Starting phenix.real_space_refine on Wed Jun 11 07:35:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1l_41816/06_2025/8u1l_41816.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1l_41816/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u1l_41816/06_2025/8u1l_41816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1l_41816/06_2025/8u1l_41816.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1l_41816/06_2025/8u1l_41816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1l_41816/06_2025/8u1l_41816.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.40, per 1000 atoms: 0.67 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: 3.40 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.73 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: 4.68 Time building geometry restraints manager: 4.04 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: 1.250 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.320 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.820 ------------------------------------------------------------------------------- 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 : 14.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (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 TRP 0.017 0.002 TRP D 31 HIS 0.006 0.001 HIS B 314 PHE 0.013 0.001 PHE A 303 TYR 0.009 0.001 TYR B 483 ARG 0.016 0.001 ARG C 518 Details of bonding type rmsd hydrogen bonds : bond 0.20045 ( 581) hydrogen bonds : angle 7.59032 ( 1647) covalent geometry : bond 0.00465 (12813) covalent geometry : angle 1.06642 (17239) *********************** 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 : 1.679 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: 0.3132 time to fit residues: 48.7396 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 : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 39 optimal weight: 0.0970 chunk 77 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 119 optimal weight: 40.0000 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 overall best weight: 6.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN 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 445 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.054571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.040734 restraints weight = 119202.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.041433 restraints weight = 89656.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.041937 restraints weight = 74816.015| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12813 Z= 0.211 Angle : 0.666 10.026 17239 Z= 0.351 Chirality : 0.043 0.254 1894 Planarity : 0.005 0.070 2194 Dihedral : 8.747 81.083 1741 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.09 % Allowed : 12.82 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1524 helix: 0.96 (0.20), residues: 641 sheet: 0.80 (0.39), residues: 197 loop : -0.45 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 423 HIS 0.009 0.002 HIS A 314 PHE 0.014 0.002 PHE A 303 TYR 0.027 0.002 TYR A 595 ARG 0.006 0.001 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 581) hydrogen bonds : angle 5.82868 ( 1647) covalent geometry : bond 0.00453 (12813) covalent geometry : angle 0.66569 (17239) *********************** 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 115 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 1.529 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: 0.8470 (OUTLIER) cc_final: 0.8105 (p) REVERT: C 429 LEU cc_start: 0.9450 (mm) cc_final: 0.9229 (mm) REVERT: C 512 MET cc_start: 0.3767 (mmt) cc_final: 0.3561 (mmt) REVERT: C 542 MET cc_start: 0.6064 (mmp) cc_final: 0.5515 (mmp) outliers start: 29 outliers final: 15 residues processed: 107 average time/residue: 0.2806 time to fit residues: 44.6068 Evaluate side-chains 96 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 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 9 HIS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- 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 146 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 D 9 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.053449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.039717 restraints weight = 121313.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.040392 restraints weight = 92308.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.040868 restraints weight = 77251.231| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 12813 Z= 0.218 Angle : 0.637 7.618 17239 Z= 0.339 Chirality : 0.043 0.295 1894 Planarity : 0.004 0.074 2194 Dihedral : 8.729 80.385 1741 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.60 % Allowed : 12.25 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1524 helix: 0.96 (0.20), residues: 637 sheet: 0.43 (0.40), residues: 191 loop : -0.57 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 423 HIS 0.017 0.002 HIS D 9 PHE 0.016 0.002 PHE B 133 TYR 0.017 0.002 TYR A 372 ARG 0.006 0.001 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 581) hydrogen bonds : angle 5.67165 ( 1647) covalent geometry : bond 0.00460 (12813) covalent geometry : angle 0.63667 (17239) *********************** 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 134 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 84 time to evaluate : 1.652 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: A 31 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8059 (p) REVERT: A 123 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7425 (mm) REVERT: B 193 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8249 (mm) REVERT: C 512 MET cc_start: 0.3449 (mmt) cc_final: 0.3143 (mmt) REVERT: C 542 MET cc_start: 0.6420 (mmp) cc_final: 0.5910 (mmp) outliers start: 50 outliers final: 26 residues processed: 124 average time/residue: 0.2622 time to fit residues: 47.7955 Evaluate side-chains 111 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 563 CYS 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 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 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 477 HIS Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 558 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 71 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 84 optimal weight: 0.0870 overall best weight: 4.6166 ------------------------------------------------------------------------------- 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 146 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** D 9 HIS D 20 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.053993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.040795 restraints weight = 123990.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.041309 restraints weight = 92723.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.041737 restraints weight = 77460.972| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12813 Z= 0.169 Angle : 0.598 8.815 17239 Z= 0.316 Chirality : 0.043 0.309 1894 Planarity : 0.004 0.075 2194 Dihedral : 8.632 80.108 1741 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.17 % Allowed : 13.33 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1524 helix: 1.05 (0.21), residues: 634 sheet: 0.24 (0.38), residues: 199 loop : -0.56 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 7 HIS 0.006 0.001 HIS A 314 PHE 0.013 0.001 PHE B 133 TYR 0.016 0.002 TYR A 372 ARG 0.008 0.001 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 581) hydrogen bonds : angle 5.50096 ( 1647) covalent geometry : bond 0.00362 (12813) covalent geometry : angle 0.59835 (17239) *********************** 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 128 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 84 time to evaluate : 1.416 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: 0.8381 (OUTLIER) cc_final: 0.8030 (p) REVERT: A 123 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7450 (mm) REVERT: B 125 MET cc_start: 0.8692 (mmm) cc_final: 0.6979 (mmm) REVERT: B 193 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8210 (mm) REVERT: B 332 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8199 (mm) REVERT: B 622 LYS cc_start: 0.7356 (tptt) cc_final: 0.6898 (tptt) REVERT: C 542 MET cc_start: 0.6458 (mmp) cc_final: 0.6018 (mmp) outliers start: 44 outliers final: 27 residues processed: 118 average time/residue: 0.2728 time to fit residues: 46.8140 Evaluate side-chains 112 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 426 LYS 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 542 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 578 VAL 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 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 C residue 464 ILE Chi-restraints excluded: chain C residue 477 HIS 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 9 HIS 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 131 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 20.0000 chunk 33 optimal weight: 0.2980 chunk 125 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 148 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 106 optimal weight: 0.0010 overall best weight: 2.0390 ------------------------------------------------------------------------------- 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 146 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 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.054730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.040923 restraints weight = 119020.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.041657 restraints weight = 88894.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.042159 restraints weight = 73801.621| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12813 Z= 0.116 Angle : 0.581 9.624 17239 Z= 0.300 Chirality : 0.042 0.318 1894 Planarity : 0.004 0.078 2194 Dihedral : 8.457 82.436 1741 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.31 % Allowed : 14.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1524 helix: 1.19 (0.21), residues: 634 sheet: 0.36 (0.38), residues: 204 loop : -0.53 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 157 HIS 0.010 0.001 HIS D 20 PHE 0.011 0.001 PHE C 559 TYR 0.012 0.001 TYR A 372 ARG 0.006 0.000 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 581) hydrogen bonds : angle 5.28759 ( 1647) covalent geometry : bond 0.00252 (12813) covalent geometry : angle 0.58107 (17239) *********************** 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 120 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 1.602 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: 0.8370 (OUTLIER) cc_final: 0.8061 (p) REVERT: A 125 MET cc_start: 0.8260 (mmm) cc_final: 0.7603 (mmp) REVERT: B 125 MET cc_start: 0.8797 (mmm) cc_final: 0.7010 (mmm) REVERT: B 193 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8272 (mm) REVERT: B 332 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8284 (mm) REVERT: B 622 LYS cc_start: 0.7501 (tptt) cc_final: 0.7089 (tptt) REVERT: C 469 MET cc_start: 0.4669 (mmm) cc_final: 0.4419 (mmm) REVERT: C 542 MET cc_start: 0.6681 (mmp) cc_final: 0.6331 (mmp) outliers start: 32 outliers final: 19 residues processed: 108 average time/residue: 0.2823 time to fit residues: 43.8356 Evaluate side-chains 106 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 426 LYS 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 563 CYS 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 545 ASP Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 481 THR 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 108 LYS 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 143 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 146 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 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.053674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.040005 restraints weight = 122607.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.040726 restraints weight = 92126.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.041042 restraints weight = 76390.949| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12813 Z= 0.163 Angle : 0.605 10.104 17239 Z= 0.313 Chirality : 0.042 0.281 1894 Planarity : 0.004 0.079 2194 Dihedral : 8.486 83.230 1741 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.24 % Allowed : 14.05 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1524 helix: 1.08 (0.21), residues: 640 sheet: 0.30 (0.38), residues: 198 loop : -0.59 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 423 HIS 0.006 0.001 HIS A 314 PHE 0.016 0.001 PHE D 124 TYR 0.016 0.001 TYR A 372 ARG 0.005 0.000 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 581) hydrogen bonds : angle 5.31635 ( 1647) covalent geometry : bond 0.00350 (12813) covalent geometry : angle 0.60473 (17239) *********************** 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 135 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 90 time to evaluate : 1.598 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: 0.8392 (OUTLIER) cc_final: 0.8064 (p) REVERT: A 123 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7188 (mm) REVERT: A 125 MET cc_start: 0.8253 (mmm) cc_final: 0.7459 (mmp) REVERT: B 193 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8348 (mm) REVERT: B 622 LYS cc_start: 0.7600 (tptt) cc_final: 0.7190 (tptt) REVERT: C 542 MET cc_start: 0.6820 (mmp) cc_final: 0.6510 (mmp) outliers start: 45 outliers final: 32 residues processed: 121 average time/residue: 0.2785 time to fit residues: 48.4210 Evaluate side-chains 119 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 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 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 578 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 685 LEU 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 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 28 LEU Chi-restraints excluded: chain D residue 126 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 26 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 150 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 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** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 HIS D 9 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.052132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.038708 restraints weight = 125905.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.039370 restraints weight = 96813.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.039655 restraints weight = 81122.809| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 12813 Z= 0.236 Angle : 0.694 10.952 17239 Z= 0.360 Chirality : 0.044 0.387 1894 Planarity : 0.004 0.084 2194 Dihedral : 8.698 83.973 1741 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.60 % Allowed : 14.55 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1524 helix: 0.84 (0.20), residues: 637 sheet: 0.09 (0.38), residues: 197 loop : -0.75 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 7 HIS 0.008 0.001 HIS A 314 PHE 0.015 0.002 PHE B 133 TYR 0.021 0.002 TYR A 372 ARG 0.007 0.001 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 581) hydrogen bonds : angle 5.54025 ( 1647) covalent geometry : bond 0.00499 (12813) covalent geometry : angle 0.69390 (17239) *********************** 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 136 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 86 time to evaluate : 1.509 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 123 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7474 (mm) REVERT: A 125 MET cc_start: 0.8173 (mmm) cc_final: 0.7785 (mmp) REVERT: B 123 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7900 (mm) REVERT: B 193 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8454 (mm) REVERT: C 542 MET cc_start: 0.6882 (mmp) cc_final: 0.6616 (mmp) outliers start: 50 outliers final: 34 residues processed: 124 average time/residue: 0.2905 time to fit residues: 52.8062 Evaluate side-chains 121 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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 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 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 123 ILE 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 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 20 HIS Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 126 LYS 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 32 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** A 673 GLN ** B 146 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 395 GLN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.053057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.039482 restraints weight = 123784.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.040212 restraints weight = 94020.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.040550 restraints weight = 78052.486| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12813 Z= 0.156 Angle : 0.640 11.495 17239 Z= 0.329 Chirality : 0.043 0.319 1894 Planarity : 0.004 0.083 2194 Dihedral : 8.483 84.306 1741 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.03 % Allowed : 15.56 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1524 helix: 0.96 (0.21), residues: 638 sheet: -0.03 (0.37), residues: 201 loop : -0.65 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP D 7 HIS 0.006 0.001 HIS A 146 PHE 0.013 0.001 PHE D 43 TYR 0.020 0.001 TYR B 428 ARG 0.007 0.001 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 581) hydrogen bonds : angle 5.36884 ( 1647) covalent geometry : bond 0.00337 (12813) covalent geometry : angle 0.63989 (17239) *********************** 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 128 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 86 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8112 (p) REVERT: A 123 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7095 (mm) REVERT: A 125 MET cc_start: 0.8178 (mmm) cc_final: 0.7227 (mmp) REVERT: B 123 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7559 (mm) REVERT: B 193 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8409 (mm) REVERT: C 457 ASP cc_start: 0.9170 (t70) cc_final: 0.8877 (t70) REVERT: D 20 HIS cc_start: 0.7833 (OUTLIER) cc_final: 0.7290 (t-170) outliers start: 42 outliers final: 25 residues processed: 119 average time/residue: 0.2705 time to fit residues: 47.0074 Evaluate side-chains 112 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 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 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 123 ILE 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 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 20 HIS 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 95 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 55 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 84 optimal weight: 40.0000 chunk 88 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 146 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 = 0.3767 r_free = 0.3767 target = 0.053414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.039756 restraints weight = 120484.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.040512 restraints weight = 90400.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.040996 restraints weight = 74924.513| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12813 Z= 0.132 Angle : 0.647 12.027 17239 Z= 0.327 Chirality : 0.043 0.312 1894 Planarity : 0.004 0.083 2194 Dihedral : 8.381 85.912 1741 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.16 % Allowed : 16.35 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1524 helix: 1.03 (0.21), residues: 638 sheet: 0.20 (0.37), residues: 201 loop : -0.64 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 7 HIS 0.005 0.001 HIS A 146 PHE 0.013 0.001 PHE D 43 TYR 0.018 0.001 TYR B 428 ARG 0.007 0.000 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 581) hydrogen bonds : angle 5.27362 ( 1647) covalent geometry : bond 0.00290 (12813) covalent geometry : angle 0.64684 (17239) *********************** 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 116 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 1.724 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: 0.8363 (OUTLIER) cc_final: 0.8109 (p) REVERT: A 125 MET cc_start: 0.8106 (mmm) cc_final: 0.7352 (mmp) REVERT: B 114 MET cc_start: 0.9267 (mtt) cc_final: 0.8930 (mmm) REVERT: B 193 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8488 (mm) REVERT: C 457 ASP cc_start: 0.9183 (t70) cc_final: 0.8869 (t70) REVERT: C 512 MET cc_start: 0.4317 (mmt) cc_final: 0.3898 (mmt) REVERT: D 20 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7246 (t-170) outliers start: 30 outliers final: 23 residues processed: 109 average time/residue: 0.2969 time to fit residues: 47.7551 Evaluate side-chains 106 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR 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 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 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 9 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 HIS 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 46 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 146 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 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 556 GLN D 9 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.053072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.039532 restraints weight = 121121.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.040191 restraints weight = 92053.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.040494 restraints weight = 77330.555| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3599 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= 0.153 Angle : 0.672 12.466 17239 Z= 0.341 Chirality : 0.043 0.308 1894 Planarity : 0.004 0.084 2194 Dihedral : 8.423 85.990 1741 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.87 % Allowed : 16.86 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1524 helix: 0.97 (0.21), residues: 638 sheet: 0.12 (0.38), residues: 196 loop : -0.59 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 7 HIS 0.005 0.001 HIS A 146 PHE 0.018 0.001 PHE B 113 TYR 0.017 0.001 TYR A 372 ARG 0.009 0.001 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 581) hydrogen bonds : angle 5.32457 ( 1647) covalent geometry : bond 0.00334 (12813) covalent geometry : angle 0.67228 (17239) ********************** 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 109 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 1.431 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: A 31 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8152 (p) REVERT: A 123 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7512 (mm) REVERT: A 125 MET cc_start: 0.8099 (mmm) cc_final: 0.7739 (mmp) REVERT: B 114 MET cc_start: 0.9220 (mtt) cc_final: 0.8926 (mmm) REVERT: B 193 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8513 (mm) REVERT: C 457 ASP cc_start: 0.9199 (t70) cc_final: 0.8879 (t70) REVERT: C 512 MET cc_start: 0.4335 (mmt) cc_final: 0.4047 (mmt) REVERT: D 20 HIS cc_start: 0.7895 (OUTLIER) cc_final: 0.7296 (t-170) outliers start: 26 outliers final: 21 residues processed: 103 average time/residue: 0.2686 time to fit residues: 39.8732 Evaluate side-chains 106 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 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 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 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL 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 20 HIS 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 151 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 103 optimal weight: 0.0050 chunk 64 optimal weight: 6.9990 overall best weight: 4.3600 ------------------------------------------------------------------------------- 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 146 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** D 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.052596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.039019 restraints weight = 123617.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.039708 restraints weight = 93265.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.040175 restraints weight = 77870.387| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12813 Z= 0.165 Angle : 0.673 12.299 17239 Z= 0.343 Chirality : 0.043 0.305 1894 Planarity : 0.004 0.084 2194 Dihedral : 8.474 84.763 1741 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.22), residues: 1524 helix: 0.89 (0.21), residues: 644 sheet: 0.07 (0.38), residues: 195 loop : -0.60 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 7 HIS 0.007 0.001 HIS D 33 PHE 0.017 0.002 PHE B 113 TYR 0.018 0.002 TYR A 372 ARG 0.016 0.001 ARG D 36 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 581) hydrogen bonds : angle 5.36839 ( 1647) covalent geometry : bond 0.00358 (12813) covalent geometry : angle 0.67258 (17239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4967.90 seconds wall clock time: 87 minutes 22.22 seconds (5242.22 seconds total)