Starting phenix.real_space_refine on Sat Oct 11 06:58:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1l_41816/10_2025/8u1l_41816.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1l_41816/10_2025/8u1l_41816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u1l_41816/10_2025/8u1l_41816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1l_41816/10_2025/8u1l_41816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u1l_41816/10_2025/8u1l_41816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1l_41816/10_2025/8u1l_41816.map" } resolution = 3.7 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= 0.003 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 61 5.16 5 C 7959 2.51 5 N 2133 2.21 5 O 2433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12595 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5171 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 14, 'TRANS': 623} Chain breaks: 1 Chain: "B" Number of atoms: 5171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5171 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 14, 'TRANS': 623} Chain breaks: 1 Chain: "C" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1483 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain breaks: 1 Chain: "D" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 706 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain breaks: 1 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} Time building chain proxies: 2.89, per 1000 atoms: 0.23 Number of scatterers: 12595 At special positions: 0 Unit cell: (134.706, 117.546, 100.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 61 16.00 P 7 15.00 Mg 2 11.99 O 2433 8.00 N 2133 7.00 C 7959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 490.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2936 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 47.7% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.952A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 61 removed outlier: 4.081A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.630A pdb=" N LEU A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 187 through 193 removed outlier: 4.186A pdb=" N ALA A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLU A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 192 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 397 through 420 removed outlier: 3.815A pdb=" N LYS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 443 removed outlier: 6.394A pdb=" N LYS A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 453 removed outlier: 3.810A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 489 through 495 removed outlier: 3.513A pdb=" N ASN A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 removed outlier: 4.474A pdb=" N VAL A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'A' and resid 545 through 571 removed outlier: 5.142A pdb=" N GLY A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 612 through 617 removed outlier: 3.630A pdb=" N MET A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 631 through 644 Processing helix chain 'A' and resid 647 through 665 Processing helix chain 'A' and resid 671 through 688 removed outlier: 3.694A pdb=" N HIS A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 38 through 59 removed outlier: 3.514A pdb=" N GLU B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 removed outlier: 6.653A pdb=" N SER B 63 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 187 through 193 removed outlier: 3.629A pdb=" N ALA B 190 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU B 191 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.598A pdb=" N ILE B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.605A pdb=" N LEU B 373 " --> pdb=" O PRO B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 419 removed outlier: 3.991A pdb=" N LYS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 443 removed outlier: 6.462A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS B 441 " --> pdb=" O LYS B 437 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 452 removed outlier: 3.990A pdb=" N ASP B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 474 Processing helix chain 'B' and resid 489 through 495 Processing helix chain 'B' and resid 498 through 505 removed outlier: 4.345A pdb=" N VAL B 502 " --> pdb=" O PHE B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 3.922A pdb=" N GLN B 523 " --> pdb=" O TYR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 571 removed outlier: 5.565A pdb=" N GLY B 561 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 removed outlier: 3.694A pdb=" N ARG B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 644 Processing helix chain 'B' and resid 647 through 665 Processing helix chain 'B' and resid 671 through 688 removed outlier: 3.783A pdb=" N HIS B 675 " --> pdb=" O GLU B 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 441 through 462 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 526 through 544 Processing helix chain 'C' and resid 553 through 564 Processing helix chain 'C' and resid 569 through 573 Processing helix chain 'C' and resid 578 through 589 Processing helix chain 'C' and resid 598 through 612 removed outlier: 3.542A pdb=" N SER C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 48 Processing helix chain 'D' and resid 103 through 112 removed outlier: 3.642A pdb=" N LYS D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU D 109 " --> pdb=" O MET D 105 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 119 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.858A pdb=" N SER B 147 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 178 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 85 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 73 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 75 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 217 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.652A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.584A pdb=" N VAL A 217 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 278 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 178 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 148 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 322 removed outlier: 6.803A pdb=" N VAL A 334 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 317 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 332 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N HIS A 319 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA A 330 " --> pdb=" O HIS A 319 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER A 321 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE A 328 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET A 362 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL A 356 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA7, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 579 removed outlier: 6.903A pdb=" N LYS A 576 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE A 627 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 578 " --> pdb=" O ILE A 627 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 359 through 362 removed outlier: 5.226A pdb=" N PHE B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 356 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET B 362 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B 351 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL B 380 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS B 353 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N SER B 382 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR B 355 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 316 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 359 through 362 removed outlier: 5.226A pdb=" N PHE B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 356 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET B 362 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B 351 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL B 380 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS B 353 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N SER B 382 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR B 355 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 316 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AB3, first strand: chain 'B' and resid 510 through 512 removed outlier: 8.737A pdb=" N VAL B 510 " --> pdb=" O HIS B 481 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 483 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N MET B 512 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 485 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 576 through 579 removed outlier: 6.697A pdb=" N LYS B 576 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE B 627 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 578 " --> pdb=" O ILE B 627 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 426 through 428 removed outlier: 3.649A pdb=" N PHE C 475 " --> pdb=" O LYS C 483 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4108 1.34 - 1.46: 2486 1.46 - 1.58: 6104 1.58 - 1.70: 10 1.70 - 1.82: 105 Bond restraints: 12813 Sorted by residual: bond pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " ideal model delta sigma weight residual 1.443 1.219 0.224 1.00e-02 1.00e+04 5.02e+02 bond pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 1.443 1.224 0.219 1.00e-02 1.00e+04 4.80e+02 bond pdb=" C4' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.444 1.397 0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C3' ATP B 801 " pdb=" O3' ATP B 801 " ideal model delta sigma weight residual 1.423 1.378 0.045 1.10e-02 8.26e+03 1.66e+01 bond pdb=" C3' ATP A 801 " pdb=" O3' ATP A 801 " ideal model delta sigma weight residual 1.423 1.378 0.045 1.10e-02 8.26e+03 1.64e+01 ... (remaining 12808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.99: 17202 6.99 - 13.99: 23 13.99 - 20.98: 6 20.98 - 27.98: 0 27.98 - 34.97: 8 Bond angle restraints: 17239 Sorted by residual: angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 156.24 -34.97 1.00e+00 1.00e+00 1.22e+03 angle pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 121.27 155.38 -34.11 1.00e+00 1.00e+00 1.16e+03 angle pdb=" C3' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" C5' ATP B 801 " ideal model delta sigma weight residual 115.19 83.09 32.10 1.76e+00 3.23e-01 3.33e+02 angle pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " ideal model delta sigma weight residual 115.19 85.19 30.00 1.76e+00 3.23e-01 2.91e+02 angle pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 108.83 140.57 -31.74 2.33e+00 1.85e-01 1.86e+02 ... (remaining 17234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 7120 18.23 - 36.47: 633 36.47 - 54.70: 120 54.70 - 72.93: 30 72.93 - 91.17: 13 Dihedral angle restraints: 7916 sinusoidal: 3380 harmonic: 4536 Sorted by residual: dihedral pdb=" CA MET A 475 " pdb=" C MET A 475 " pdb=" N LYS A 476 " pdb=" CA LYS A 476 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA MET B 93 " pdb=" C MET B 93 " pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LEU C 598 " pdb=" C LEU C 598 " pdb=" N PHE C 599 " pdb=" CA PHE C 599 " ideal model delta harmonic sigma weight residual 180.00 -157.70 -22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1816 0.099 - 0.198: 71 0.198 - 0.297: 4 0.297 - 0.396: 1 0.396 - 0.495: 2 Chirality restraints: 1894 Sorted by residual: chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.99 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" C4' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" C5' ATP B 801 " pdb=" O4' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.97 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CG LEU C 538 " pdb=" CB LEU C 538 " pdb=" CD1 LEU C 538 " pdb=" CD2 LEU C 538 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 1891 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 542 " 0.089 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO A 543 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 112 " 0.072 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO D 113 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 542 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO B 543 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " -0.032 5.00e-02 4.00e+02 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 169 2.54 - 3.13: 9989 3.13 - 3.72: 20723 3.72 - 4.31: 28318 4.31 - 4.90: 45173 Nonbonded interactions: 104372 Sorted by model distance: nonbonded pdb=" O3G ATP B 801 " pdb="MG MG B 802 " model vdw 1.947 2.170 nonbonded pdb=" O3A ATP A 801 " pdb="MG MG A 802 " model vdw 2.030 2.170 nonbonded pdb=" O1G ATP A 801 " pdb="MG MG A 802 " model vdw 2.099 2.170 nonbonded pdb=" OH TYR A 425 " pdb=" O LEU A 453 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR A 372 " pdb=" OD2 ASP A 443 " model vdw 2.206 3.040 ... (remaining 104367 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.050 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 : 0.005 0.224 12813 Z= 0.346 Angle : 1.066 34.971 17239 Z= 0.636 Chirality : 0.046 0.495 1894 Planarity : 0.005 0.128 2194 Dihedral : 14.738 91.169 4980 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.22), residues: 1524 helix: 0.86 (0.21), residues: 643 sheet: 0.85 (0.37), residues: 201 loop : -0.42 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 518 TYR 0.009 0.001 TYR B 483 PHE 0.013 0.001 PHE A 303 TRP 0.017 0.002 TRP D 31 HIS 0.006 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00465 (12813) covalent geometry : angle 1.06642 (17239) hydrogen bonds : bond 0.20045 ( 581) hydrogen bonds : angle 7.59032 ( 1647) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.534 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: A 512 MET cc_start: 0.8046 (mmm) cc_final: 0.7781 (mmm) REVERT: B 475 MET cc_start: 0.4892 (mmt) cc_final: 0.4605 (mmt) REVERT: C 457 ASP cc_start: 0.9102 (t70) cc_final: 0.8640 (t0) REVERT: D 105 MET cc_start: 0.3884 (tpp) cc_final: 0.1675 (ptm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1332 time to fit residues: 20.6869 Evaluate side-chains 94 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 GLN C 556 GLN D 9 HIS ** D 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 HIS D 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.053568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.040016 restraints weight = 122109.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.040512 restraints weight = 93117.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.041143 restraints weight = 79516.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.041389 restraints weight = 70473.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.041394 restraints weight = 65813.976| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 12813 Z= 0.270 Angle : 0.727 9.579 17239 Z= 0.385 Chirality : 0.045 0.258 1894 Planarity : 0.005 0.071 2194 Dihedral : 8.888 81.319 1741 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.67 % Allowed : 12.82 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.21), residues: 1524 helix: 0.77 (0.20), residues: 642 sheet: 0.70 (0.40), residues: 192 loop : -0.54 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 638 TYR 0.024 0.002 TYR A 595 PHE 0.016 0.002 PHE A 303 TRP 0.020 0.002 TRP C 423 HIS 0.011 0.002 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00572 (12813) covalent geometry : angle 0.72719 (17239) hydrogen bonds : bond 0.04921 ( 581) hydrogen bonds : angle 5.97696 ( 1647) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.520 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: A 31 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8063 (p) REVERT: B 193 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8057 (mm) REVERT: C 429 LEU cc_start: 0.9442 (mm) cc_final: 0.9222 (mm) REVERT: C 512 MET cc_start: 0.4067 (mmt) cc_final: 0.3837 (mmt) REVERT: C 542 MET cc_start: 0.6099 (mmp) cc_final: 0.5553 (mmp) outliers start: 37 outliers final: 16 residues processed: 113 average time/residue: 0.1122 time to fit residues: 18.8995 Evaluate side-chains 99 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 8.9990 chunk 52 optimal weight: 30.0000 chunk 127 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 139 optimal weight: 40.0000 chunk 60 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.053144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.039665 restraints weight = 123532.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.040316 restraints weight = 93414.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.040613 restraints weight = 78178.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.040996 restraints weight = 70847.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.041286 restraints weight = 65712.390| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 12813 Z= 0.215 Angle : 0.639 7.502 17239 Z= 0.341 Chirality : 0.043 0.309 1894 Planarity : 0.004 0.061 2194 Dihedral : 8.776 81.013 1741 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.60 % Allowed : 13.11 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.21), residues: 1524 helix: 0.88 (0.20), residues: 637 sheet: 0.23 (0.38), residues: 197 loop : -0.67 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 39 TYR 0.018 0.002 TYR A 372 PHE 0.015 0.002 PHE B 133 TRP 0.019 0.002 TRP C 423 HIS 0.008 0.002 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00458 (12813) covalent geometry : angle 0.63941 (17239) hydrogen bonds : bond 0.04295 ( 581) hydrogen bonds : angle 5.69272 ( 1647) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 83 time to evaluate : 0.537 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: A 31 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8101 (p) REVERT: A 123 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7392 (mm) REVERT: B 125 MET cc_start: 0.8700 (mmm) cc_final: 0.7169 (mmm) REVERT: B 622 LYS cc_start: 0.7354 (tptt) cc_final: 0.6908 (tptt) REVERT: C 457 ASP cc_start: 0.9084 (t70) cc_final: 0.8799 (t70) REVERT: C 512 MET cc_start: 0.3758 (mmt) cc_final: 0.3487 (mmt) REVERT: C 542 MET cc_start: 0.6433 (mmp) cc_final: 0.5927 (mmp) outliers start: 50 outliers final: 25 residues processed: 123 average time/residue: 0.1134 time to fit residues: 20.6150 Evaluate side-chains 107 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 20 HIS Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 2.9990 chunk 135 optimal weight: 20.0000 chunk 139 optimal weight: 50.0000 chunk 57 optimal weight: 40.0000 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.054069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.040632 restraints weight = 124607.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.041264 restraints weight = 94087.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.041607 restraints weight = 78973.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.041986 restraints weight = 69735.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.042222 restraints weight = 65331.093| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12813 Z= 0.145 Angle : 0.584 8.391 17239 Z= 0.308 Chirality : 0.042 0.322 1894 Planarity : 0.004 0.069 2194 Dihedral : 8.578 81.145 1741 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.10 % Allowed : 13.90 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.22), residues: 1524 helix: 1.10 (0.21), residues: 634 sheet: 0.21 (0.38), residues: 199 loop : -0.57 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 39 TYR 0.014 0.001 TYR A 372 PHE 0.012 0.001 PHE B 133 TRP 0.014 0.002 TRP B 157 HIS 0.006 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00314 (12813) covalent geometry : angle 0.58375 (17239) hydrogen bonds : bond 0.03703 ( 581) hydrogen bonds : angle 5.46960 ( 1647) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 84 time to evaluate : 0.596 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: A 31 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8034 (p) REVERT: A 123 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7210 (mm) REVERT: A 125 MET cc_start: 0.8239 (mmm) cc_final: 0.7544 (mmp) REVERT: B 125 MET cc_start: 0.8748 (mmm) cc_final: 0.7449 (mmm) REVERT: B 193 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8216 (mm) REVERT: B 332 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8225 (mm) REVERT: B 622 LYS cc_start: 0.7612 (tptt) cc_final: 0.7200 (tptt) REVERT: C 512 MET cc_start: 0.3608 (mmt) cc_final: 0.3271 (mmt) REVERT: C 542 MET cc_start: 0.6615 (mmp) cc_final: 0.6192 (mmp) REVERT: D 20 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7115 (t-90) outliers start: 43 outliers final: 23 residues processed: 118 average time/residue: 0.1288 time to fit residues: 22.1033 Evaluate side-chains 107 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 HIS Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 9 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.052107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.038725 restraints weight = 127370.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.039354 restraints weight = 97397.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.039706 restraints weight = 81936.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.040208 restraints weight = 71900.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.040376 restraints weight = 67187.978| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 12813 Z= 0.246 Angle : 0.681 9.960 17239 Z= 0.356 Chirality : 0.043 0.244 1894 Planarity : 0.004 0.077 2194 Dihedral : 8.787 82.871 1741 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.96 % Allowed : 13.98 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.21), residues: 1524 helix: 0.84 (0.20), residues: 632 sheet: 0.07 (0.38), residues: 197 loop : -0.79 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 638 TYR 0.020 0.002 TYR A 372 PHE 0.016 0.002 PHE B 133 TRP 0.019 0.002 TRP D 7 HIS 0.010 0.002 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00518 (12813) covalent geometry : angle 0.68056 (17239) hydrogen bonds : bond 0.04080 ( 581) hydrogen bonds : angle 5.63533 ( 1647) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 79 time to evaluate : 0.567 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: B 193 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8299 (mm) outliers start: 55 outliers final: 38 residues processed: 119 average time/residue: 0.1282 time to fit residues: 22.3495 Evaluate side-chains 112 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 40.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.052867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.039369 restraints weight = 122592.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.040010 restraints weight = 93267.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.040412 restraints weight = 78477.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.040735 restraints weight = 70585.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.040993 restraints weight = 65652.374| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12813 Z= 0.156 Angle : 0.618 10.101 17239 Z= 0.319 Chirality : 0.043 0.343 1894 Planarity : 0.004 0.081 2194 Dihedral : 8.568 83.807 1741 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.17 % Allowed : 15.71 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.15 (0.22), residues: 1524 helix: 1.02 (0.21), residues: 633 sheet: -0.02 (0.37), residues: 199 loop : -0.67 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 39 TYR 0.016 0.001 TYR A 372 PHE 0.015 0.001 PHE D 124 TRP 0.015 0.002 TRP D 7 HIS 0.006 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00337 (12813) covalent geometry : angle 0.61800 (17239) hydrogen bonds : bond 0.03664 ( 581) hydrogen bonds : angle 5.44351 ( 1647) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 0.558 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: A 31 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8046 (p) REVERT: A 125 MET cc_start: 0.8361 (mmm) cc_final: 0.7530 (mmp) REVERT: B 114 MET cc_start: 0.9198 (mtt) cc_final: 0.8871 (mmm) REVERT: B 193 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8357 (mm) REVERT: C 469 MET cc_start: 0.5107 (mmm) cc_final: 0.4790 (mmm) outliers start: 44 outliers final: 28 residues processed: 116 average time/residue: 0.1312 time to fit residues: 22.2429 Evaluate side-chains 110 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 HIS Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 10 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.052534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.039084 restraints weight = 124546.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.039729 restraints weight = 95503.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.040095 restraints weight = 80196.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.040585 restraints weight = 70257.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.040718 restraints weight = 65602.792| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12813 Z= 0.179 Angle : 0.636 10.946 17239 Z= 0.332 Chirality : 0.043 0.305 1894 Planarity : 0.004 0.083 2194 Dihedral : 8.570 84.943 1741 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.88 % Allowed : 16.28 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.22), residues: 1524 helix: 1.03 (0.21), residues: 633 sheet: -0.05 (0.37), residues: 199 loop : -0.66 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 638 TYR 0.019 0.002 TYR B 428 PHE 0.013 0.002 PHE B 133 TRP 0.016 0.002 TRP D 7 HIS 0.009 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00381 (12813) covalent geometry : angle 0.63600 (17239) hydrogen bonds : bond 0.03722 ( 581) hydrogen bonds : angle 5.44691 ( 1647) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 0.583 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: A 31 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8056 (p) REVERT: A 125 MET cc_start: 0.8233 (mmm) cc_final: 0.7386 (mmp) REVERT: B 193 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8407 (mm) REVERT: C 542 MET cc_start: 0.6617 (mmp) cc_final: 0.5863 (mmp) REVERT: C 581 MET cc_start: 0.8122 (mmt) cc_final: 0.7496 (tmm) outliers start: 40 outliers final: 27 residues processed: 111 average time/residue: 0.1232 time to fit residues: 20.1078 Evaluate side-chains 107 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.052695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.039135 restraints weight = 121777.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.039811 restraints weight = 92310.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.040248 restraints weight = 77405.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.040426 restraints weight = 69265.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.040807 restraints weight = 65257.897| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12813 Z= 0.150 Angle : 0.631 11.740 17239 Z= 0.325 Chirality : 0.042 0.330 1894 Planarity : 0.004 0.084 2194 Dihedral : 8.511 85.284 1741 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.74 % Allowed : 16.79 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.22), residues: 1524 helix: 1.08 (0.21), residues: 633 sheet: -0.07 (0.37), residues: 201 loop : -0.60 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 39 TYR 0.016 0.001 TYR A 372 PHE 0.015 0.001 PHE B 113 TRP 0.044 0.002 TRP D 7 HIS 0.005 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00325 (12813) covalent geometry : angle 0.63084 (17239) hydrogen bonds : bond 0.03551 ( 581) hydrogen bonds : angle 5.39625 ( 1647) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 0.531 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 31 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8088 (p) REVERT: A 125 MET cc_start: 0.8242 (mmm) cc_final: 0.7389 (mmp) REVERT: B 193 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8392 (mm) REVERT: C 457 ASP cc_start: 0.9109 (t70) cc_final: 0.8784 (t70) REVERT: C 542 MET cc_start: 0.6683 (mmp) cc_final: 0.6424 (mmp) REVERT: C 581 MET cc_start: 0.8121 (mmt) cc_final: 0.7810 (ptp) REVERT: D 39 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8295 (tmm-80) outliers start: 38 outliers final: 29 residues processed: 113 average time/residue: 0.1214 time to fit residues: 20.3570 Evaluate side-chains 111 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.053233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.039590 restraints weight = 121475.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.040291 restraints weight = 91642.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.040596 restraints weight = 76467.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.041062 restraints weight = 69162.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.041188 restraints weight = 64003.186| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12813 Z= 0.130 Angle : 0.623 12.129 17239 Z= 0.320 Chirality : 0.042 0.330 1894 Planarity : 0.004 0.083 2194 Dihedral : 8.434 85.965 1741 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.52 % Allowed : 16.50 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.22), residues: 1524 helix: 1.10 (0.21), residues: 639 sheet: 0.19 (0.37), residues: 203 loop : -0.54 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 39 TYR 0.015 0.001 TYR A 372 PHE 0.017 0.001 PHE B 113 TRP 0.062 0.003 TRP D 7 HIS 0.008 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00284 (12813) covalent geometry : angle 0.62308 (17239) hydrogen bonds : bond 0.03392 ( 581) hydrogen bonds : angle 5.31857 ( 1647) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.540 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: A 31 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8165 (p) REVERT: A 125 MET cc_start: 0.8140 (mmm) cc_final: 0.7350 (mmp) REVERT: B 193 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8430 (mm) REVERT: C 457 ASP cc_start: 0.9135 (t70) cc_final: 0.8766 (t70) REVERT: C 542 MET cc_start: 0.6627 (mmp) cc_final: 0.6394 (mmp) REVERT: C 581 MET cc_start: 0.8182 (mmt) cc_final: 0.7875 (ptp) REVERT: D 39 ARG cc_start: 0.8487 (ttp80) cc_final: 0.8244 (tmm-80) REVERT: D 105 MET cc_start: 0.6892 (tpp) cc_final: 0.6370 (mtp) outliers start: 35 outliers final: 27 residues processed: 108 average time/residue: 0.1164 time to fit residues: 18.9001 Evaluate side-chains 109 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 118 optimal weight: 20.0000 chunk 119 optimal weight: 40.0000 chunk 108 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 97 optimal weight: 0.0370 chunk 80 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 overall best weight: 4.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN D 9 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.052695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.039092 restraints weight = 122425.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.039784 restraints weight = 93105.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.040206 restraints weight = 77830.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.040384 restraints weight = 69714.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.040624 restraints weight = 65710.514| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12813 Z= 0.157 Angle : 0.647 12.380 17239 Z= 0.332 Chirality : 0.043 0.332 1894 Planarity : 0.004 0.084 2194 Dihedral : 8.480 86.135 1741 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.23 % Allowed : 16.64 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.28 (0.22), residues: 1524 helix: 1.03 (0.21), residues: 639 sheet: 0.15 (0.38), residues: 196 loop : -0.53 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 39 TYR 0.017 0.001 TYR A 372 PHE 0.017 0.002 PHE B 113 TRP 0.041 0.002 TRP D 7 HIS 0.009 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00340 (12813) covalent geometry : angle 0.64711 (17239) hydrogen bonds : bond 0.03454 ( 581) hydrogen bonds : angle 5.34542 ( 1647) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.517 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: A 31 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8191 (p) REVERT: A 125 MET cc_start: 0.8148 (mmm) cc_final: 0.7325 (mmp) REVERT: B 193 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8451 (mm) REVERT: C 512 MET cc_start: 0.3813 (mmt) cc_final: 0.3469 (mmt) REVERT: C 542 MET cc_start: 0.6705 (mmp) cc_final: 0.6299 (mmp) REVERT: D 39 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8323 (tmm-80) REVERT: D 109 GLU cc_start: 0.6250 (mp0) cc_final: 0.5901 (mp0) outliers start: 31 outliers final: 28 residues processed: 107 average time/residue: 0.1196 time to fit residues: 19.0558 Evaluate side-chains 110 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 22 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN D 9 HIS D 20 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.052608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.039121 restraints weight = 124447.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.039769 restraints weight = 95104.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.040190 restraints weight = 79571.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.040527 restraints weight = 71455.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.040635 restraints weight = 66419.815| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12813 Z= 0.157 Angle : 0.655 12.215 17239 Z= 0.336 Chirality : 0.043 0.342 1894 Planarity : 0.004 0.084 2194 Dihedral : 8.477 85.626 1741 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.38 % Allowed : 16.86 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.22), residues: 1524 helix: 0.93 (0.21), residues: 645 sheet: 0.15 (0.38), residues: 196 loop : -0.57 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 39 TYR 0.017 0.001 TYR A 372 PHE 0.016 0.001 PHE B 113 TRP 0.034 0.002 TRP D 7 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00338 (12813) covalent geometry : angle 0.65545 (17239) hydrogen bonds : bond 0.03499 ( 581) hydrogen bonds : angle 5.36057 ( 1647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2856.39 seconds wall clock time: 50 minutes 12.25 seconds (3012.25 seconds total)