Starting phenix.real_space_refine on Fri Jun 27 15:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffv_29068/06_2025/8ffv_29068_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffv_29068/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ffv_29068/06_2025/8ffv_29068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffv_29068/06_2025/8ffv_29068.map" model { file = "/net/cci-nas-00/data/ceres_data/8ffv_29068/06_2025/8ffv_29068_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffv_29068/06_2025/8ffv_29068_trim.cif" } resolution = 3.01 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= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.43, per 1000 atoms: 0.49 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: 8.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 3.06 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: 12.78 Time building geometry restraints manager: 10.33 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: 2.260 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: 0.530 Extract box with map and model: 1.230 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 68.150 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.050 ------------------------------------------------------------------------------- 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 (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: 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 TRP 0.043 0.010 TRP B 162 HIS 0.012 0.003 HIS C 645 PHE 0.057 0.007 PHE B 337 TYR 0.063 0.008 TYR D 245 ARG 0.009 0.001 ARG A 591 Details of bonding type rmsd hydrogen bonds : bond 0.18140 ( 800) hydrogen bonds : angle 7.20845 ( 2190) covalent geometry : bond 0.02270 (16108) covalent geometry : angle 1.85378 (21701) *********************** 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 : 2.877 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: 0.8699 (mmm) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.8109 time to fit residues: 179.4250 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 : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 30.0000 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN B 531 GLN D 104 HIS D 269 GLN D 322 HIS D 329 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.103624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.061757 restraints weight = 125772.367| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.34 r_work: 0.2997 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16108 Z= 0.279 Angle : 0.757 19.684 21701 Z= 0.433 Chirality : 0.045 0.161 2398 Planarity : 0.004 0.035 2767 Dihedral : 8.353 88.922 2249 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.52 % Allowed : 2.30 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.85 (0.18), residues: 1928 helix: 0.81 (0.17), residues: 860 sheet: 1.04 (0.30), residues: 279 loop : 0.30 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 600 HIS 0.006 0.001 HIS A 154 PHE 0.026 0.002 PHE C 715 TYR 0.020 0.002 TYR B 309 ARG 0.004 0.001 ARG B 483 Details of bonding type rmsd hydrogen bonds : bond 0.07267 ( 800) hydrogen bonds : angle 5.67299 ( 2190) covalent geometry : bond 0.00620 (16108) covalent geometry : angle 0.75710 (21701) *********************** 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 108 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 3.689 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: 0.8904 (t) cc_final: 0.8588 (p) REVERT: C 593 MET cc_start: 0.9165 (mmp) cc_final: 0.8557 (mmm) REVERT: C 600 TRP cc_start: 0.9117 (p-90) cc_final: 0.8846 (p-90) REVERT: D 211 MET cc_start: 0.6947 (mtp) cc_final: 0.6618 (mtp) outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.6186 time to fit residues: 105.7851 Evaluate side-chains 89 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 2.756 ------------------------------------------------------------------------------- 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 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 77 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 182 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 363 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.103739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.061751 restraints weight = 127074.231| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.36 r_work: 0.2995 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16108 Z= 0.182 Angle : 0.618 19.107 21701 Z= 0.353 Chirality : 0.040 0.144 2398 Planarity : 0.003 0.038 2767 Dihedral : 7.262 85.448 2249 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.29 % Allowed : 3.16 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.94 (0.19), residues: 1928 helix: 1.21 (0.18), residues: 853 sheet: 0.63 (0.30), residues: 274 loop : 0.12 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 600 HIS 0.005 0.001 HIS B 684 PHE 0.020 0.002 PHE C 606 TYR 0.015 0.002 TYR A 434 ARG 0.002 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.05679 ( 800) hydrogen bonds : angle 5.06927 ( 2190) covalent geometry : bond 0.00392 (16108) covalent geometry : angle 0.61787 (21701) *********************** 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 92 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 2.808 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: B 222 VAL cc_start: 0.8899 (t) cc_final: 0.8608 (p) REVERT: C 593 MET cc_start: 0.9222 (mmp) cc_final: 0.8529 (mmm) REVERT: C 600 TRP cc_start: 0.9134 (p-90) cc_final: 0.8845 (p-90) REVERT: C 666 MET cc_start: 0.9584 (mtm) cc_final: 0.9144 (mtp) REVERT: D 211 MET cc_start: 0.6986 (mtp) cc_final: 0.6594 (mtp) outliers start: 5 outliers final: 5 residues processed: 92 average time/residue: 0.6037 time to fit residues: 87.5566 Evaluate side-chains 85 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 3.316 ------------------------------------------------------------------------------- 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 187 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 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 334 GLN A 490 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.103606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061316 restraints weight = 126494.296| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 4.04 r_work: 0.2911 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16108 Z= 0.195 Angle : 0.583 18.921 21701 Z= 0.331 Chirality : 0.040 0.145 2398 Planarity : 0.003 0.039 2767 Dihedral : 7.109 87.398 2249 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.40 % Allowed : 2.93 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.86 (0.19), residues: 1928 helix: 1.29 (0.18), residues: 860 sheet: 0.47 (0.30), residues: 270 loop : -0.07 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.007 0.001 HIS B 684 PHE 0.017 0.001 PHE C 715 TYR 0.014 0.001 TYR A 434 ARG 0.003 0.000 ARG D 152 Details of bonding type rmsd hydrogen bonds : bond 0.05210 ( 800) hydrogen bonds : angle 4.90688 ( 2190) covalent geometry : bond 0.00434 (16108) covalent geometry : angle 0.58297 (21701) *********************** 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 93 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 2.433 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: B 222 VAL cc_start: 0.8951 (t) cc_final: 0.8638 (p) REVERT: C 593 MET cc_start: 0.9315 (mmp) cc_final: 0.8624 (mmm) REVERT: C 600 TRP cc_start: 0.9206 (p-90) cc_final: 0.8957 (p-90) REVERT: D 211 MET cc_start: 0.6883 (mtp) cc_final: 0.6480 (mtp) outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.5246 time to fit residues: 78.5629 Evaluate side-chains 86 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 2.414 ------------------------------------------------------------------------------- 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 117 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 157 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS D 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.102962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.060768 restraints weight = 126138.869| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.98 r_work: 0.2886 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16108 Z= 0.220 Angle : 0.583 19.059 21701 Z= 0.330 Chirality : 0.040 0.148 2398 Planarity : 0.003 0.038 2767 Dihedral : 7.096 80.332 2249 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.40 % Allowed : 3.51 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.72 (0.19), residues: 1928 helix: 1.35 (0.18), residues: 860 sheet: 0.20 (0.29), residues: 274 loop : -0.29 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 162 HIS 0.007 0.001 HIS B 684 PHE 0.015 0.001 PHE C 715 TYR 0.016 0.002 TYR A 434 ARG 0.003 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.05148 ( 800) hydrogen bonds : angle 4.85532 ( 2190) covalent geometry : bond 0.00496 (16108) covalent geometry : angle 0.58317 (21701) *********************** 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 88 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 2.655 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 593 MET cc_start: 0.9369 (mmp) cc_final: 0.8700 (mmm) REVERT: C 601 MET cc_start: 0.9176 (mmm) cc_final: 0.8942 (mmm) REVERT: D 211 MET cc_start: 0.7132 (mtp) cc_final: 0.6722 (mtp) outliers start: 7 outliers final: 6 residues processed: 88 average time/residue: 0.5852 time to fit residues: 85.2240 Evaluate side-chains 82 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 2.505 ------------------------------------------------------------------------------- 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 451 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 90 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 155 optimal weight: 30.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.103705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.060658 restraints weight = 125549.628| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.39 r_work: 0.2930 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16108 Z= 0.140 Angle : 0.543 18.910 21701 Z= 0.306 Chirality : 0.039 0.142 2398 Planarity : 0.003 0.039 2767 Dihedral : 6.842 80.742 2249 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.40 % Allowed : 3.97 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.84 (0.19), residues: 1928 helix: 1.51 (0.18), residues: 859 sheet: 0.10 (0.29), residues: 269 loop : -0.24 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.014 0.001 HIS B 633 PHE 0.016 0.001 PHE C 715 TYR 0.014 0.001 TYR A 434 ARG 0.002 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 800) hydrogen bonds : angle 4.69464 ( 2190) covalent geometry : bond 0.00308 (16108) covalent geometry : angle 0.54334 (21701) *********************** 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 88 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 2.749 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: C 593 MET cc_start: 0.9361 (mmp) cc_final: 0.8732 (mmm) REVERT: C 601 MET cc_start: 0.9160 (mmm) cc_final: 0.8955 (mmm) outliers start: 7 outliers final: 7 residues processed: 87 average time/residue: 0.7067 time to fit residues: 98.5665 Evaluate side-chains 85 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 4.157 ------------------------------------------------------------------------------- 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 B residue 451 GLU Chi-restraints excluded: chain C residue 560 MET 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 101 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 133 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 154 optimal weight: 40.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.103765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060704 restraints weight = 125776.115| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.39 r_work: 0.2945 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16108 Z= 0.145 Angle : 0.535 18.939 21701 Z= 0.300 Chirality : 0.039 0.142 2398 Planarity : 0.003 0.039 2767 Dihedral : 6.695 76.304 2249 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.35 % Allowed : 4.37 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.89 (0.19), residues: 1928 helix: 1.63 (0.18), residues: 859 sheet: -0.02 (0.30), residues: 258 loop : -0.25 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.006 0.001 HIS B 684 PHE 0.016 0.001 PHE C 715 TYR 0.014 0.001 TYR A 434 ARG 0.002 0.000 ARG A 620 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 800) hydrogen bonds : angle 4.60078 ( 2190) covalent geometry : bond 0.00323 (16108) covalent geometry : angle 0.53525 (21701) *********************** 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 88 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 2.636 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: 0.9382 (mmp) cc_final: 0.8741 (mmm) REVERT: D 211 MET cc_start: 0.7617 (mtp) cc_final: 0.6864 (mmm) outliers start: 6 outliers final: 6 residues processed: 87 average time/residue: 0.6826 time to fit residues: 96.1488 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 : 2.858 ------------------------------------------------------------------------------- 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 560 MET Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 126 optimal weight: 30.0000 chunk 49 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.103445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060819 restraints weight = 126053.314| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.98 r_work: 0.2884 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16108 Z= 0.158 Angle : 0.538 18.904 21701 Z= 0.301 Chirality : 0.039 0.150 2398 Planarity : 0.003 0.038 2767 Dihedral : 6.692 79.345 2249 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.35 % Allowed : 4.66 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.91 (0.19), residues: 1928 helix: 1.67 (0.18), residues: 859 sheet: 0.00 (0.30), residues: 252 loop : -0.28 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 600 HIS 0.006 0.001 HIS B 684 PHE 0.016 0.001 PHE C 715 TYR 0.014 0.001 TYR A 434 ARG 0.002 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 800) hydrogen bonds : angle 4.59810 ( 2190) covalent geometry : bond 0.00353 (16108) covalent geometry : angle 0.53804 (21701) *********************** 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 89 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 2.567 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: C 593 MET cc_start: 0.9407 (mmp) cc_final: 0.8755 (mmm) REVERT: C 725 MET cc_start: 0.9573 (mmm) cc_final: 0.9354 (mmt) REVERT: D 211 MET cc_start: 0.7458 (mtp) cc_final: 0.6573 (mmm) outliers start: 6 outliers final: 6 residues processed: 88 average time/residue: 0.5679 time to fit residues: 80.2698 Evaluate side-chains 88 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 2.501 ------------------------------------------------------------------------------- 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 B residue 451 GLU Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 40 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.103651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060725 restraints weight = 125487.335| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.36 r_work: 0.2920 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16108 Z= 0.144 Angle : 0.534 18.874 21701 Z= 0.299 Chirality : 0.039 0.142 2398 Planarity : 0.003 0.038 2767 Dihedral : 6.627 83.654 2249 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.35 % Allowed : 4.95 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.89 (0.19), residues: 1928 helix: 1.70 (0.18), residues: 866 sheet: -0.20 (0.29), residues: 265 loop : -0.31 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 600 HIS 0.005 0.001 HIS B 684 PHE 0.019 0.001 PHE C 606 TYR 0.014 0.001 TYR A 434 ARG 0.002 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 800) hydrogen bonds : angle 4.55097 ( 2190) covalent geometry : bond 0.00321 (16108) covalent geometry : angle 0.53375 (21701) *********************** 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 89 residues out of total 1739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 2.470 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: C 593 MET cc_start: 0.9413 (mmp) cc_final: 0.8760 (mmm) REVERT: D 211 MET cc_start: 0.7619 (mtp) cc_final: 0.6658 (mmm) outliers start: 6 outliers final: 5 residues processed: 88 average time/residue: 0.5397 time to fit residues: 76.5583 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 : 2.492 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 128 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 182 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 164 optimal weight: 40.0000 chunk 100 optimal weight: 1.9990 chunk 170 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 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 = 0.4033 r_free = 0.4033 target = 0.103408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060190 restraints weight = 125479.229| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.40 r_work: 0.2909 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16108 Z= 0.168 Angle : 0.543 18.924 21701 Z= 0.304 Chirality : 0.039 0.144 2398 Planarity : 0.003 0.038 2767 Dihedral : 6.709 89.853 2249 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.29 % Allowed : 5.06 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.88 (0.19), residues: 1928 helix: 1.73 (0.18), residues: 867 sheet: -0.14 (0.30), residues: 262 loop : -0.38 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 600 HIS 0.006 0.001 HIS B 684 PHE 0.015 0.001 PHE C 715 TYR 0.015 0.001 TYR A 434 ARG 0.002 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 800) hydrogen bonds : angle 4.56941 ( 2190) covalent geometry : bond 0.00377 (16108) covalent geometry : angle 0.54299 (21701) ********************** 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: 5 poor density : 81 time to evaluate : 2.854 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: C 593 MET cc_start: 0.9427 (mmp) cc_final: 0.8789 (mmm) REVERT: D 211 MET cc_start: 0.7720 (mtp) cc_final: 0.6745 (mmm) outliers start: 5 outliers final: 5 residues processed: 85 average time/residue: 0.5948 time to fit residues: 81.7936 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 : 2.861 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 36 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.104131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061169 restraints weight = 125224.027| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.41 r_work: 0.2937 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16108 Z= 0.105 Angle : 0.524 18.811 21701 Z= 0.290 Chirality : 0.039 0.137 2398 Planarity : 0.003 0.038 2767 Dihedral : 6.412 88.588 2249 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.29 % Allowed : 5.18 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 1.03 (0.19), residues: 1928 helix: 1.90 (0.18), residues: 867 sheet: -0.12 (0.30), residues: 262 loop : -0.33 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 600 HIS 0.005 0.001 HIS B 684 PHE 0.016 0.001 PHE C 715 TYR 0.013 0.001 TYR A 434 ARG 0.003 0.000 ARG A 620 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 800) hydrogen bonds : angle 4.41822 ( 2190) covalent geometry : bond 0.00225 (16108) covalent geometry : angle 0.52389 (21701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17035.09 seconds wall clock time: 294 minutes 48.21 seconds (17688.21 seconds total)