (0.64), residues: 64 loop : -0.36 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 322 HIS 0.005 0.001 HIS B 670 PHE 0.017 0.001 PHE B 588 TYR 0.016 0.001 TYR B 541 ARG 0.007 0.000 ARG C 1 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1970.72 seconds wall clock time: 37 minutes 15.32 seconds (2235.32 seconds total)