Starting phenix.real_space_refine on Tue Aug 26 00:27:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffv_29068/08_2025/8ffv_29068_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffv_29068/08_2025/8ffv_29068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ffv_29068/08_2025/8ffv_29068_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffv_29068/08_2025/8ffv_29068_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ffv_29068/08_2025/8ffv_29068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffv_29068/08_2025/8ffv_29068.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 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: 8 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 78 5.16 5 C 10037 2.51 5 N 2649 2.21 5 O 3054 1.98 5 F 1 1.80 5 H 15804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31631 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10279 Classifications: {'peptide': 630} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 614} Chain breaks: 1 Chain: "B" Number of atoms: 10478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 10478 Classifications: {'peptide': 644} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 627} Chain breaks: 2 Chain: "C" Number of atoms: 4235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4235 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 247} Chain: "D" Number of atoms: 6547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 6547 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 393} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'DEX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.11, per 1000 atoms: 0.19 Number of scatterers: 31631 At special positions: 0 Unit cell: (143.62, 127.755, 118.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 78 16.00 P 6 15.00 Mg 2 11.99 F 1 9.00 O 3054 8.00 N 2649 7.00 C 10037 6.00 H 15804 1.00 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: 2.96 Conformation dependent library (CDL) restraints added in 935.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3692 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 14 sheets defined 50.6% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 42 through 63 removed outlier: 3.626A pdb=" N ARG A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 65 No H-bonds generated for 'chain 'A' and resid 64 through 65' Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 199 through 212 removed outlier: 4.145A pdb=" N GLN A 212 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 406 through 428 removed outlier: 3.512A pdb=" N LYS A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 451 removed outlier: 3.847A pdb=" N GLN A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 455 through 460 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 498 through 504 removed outlier: 3.734A pdb=" N VAL A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 508 through 514 Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.880A pdb=" N CYS A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 578 removed outlier: 4.008A pdb=" N THR A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASN A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 640 through 653 Processing helix chain 'A' and resid 656 through 674 Processing helix chain 'A' and resid 681 through 696 Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.829A pdb=" N PHE B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 43 through 64 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 113 through 122 Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.714A pdb=" N ASP B 303 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 318 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 406 through 428 Processing helix chain 'B' and resid 430 through 452 removed outlier: 3.727A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 460 Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 498 through 504 Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 508 through 514 Processing helix chain 'B' and resid 525 through 534 removed outlier: 4.356A pdb=" N GLN B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 564 Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 568 through 579 Processing helix chain 'B' and resid 609 through 616 Processing helix chain 'B' and resid 621 through 627 Processing helix chain 'B' and resid 640 through 653 Processing helix chain 'B' and resid 656 through 674 Processing helix chain 'B' and resid 681 through 696 removed outlier: 4.459A pdb=" N ARG B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 730 Processing helix chain 'C' and resid 531 through 540 Processing helix chain 'C' and resid 555 through 580 Processing helix chain 'C' and resid 583 through 587 Processing helix chain 'C' and resid 588 through 616 removed outlier: 5.041A pdb=" N MET C 601 " --> pdb=" O GLN C 597 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER C 602 " --> pdb=" O TYR C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 636 through 656 removed outlier: 5.071A pdb=" N LYS C 644 " --> pdb=" O TYR C 640 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N HIS C 645 " --> pdb=" O ASP C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 672 Processing helix chain 'C' and resid 682 through 706 removed outlier: 4.995A pdb=" N GLU C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 704 " --> pdb=" O ALA C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 742 removed outlier: 4.015A pdb=" N LEU C 721 " --> pdb=" O GLN C 717 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS C 726 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU C 727 " --> pdb=" O ASP C 723 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 735 " --> pdb=" O ASN C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 766 Proline residue: C 762 - end of helix Processing helix chain 'D' and resid 19 through 23 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 87 through 96 Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 113 through 117 removed outlier: 4.158A pdb=" N GLY D 117 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 209 removed outlier: 3.654A pdb=" N ARG D 206 " --> pdb=" O TYR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 262 through 283 Processing helix chain 'D' and resid 285 through 302 removed outlier: 3.694A pdb=" N LYS D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE D 296 " --> pdb=" O GLN D 292 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 332 Processing helix chain 'D' and resid 334 through 349 Processing helix chain 'D' and resid 352 through 365 Processing helix chain 'D' and resid 368 through 383 Processing helix chain 'D' and resid 386 through 411 Processing helix chain 'D' and resid 413 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 6.935A pdb=" N HIS B 189 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL B 148 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 187 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL B 150 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 185 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 152 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 183 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU B 223 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE B 218 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 284 through 289 removed outlier: 6.742A pdb=" N GLU A 223 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 332 removed outlier: 6.604A pdb=" N VAL A 343 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL A 326 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 341 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N HIS A 328 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 339 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER A 330 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE A 337 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 363 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 466 through 467 removed outlier: 4.302A pdb=" N TYR A 466 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N ILE A 519 " --> pdb=" O HIS A 490 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TYR A 492 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N MET A 521 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 494 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE A 491 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 588 removed outlier: 4.366A pdb=" N LYS A 585 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 331 removed outlier: 6.680A pdb=" N VAL B 343 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL B 326 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 341 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS B 328 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA B 339 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER B 330 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE B 337 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL B 365 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 466 through 467 removed outlier: 4.334A pdb=" N TYR B 466 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ILE B 519 " --> pdb=" O HIS B 490 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N TYR B 492 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N MET B 521 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 494 " --> pdb=" O MET B 521 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 585 through 588 removed outlier: 6.715A pdb=" N LYS B 585 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE B 636 " --> pdb=" O LYS B 585 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 621 through 624 removed outlier: 6.660A pdb=" N LEU C 627 " --> pdb=" O PHE C 623 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 674 through 676 Processing sheet with id=AB3, first strand: chain 'D' and resid 65 through 66 Processing sheet with id=AB4, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.493A pdb=" N ARG D 52 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE D 137 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE D 54 " --> pdb=" O PHE D 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 140 through 141 removed outlier: 6.952A pdb=" N GLU D 171 " --> pdb=" O LYS D 250 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE D 252 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE D 169 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY D 176 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP D 184 " --> pdb=" O GLY D 176 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR D 178 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU D 182 " --> pdb=" O TYR D 178 " (cutoff:3.500A) 802 hydrogen bonds defined for protein. 2190 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: 7.81 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 15780 1.13 - 1.31: 2927 1.31 - 1.48: 6619 1.48 - 1.66: 6454 1.66 - 1.84: 132 Bond restraints: 31912 Sorted by residual: bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.491 -0.103 1.00e-02 1.00e+04 1.06e+02 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.490 -0.102 1.00e-02 1.00e+04 1.04e+02 bond pdb=" NE1 TRP B 297 " pdb=" HE1 TRP B 297 " ideal model delta sigma weight residual 0.860 1.053 -0.193 2.00e-02 2.50e+03 9.32e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.506 -0.097 1.00e-02 1.00e+04 9.32e+01 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.505 -0.096 1.00e-02 1.00e+04 9.30e+01 ... (remaining 31907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.94: 57760 9.94 - 19.89: 54 19.89 - 29.83: 0 29.83 - 39.77: 8 39.77 - 49.72: 4 Bond angle restraints: 57826 Sorted by residual: angle pdb=" C TYR A 528 " pdb=" N CYS A 529 " pdb=" CA CYS A 529 " ideal model delta sigma weight residual 120.44 153.95 -33.51 1.36e+00 5.41e-01 6.07e+02 angle pdb=" C THR B 594 " pdb=" N SER B 595 " pdb=" CA SER B 595 " ideal model delta sigma weight residual 120.49 153.08 -32.59 1.42e+00 4.96e-01 5.27e+02 angle pdb=" C MET B 484 " pdb=" N LYS B 485 " pdb=" CA LYS B 485 " ideal model delta sigma weight residual 120.97 152.91 -31.94 1.82e+00 3.02e-01 3.08e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 122.46 17.41 1.00e+00 1.00e+00 3.03e+02 angle pdb=" C THR B 594 " pdb=" N SER B 595 " pdb=" H SER B 595 " ideal model delta sigma weight residual 124.91 75.19 49.72 3.00e+00 1.11e-01 2.75e+02 ... (remaining 57821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 14210 16.49 - 32.98: 456 32.98 - 49.47: 177 49.47 - 65.96: 88 65.96 - 82.45: 23 Dihedral angle restraints: 14954 sinusoidal: 8337 harmonic: 6617 Sorted by residual: dihedral pdb=" CA ALA B 469 " pdb=" C ALA B 469 " pdb=" N SER B 470 " pdb=" CA SER B 470 " ideal model delta harmonic sigma weight residual -180.00 -149.39 -30.61 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA ASN D 197 " pdb=" C ASN D 197 " pdb=" N LEU D 198 " pdb=" CA LEU D 198 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PHE A 437 " pdb=" C PHE A 437 " pdb=" N TYR A 438 " pdb=" CA TYR A 438 " ideal model delta harmonic sigma weight residual -180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 14951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 2071 0.144 - 0.289: 316 0.289 - 0.433: 9 0.433 - 0.577: 1 0.577 - 0.721: 1 Chirality restraints: 2398 Sorted by residual: chirality pdb=" C8 DEX C 801 " pdb=" C14 DEX C 801 " pdb=" C7 DEX C 801 " pdb=" C9 DEX C 801 " both_signs ideal model delta sigma weight residual False 2.68 1.96 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CB ILE B 378 " pdb=" CA ILE B 378 " pdb=" CG1 ILE B 378 " pdb=" CG2 ILE B 378 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" CA GLU D 215 " pdb=" N GLU D 215 " pdb=" C GLU D 215 " pdb=" CB GLU D 215 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 2395 not shown) Planarity restraints: 4645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 168 " -0.086 2.00e-02 2.50e+03 1.54e-01 2.37e+02 pdb=" N SER A 169 " 0.265 2.00e-02 2.50e+03 pdb=" CA SER A 169 " -0.072 2.00e-02 2.50e+03 pdb=" H SER A 169 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 578 " -0.084 2.00e-02 2.50e+03 1.53e-01 2.34e+02 pdb=" N LEU A 579 " 0.264 2.00e-02 2.50e+03 pdb=" CA LEU A 579 " -0.068 2.00e-02 2.50e+03 pdb=" H LEU A 579 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 638 " 0.084 2.00e-02 2.50e+03 1.52e-01 2.31e+02 pdb=" N ASP A 639 " -0.263 2.00e-02 2.50e+03 pdb=" CA ASP A 639 " 0.075 2.00e-02 2.50e+03 pdb=" H ASP A 639 " 0.104 2.00e-02 2.50e+03 ... (remaining 4642 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.86: 264 1.86 - 2.55: 28827 2.55 - 3.23: 99320 3.23 - 3.92: 125976 3.92 - 4.60: 198014 Nonbonded interactions: 452401 Sorted by model distance: nonbonded pdb=" H GLY B 168 " pdb=" H SER B 169 " model vdw 1.175 2.100 nonbonded pdb=" H ASP A 639 " pdb=" H HIS A 640 " model vdw 1.181 2.100 nonbonded pdb=" H VAL A 544 " pdb=" H THR A 545 " model vdw 1.199 2.100 nonbonded pdb=" H PHE B 384 " pdb=" H ILE B 385 " model vdw 1.219 2.100 nonbonded pdb=" H GLN B 532 " pdb=" H LEU B 533 " model vdw 1.219 2.100 ... (remaining 452396 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 701 or resid 801 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.200 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.060 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.023 0.156 16108 Z= 1.237 Angle : 1.854 33.507 21701 Z= 1.272 Chirality : 0.098 0.721 2398 Planarity : 0.017 0.148 2767 Dihedral : 11.224 82.452 6313 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.19 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 1928 helix: -0.19 (0.16), residues: 848 sheet: 1.43 (0.31), residues: 282 loop : 1.04 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 591 TYR 0.063 0.008 TYR D 245 PHE 0.057 0.007 PHE B 337 TRP 0.043 0.010 TRP B 162 HIS 0.012 0.003 HIS C 645 Details of bonding type rmsd covalent geometry : bond 0.02270 (16108) covalent geometry : angle 1.85378 (21701) hydrogen bonds : bond 0.18140 ( 800) hydrogen bonds : angle 7.20845 ( 2190) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 349 PHE cc_start: 0.9047 (p90) cc_final: 0.8539 (p90) REVERT: B 359 ASN cc_start: 0.7383 (m-40) cc_final: 0.7133 (p0) REVERT: B 373 ASN cc_start: 0.8187 (m-40) cc_final: 0.7926 (m-40) REVERT: C 593 MET cc_start: 0.9090 (mmp) cc_final: 0.8700 (mmm) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.3380 time to fit residues: 73.2972 Evaluate side-chains 90 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN D 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.105457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.063936 restraints weight = 126021.028| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.40 r_work: 0.3064 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16108 Z= 0.169 Angle : 0.728 19.851 21701 Z= 0.420 Chirality : 0.043 0.163 2398 Planarity : 0.004 0.037 2767 Dihedral : 8.487 89.800 2249 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.46 % Allowed : 2.24 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.19), residues: 1928 helix: 0.91 (0.17), residues: 856 sheet: 1.20 (0.30), residues: 274 loop : 0.54 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.019 0.002 TYR A 434 PHE 0.026 0.002 PHE C 715 TRP 0.027 0.002 TRP C 600 HIS 0.006 0.001 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00339 (16108) covalent geometry : angle 0.72758 (21701) hydrogen bonds : bond 0.07320 ( 800) hydrogen bonds : angle 5.59294 ( 2190) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.8855 (t) cc_final: 0.8528 (p) REVERT: B 359 ASN cc_start: 0.7673 (m-40) cc_final: 0.7308 (p0) REVERT: C 593 MET cc_start: 0.9126 (mmp) cc_final: 0.8489 (mmm) REVERT: C 600 TRP cc_start: 0.9053 (p-90) cc_final: 0.8766 (p-90) REVERT: D 211 MET cc_start: 0.6939 (mtp) cc_final: 0.6613 (mtp) outliers start: 8 outliers final: 8 residues processed: 109 average time/residue: 0.2535 time to fit residues: 44.2237 Evaluate side-chains 90 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain D residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 0.0000 chunk 166 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 156 optimal weight: 50.0000 chunk 10 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS D 56 HIS D 322 HIS D 363 HIS D 403 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.104131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062226 restraints weight = 126454.718| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.35 r_work: 0.3022 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16108 Z= 0.182 Angle : 0.610 19.105 21701 Z= 0.347 Chirality : 0.040 0.143 2398 Planarity : 0.003 0.039 2767 Dihedral : 7.401 87.570 2249 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.35 % Allowed : 2.88 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 1928 helix: 1.18 (0.18), residues: 857 sheet: 0.69 (0.29), residues: 274 loop : 0.24 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.016 0.002 TYR A 434 PHE 0.022 0.002 PHE B 349 TRP 0.019 0.002 TRP C 600 HIS 0.004 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00392 (16108) covalent geometry : angle 0.61045 (21701) hydrogen bonds : bond 0.05593 ( 800) hydrogen bonds : angle 5.07625 ( 2190) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.8920 (t) cc_final: 0.8621 (p) REVERT: C 593 MET cc_start: 0.9204 (mmp) cc_final: 0.8525 (mmm) REVERT: C 600 TRP cc_start: 0.9116 (p-90) cc_final: 0.8828 (p-90) REVERT: D 211 MET cc_start: 0.6945 (mtp) cc_final: 0.6544 (mtp) outliers start: 6 outliers final: 5 residues processed: 95 average time/residue: 0.2725 time to fit residues: 40.2450 Evaluate side-chains 88 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 30 optimal weight: 2.9990 chunk 170 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 167 optimal weight: 50.0000 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 157 optimal weight: 30.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.103759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060886 restraints weight = 125467.616| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.45 r_work: 0.2940 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16108 Z= 0.185 Angle : 0.578 18.885 21701 Z= 0.327 Chirality : 0.040 0.144 2398 Planarity : 0.003 0.038 2767 Dihedral : 7.063 89.115 2249 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.29 % Allowed : 3.22 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.19), residues: 1928 helix: 1.35 (0.18), residues: 856 sheet: 0.52 (0.30), residues: 268 loop : -0.06 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 345 TYR 0.015 0.002 TYR A 434 PHE 0.026 0.002 PHE C 606 TRP 0.012 0.001 TRP A 606 HIS 0.007 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00410 (16108) covalent geometry : angle 0.57825 (21701) hydrogen bonds : bond 0.05106 ( 800) hydrogen bonds : angle 4.83759 ( 2190) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.8931 (t) cc_final: 0.8636 (p) REVERT: C 593 MET cc_start: 0.9308 (mmp) cc_final: 0.8612 (mmm) REVERT: C 600 TRP cc_start: 0.9217 (p-90) cc_final: 0.8931 (p-90) REVERT: C 606 PHE cc_start: 0.8938 (t80) cc_final: 0.8654 (t80) REVERT: C 666 MET cc_start: 0.9659 (mtm) cc_final: 0.9201 (mtp) REVERT: D 211 MET cc_start: 0.7154 (mtp) cc_final: 0.6741 (mtp) outliers start: 5 outliers final: 4 residues processed: 96 average time/residue: 0.2497 time to fit residues: 39.2962 Evaluate side-chains 88 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.104521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.061528 restraints weight = 126027.425| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.41 r_work: 0.2960 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16108 Z= 0.122 Angle : 0.534 18.818 21701 Z= 0.301 Chirality : 0.039 0.146 2398 Planarity : 0.003 0.040 2767 Dihedral : 6.699 85.136 2249 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.46 % Allowed : 3.68 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.19), residues: 1928 helix: 1.55 (0.18), residues: 855 sheet: 0.35 (0.30), residues: 263 loop : -0.06 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 152 TYR 0.014 0.001 TYR A 434 PHE 0.017 0.001 PHE C 715 TRP 0.012 0.001 TRP A 162 HIS 0.004 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00261 (16108) covalent geometry : angle 0.53403 (21701) hydrogen bonds : bond 0.04617 ( 800) hydrogen bonds : angle 4.64376 ( 2190) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 593 MET cc_start: 0.9330 (mmp) cc_final: 0.8684 (mmm) REVERT: C 600 TRP cc_start: 0.9192 (p-90) cc_final: 0.8943 (p-90) REVERT: C 725 MET cc_start: 0.9567 (mmm) cc_final: 0.9366 (mmt) outliers start: 8 outliers final: 4 residues processed: 92 average time/residue: 0.2698 time to fit residues: 39.4496 Evaluate side-chains 85 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 145 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.103443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060291 restraints weight = 125803.963| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.36 r_work: 0.2920 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16108 Z= 0.211 Angle : 0.564 18.945 21701 Z= 0.317 Chirality : 0.040 0.147 2398 Planarity : 0.003 0.038 2767 Dihedral : 6.920 84.230 2249 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.29 % Allowed : 4.03 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.19), residues: 1928 helix: 1.51 (0.18), residues: 856 sheet: 0.22 (0.30), residues: 263 loop : -0.23 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 345 TYR 0.015 0.001 TYR A 434 PHE 0.019 0.001 PHE B 337 TRP 0.013 0.001 TRP A 162 HIS 0.007 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00475 (16108) covalent geometry : angle 0.56359 (21701) hydrogen bonds : bond 0.04858 ( 800) hydrogen bonds : angle 4.73508 ( 2190) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 MET cc_start: 0.4698 (mtp) cc_final: 0.3064 (ptp) REVERT: C 593 MET cc_start: 0.9375 (mmp) cc_final: 0.8732 (mmm) REVERT: D 211 MET cc_start: 0.7568 (mtp) cc_final: 0.6703 (mmm) outliers start: 5 outliers final: 5 residues processed: 87 average time/residue: 0.2486 time to fit residues: 35.5438 Evaluate side-chains 84 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 173 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.103963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.060870 restraints weight = 125953.835| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.41 r_work: 0.2932 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16108 Z= 0.150 Angle : 0.539 18.955 21701 Z= 0.302 Chirality : 0.039 0.142 2398 Planarity : 0.003 0.039 2767 Dihedral : 6.699 83.959 2249 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.35 % Allowed : 4.31 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.19), residues: 1928 helix: 1.64 (0.18), residues: 855 sheet: 0.15 (0.30), residues: 263 loop : -0.20 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.014 0.001 TYR A 434 PHE 0.016 0.001 PHE C 715 TRP 0.023 0.001 TRP C 600 HIS 0.006 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00331 (16108) covalent geometry : angle 0.53892 (21701) hydrogen bonds : bond 0.04550 ( 800) hydrogen bonds : angle 4.61178 ( 2190) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 560 MET cc_start: 0.8528 (mmp) cc_final: 0.8317 (mmp) REVERT: C 593 MET cc_start: 0.9383 (mmp) cc_final: 0.8737 (mmm) REVERT: C 725 MET cc_start: 0.9599 (mmm) cc_final: 0.9392 (mmt) REVERT: D 211 MET cc_start: 0.7568 (mtp) cc_final: 0.6670 (mmm) outliers start: 6 outliers final: 5 residues processed: 89 average time/residue: 0.2476 time to fit residues: 36.2359 Evaluate side-chains 86 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain D residue 415 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 95 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 185 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.103529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060430 restraints weight = 125752.907| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.38 r_work: 0.2921 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16108 Z= 0.169 Angle : 0.540 18.974 21701 Z= 0.303 Chirality : 0.039 0.144 2398 Planarity : 0.003 0.038 2767 Dihedral : 6.703 78.711 2249 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.35 % Allowed : 4.60 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.19), residues: 1928 helix: 1.65 (0.18), residues: 859 sheet: 0.09 (0.30), residues: 251 loop : -0.25 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.015 0.001 TYR A 434 PHE 0.017 0.001 PHE B 337 TRP 0.046 0.002 TRP C 600 HIS 0.006 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00378 (16108) covalent geometry : angle 0.54044 (21701) hydrogen bonds : bond 0.04540 ( 800) hydrogen bonds : angle 4.60420 ( 2190) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 MET cc_start: 0.4461 (mtp) cc_final: 0.3268 (ptp) REVERT: C 593 MET cc_start: 0.9398 (mmp) cc_final: 0.8757 (mmm) REVERT: C 725 MET cc_start: 0.9592 (mmm) cc_final: 0.9378 (mmt) REVERT: D 211 MET cc_start: 0.7565 (mtp) cc_final: 0.6627 (mmm) outliers start: 6 outliers final: 6 residues processed: 87 average time/residue: 0.2550 time to fit residues: 36.5168 Evaluate side-chains 86 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain D residue 415 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 168 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 167 optimal weight: 40.0000 chunk 97 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.102984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059580 restraints weight = 126376.805| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.41 r_work: 0.2905 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16108 Z= 0.205 Angle : 0.564 19.052 21701 Z= 0.316 Chirality : 0.040 0.147 2398 Planarity : 0.003 0.037 2767 Dihedral : 6.817 80.666 2249 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.35 % Allowed : 4.72 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.19), residues: 1928 helix: 1.64 (0.18), residues: 860 sheet: -0.01 (0.30), residues: 259 loop : -0.37 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 345 TYR 0.016 0.001 TYR A 434 PHE 0.029 0.001 PHE B 349 TRP 0.036 0.002 TRP C 600 HIS 0.007 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00465 (16108) covalent geometry : angle 0.56393 (21701) hydrogen bonds : bond 0.04721 ( 800) hydrogen bonds : angle 4.65099 ( 2190) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 MET cc_start: 0.4787 (mtp) cc_final: 0.3507 (ptp) REVERT: C 593 MET cc_start: 0.9392 (mmp) cc_final: 0.8746 (mmm) REVERT: C 666 MET cc_start: 0.9609 (mtm) cc_final: 0.9213 (mtp) REVERT: D 211 MET cc_start: 0.7736 (mtp) cc_final: 0.6758 (mmm) outliers start: 6 outliers final: 6 residues processed: 85 average time/residue: 0.2522 time to fit residues: 35.1999 Evaluate side-chains 86 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain D residue 415 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.103220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060188 restraints weight = 125667.260| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.34 r_work: 0.2909 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16108 Z= 0.167 Angle : 0.545 18.926 21701 Z= 0.304 Chirality : 0.039 0.145 2398 Planarity : 0.003 0.037 2767 Dihedral : 6.662 84.375 2249 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.35 % Allowed : 4.77 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.19), residues: 1928 helix: 1.70 (0.18), residues: 866 sheet: -0.02 (0.30), residues: 259 loop : -0.39 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.015 0.001 TYR A 434 PHE 0.018 0.001 PHE B 337 TRP 0.034 0.002 TRP C 600 HIS 0.006 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00376 (16108) covalent geometry : angle 0.54533 (21701) hydrogen bonds : bond 0.04489 ( 800) hydrogen bonds : angle 4.56640 ( 2190) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 593 MET cc_start: 0.9416 (mmp) cc_final: 0.8774 (mmm) REVERT: C 666 MET cc_start: 0.9621 (mtm) cc_final: 0.9242 (mtp) REVERT: C 725 MET cc_start: 0.9603 (mmm) cc_final: 0.9399 (mmt) REVERT: D 211 MET cc_start: 0.7663 (mtp) cc_final: 0.6647 (mmm) outliers start: 6 outliers final: 6 residues processed: 86 average time/residue: 0.2317 time to fit residues: 32.5268 Evaluate side-chains 84 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain D residue 415 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.103922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.062097 restraints weight = 125215.694| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.31 r_work: 0.2991 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16108 Z= 0.099 Angle : 0.522 18.769 21701 Z= 0.288 Chirality : 0.039 0.138 2398 Planarity : 0.003 0.038 2767 Dihedral : 6.322 85.809 2249 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.35 % Allowed : 4.83 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.19), residues: 1928 helix: 1.88 (0.18), residues: 868 sheet: 0.02 (0.30), residues: 265 loop : -0.28 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 338 TYR 0.013 0.001 TYR A 434 PHE 0.028 0.001 PHE B 349 TRP 0.030 0.001 TRP C 600 HIS 0.004 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00213 (16108) covalent geometry : angle 0.52201 (21701) hydrogen bonds : bond 0.03984 ( 800) hydrogen bonds : angle 4.38599 ( 2190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8789.68 seconds wall clock time: 149 minutes 57.46 seconds (8997.46 seconds total)