Starting phenix.real_space_refine on Tue Jul 29 09:29:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pek_20327/07_2025/6pek_20327.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pek_20327/07_2025/6pek_20327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pek_20327/07_2025/6pek_20327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pek_20327/07_2025/6pek_20327.map" model { file = "/net/cci-nas-00/data/ceres_data/6pek_20327/07_2025/6pek_20327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pek_20327/07_2025/6pek_20327.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 38 5.16 5 Be 4 3.05 5 C 6949 2.51 5 N 1953 2.21 5 O 2136 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11106 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2206 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 270} Chain breaks: 1 Chain: "B" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2238 Classifications: {'peptide': 288} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 275} Chain: "C" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2238 Classifications: {'peptide': 288} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 275} Chain: "D" Number of atoms: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2278 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 280} Chain: "E" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1886 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 232} Chain breaks: 2 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 105 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.60, per 1000 atoms: 0.68 Number of scatterers: 11106 At special positions: 0 Unit cell: (132, 125.664, 83.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 38 16.00 P 10 15.00 Mg 4 11.99 F 12 9.00 O 2136 8.00 N 1953 7.00 C 6949 6.00 Be 4 4.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.4 seconds 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 5 sheets defined 56.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 347 through 364 Proline residue: A 361 - end of helix Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 418 through 433 Processing helix chain 'A' and resid 455 through 472 removed outlier: 3.676A pdb=" N ASP A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 510 through 522 Processing helix chain 'A' and resid 530 through 541 Processing helix chain 'A' and resid 545 through 557 Processing helix chain 'A' and resid 558 through 563 Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 590 Processing helix chain 'A' and resid 597 through 609 Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 347 through 364 Proline residue: B 361 - end of helix Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.989A pdb=" N ASN B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 433 removed outlier: 4.390A pdb=" N VAL B 423 " --> pdb=" O GLY B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 470 removed outlier: 3.644A pdb=" N ARG B 459 " --> pdb=" O HIS B 455 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.554A pdb=" N ARG B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 522 Processing helix chain 'B' and resid 530 through 541 Processing helix chain 'B' and resid 545 through 563 Proline residue: B 560 - end of helix Processing helix chain 'B' and resid 565 through 572 Processing helix chain 'B' and resid 581 through 590 removed outlier: 3.678A pdb=" N PHE B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 590 " --> pdb=" O THR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 609 removed outlier: 3.504A pdb=" N LEU B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 332 Processing helix chain 'C' and resid 347 through 364 Proline residue: C 361 - end of helix Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.898A pdb=" N LEU C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 412' Processing helix chain 'C' and resid 417 through 433 Processing helix chain 'C' and resid 455 through 471 removed outlier: 3.808A pdb=" N ASP C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.984A pdb=" N ARG C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 522 Processing helix chain 'C' and resid 530 through 541 Processing helix chain 'C' and resid 545 through 563 Proline residue: C 560 - end of helix Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 597 through 609 Processing helix chain 'D' and resid 321 through 332 removed outlier: 3.805A pdb=" N LEU D 327 " --> pdb=" O ASN D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 364 Proline residue: D 361 - end of helix Processing helix chain 'D' and resid 387 through 400 Processing helix chain 'D' and resid 418 through 433 Processing helix chain 'D' and resid 442 through 447 removed outlier: 4.288A pdb=" N LEU D 446 " --> pdb=" O GLU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 470 removed outlier: 3.502A pdb=" N ARG D 459 " --> pdb=" O HIS D 455 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP D 470 " --> pdb=" O LEU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.757A pdb=" N ARG D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 522 Processing helix chain 'D' and resid 530 through 541 removed outlier: 3.524A pdb=" N LEU D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 564 Proline residue: D 560 - end of helix Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 589 removed outlier: 3.738A pdb=" N PHE D 585 " --> pdb=" O ARG D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 610 removed outlier: 3.764A pdb=" N ASP D 610 " --> pdb=" O ARG D 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 333 Processing helix chain 'E' and resid 340 through 344 Processing helix chain 'E' and resid 347 through 364 Proline residue: E 361 - end of helix Processing helix chain 'E' and resid 387 through 400 removed outlier: 3.644A pdb=" N ASN E 400 " --> pdb=" O ALA E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 433 removed outlier: 4.040A pdb=" N VAL E 423 " --> pdb=" O GLY E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 446 Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 493 through 500 Processing helix chain 'E' and resid 510 through 522 Processing helix chain 'E' and resid 530 through 540 Processing helix chain 'E' and resid 545 through 554 Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.679A pdb=" N ASP E 610 " --> pdb=" O ARG E 606 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 402 through 406 removed outlier: 6.784A pdb=" N THR A 402 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE A 439 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE A 404 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER A 436 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N MET A 483 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 438 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA A 485 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 440 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 378 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLY A 377 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL A 504 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 379 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 402 through 406 removed outlier: 3.913A pdb=" N ASP B 441 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER B 436 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N MET B 483 " --> pdb=" O SER B 436 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE B 438 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA B 485 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 440 " --> pdb=" O ALA B 485 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 378 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS B 502 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 379 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL B 504 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE B 381 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 333 through 334 removed outlier: 3.853A pdb=" N ASP C 334 " --> pdb=" O PHE C 403 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE C 403 " --> pdb=" O ASP C 334 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP C 441 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER C 436 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N MET C 483 " --> pdb=" O SER C 436 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 438 " --> pdb=" O MET C 483 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA C 485 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 440 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 502 " --> pdb=" O GLY C 377 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 402 through 406 removed outlier: 4.050A pdb=" N ASP D 441 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER D 436 " --> pdb=" O LEU D 481 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N MET D 483 " --> pdb=" O SER D 436 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE D 438 " --> pdb=" O MET D 483 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ALA D 485 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 440 " --> pdb=" O ALA D 485 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU D 378 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D 381 " --> pdb=" O VAL D 504 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 404 through 405 removed outlier: 6.301A pdb=" N PHE E 404 " --> pdb=" O PHE E 439 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE E 438 " --> pdb=" O MET E 483 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ALA E 485 " --> pdb=" O ILE E 438 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU E 379 " --> pdb=" O VAL E 504 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3759 1.34 - 1.46: 2098 1.46 - 1.58: 5316 1.58 - 1.69: 12 1.69 - 1.81: 66 Bond restraints: 11251 Sorted by residual: bond pdb=" C4 ADP D 701 " pdb=" C5 ADP D 701 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C4 ADP B 701 " pdb=" C5 ADP B 701 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C5 ADP D 701 " pdb=" C6 ADP D 701 " ideal model delta sigma weight residual 1.490 1.396 0.094 2.00e-02 2.50e+03 2.19e+01 ... (remaining 11246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 15099 3.68 - 7.35: 60 7.35 - 11.03: 34 11.03 - 14.71: 3 14.71 - 18.38: 1 Bond angle restraints: 15197 Sorted by residual: angle pdb=" O1B ADP D 701 " pdb=" PB ADP D 701 " pdb=" O3B ADP D 701 " ideal model delta sigma weight residual 119.90 101.52 18.38 3.00e+00 1.11e-01 3.75e+01 angle pdb=" O1B ADP B 701 " pdb=" PB ADP B 701 " pdb=" O3B ADP B 701 " ideal model delta sigma weight residual 119.90 105.20 14.70 3.00e+00 1.11e-01 2.40e+01 angle pdb=" O1B ADP C 701 " pdb=" PB ADP C 701 " pdb=" O3B ADP C 701 " ideal model delta sigma weight residual 119.90 105.37 14.53 3.00e+00 1.11e-01 2.34e+01 angle pdb=" O1B ADP A 701 " pdb=" PB ADP A 701 " pdb=" O3B ADP A 701 " ideal model delta sigma weight residual 119.90 105.39 14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C1' ADP B 701 " pdb=" C2' ADP B 701 " pdb=" C3' ADP B 701 " ideal model delta sigma weight residual 111.00 100.24 10.76 3.00e+00 1.11e-01 1.29e+01 ... (remaining 15192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 6872 35.25 - 70.51: 84 70.51 - 105.76: 10 105.76 - 141.02: 2 141.02 - 176.27: 7 Dihedral angle restraints: 6975 sinusoidal: 2908 harmonic: 4067 Sorted by residual: dihedral pdb=" O2A ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PA ADP A 701 " pdb=" PB ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 116.27 -176.27 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP C 701 " pdb=" O5' ADP C 701 " pdb=" PA ADP C 701 " pdb=" O2A ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 112.79 -172.79 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " pdb=" O2A ADP B 701 " ideal model delta sinusoidal sigma weight residual 300.00 139.26 160.74 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 6972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1485 0.041 - 0.081: 159 0.081 - 0.122: 102 0.122 - 0.163: 5 0.163 - 0.204: 2 Chirality restraints: 1753 Sorted by residual: chirality pdb=" C1' ADP D 701 " pdb=" C2' ADP D 701 " pdb=" N9 ADP D 701 " pdb=" O4' ADP D 701 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' ADP D 701 " pdb=" C2' ADP D 701 " pdb=" C4' ADP D 701 " pdb=" O3' ADP D 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" C3' ADP A 701 " pdb=" C2' ADP A 701 " pdb=" C4' ADP A 701 " pdb=" O3' ADP A 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1750 not shown) Planarity restraints: 1960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 559 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO C 560 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 560 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 560 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 356 " 0.005 2.00e-02 2.50e+03 9.77e-03 9.55e-01 pdb=" C GLU C 356 " -0.017 2.00e-02 2.50e+03 pdb=" O GLU C 356 " 0.006 2.00e-02 2.50e+03 pdb=" N ILE C 357 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 356 " 0.004 2.00e-02 2.50e+03 8.48e-03 7.20e-01 pdb=" C GLU B 356 " -0.015 2.00e-02 2.50e+03 pdb=" O GLU B 356 " 0.006 2.00e-02 2.50e+03 pdb=" N ILE B 357 " 0.005 2.00e-02 2.50e+03 ... (remaining 1957 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 104 2.51 - 3.11: 8991 3.11 - 3.71: 16817 3.71 - 4.30: 23618 4.30 - 4.90: 38870 Nonbonded interactions: 88400 Sorted by model distance: nonbonded pdb=" OG1 THR D 389 " pdb="MG MG D 703 " model vdw 1.913 2.170 nonbonded pdb=" O2B ADP D 701 " pdb="MG MG D 703 " model vdw 2.041 2.170 nonbonded pdb=" F1 BEF D 702 " pdb="MG MG D 703 " model vdw 2.043 2.120 nonbonded pdb=" O2B ADP A 701 " pdb="MG MG A 703 " model vdw 2.077 2.170 nonbonded pdb=" O2B ADP B 701 " pdb="MG MG B 703 " model vdw 2.112 2.170 ... (remaining 88395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 323 through 472 or resid 478 through 610 or resid 701 thro \ ugh 703)) selection = (chain 'C' and (resid 323 through 472 or resid 478 through 610 or resid 701 thro \ ugh 703)) selection = (chain 'D' and (resid 323 through 472 or resid 478 through 610 or resid 701 thro \ ugh 703)) } 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: 0.720 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.150 Find NCS groups from input model: 0.500 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.014 0.720 11255 Z= 1.355 Angle : 0.731 18.383 15197 Z= 0.299 Chirality : 0.034 0.204 1753 Planarity : 0.002 0.027 1960 Dihedral : 13.789 176.273 4329 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.21), residues: 1387 helix: -0.96 (0.18), residues: 748 sheet: -1.95 (0.42), residues: 112 loop : -2.45 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 607 HIS 0.001 0.000 HIS E 455 PHE 0.004 0.000 PHE D 465 TYR 0.003 0.000 TYR C 604 ARG 0.001 0.000 ARG B 503 Details of bonding type rmsd hydrogen bonds : bond 0.16155 ( 513) hydrogen bonds : angle 5.58379 ( 1500) covalent geometry : bond 0.00459 (11251) covalent geometry : angle 0.73118 (15197) Misc. bond : bond 0.70800 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ARG cc_start: 0.6130 (ptp90) cc_final: 0.5469 (mmt90) REVERT: A 487 ASN cc_start: 0.7614 (m110) cc_final: 0.6942 (m110) REVERT: B 347 GLN cc_start: 0.8560 (mp10) cc_final: 0.7896 (mp10) REVERT: B 348 ASP cc_start: 0.8438 (p0) cc_final: 0.8116 (p0) REVERT: B 390 MET cc_start: 0.8038 (ttp) cc_final: 0.7834 (ttp) REVERT: B 420 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 516 LEU cc_start: 0.8869 (mt) cc_final: 0.8571 (tp) REVERT: B 593 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8372 (mmtm) REVERT: C 343 ASP cc_start: 0.8227 (p0) cc_final: 0.7513 (p0) REVERT: C 348 ASP cc_start: 0.7627 (p0) cc_final: 0.7290 (p0) REVERT: C 412 THR cc_start: 0.6627 (p) cc_final: 0.6272 (p) REVERT: C 439 PHE cc_start: 0.8184 (t80) cc_final: 0.7492 (t80) REVERT: C 490 GLN cc_start: 0.8527 (mp10) cc_final: 0.8223 (mp10) REVERT: D 420 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8966 (mm-30) REVERT: D 441 ASP cc_start: 0.8770 (t0) cc_final: 0.8506 (t0) REVERT: D 464 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7328 (tm-30) REVERT: D 465 PHE cc_start: 0.8990 (t80) cc_final: 0.8757 (t80) REVERT: D 516 LEU cc_start: 0.8996 (pp) cc_final: 0.8126 (tt) REVERT: D 537 LEU cc_start: 0.8915 (tp) cc_final: 0.7858 (tp) REVERT: D 572 MET cc_start: 0.5426 (ptp) cc_final: 0.5190 (ptt) REVERT: D 585 PHE cc_start: 0.8252 (m-80) cc_final: 0.7864 (m-80) REVERT: D 607 TRP cc_start: 0.8299 (t60) cc_final: 0.8061 (t60) REVERT: E 465 PHE cc_start: 0.8995 (t80) cc_final: 0.8765 (t80) REVERT: E 487 ASN cc_start: 0.6859 (m-40) cc_final: 0.6595 (m-40) REVERT: E 510 ASN cc_start: 0.6437 (m-40) cc_final: 0.6234 (t0) REVERT: E 530 THR cc_start: 0.5623 (p) cc_final: 0.5029 (p) REVERT: E 536 GLN cc_start: 0.6428 (mt0) cc_final: 0.5958 (pp30) REVERT: E 597 SER cc_start: 0.0956 (p) cc_final: 0.0096 (m) REVERT: E 599 GLN cc_start: 0.6695 (tp40) cc_final: 0.6404 (pm20) REVERT: E 600 THR cc_start: 0.6761 (p) cc_final: 0.6257 (p) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.2841 time to fit residues: 168.3020 Evaluate side-chains 265 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN B 405 ASN B 487 ASN C 326 ASN C 487 ASN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.119875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100329 restraints weight = 26610.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102759 restraints weight = 17307.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104459 restraints weight = 12635.702| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 11255 Z= 0.327 Angle : 0.885 9.625 15197 Z= 0.420 Chirality : 0.049 0.222 1753 Planarity : 0.006 0.053 1960 Dihedral : 12.979 176.172 1578 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.17 % Allowed : 6.01 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.22), residues: 1387 helix: -0.52 (0.18), residues: 774 sheet: -1.33 (0.44), residues: 131 loop : -2.02 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 607 HIS 0.007 0.003 HIS A 455 PHE 0.036 0.003 PHE A 341 TYR 0.035 0.002 TYR E 604 ARG 0.012 0.001 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 513) hydrogen bonds : angle 5.15975 ( 1500) covalent geometry : bond 0.00731 (11251) covalent geometry : angle 0.88506 (15197) Misc. bond : bond 0.00389 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 315 time to evaluate : 1.133 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 372 ARG cc_start: 0.6658 (ptp90) cc_final: 0.6058 (mmt90) REVERT: A 442 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8228 (mm-30) REVERT: A 487 ASN cc_start: 0.8336 (m-40) cc_final: 0.7168 (m110) REVERT: A 512 GLU cc_start: 0.8250 (mp0) cc_final: 0.7961 (tm-30) REVERT: A 568 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8497 (tp-100) REVERT: B 347 GLN cc_start: 0.8775 (mp10) cc_final: 0.8080 (mp10) REVERT: B 348 ASP cc_start: 0.8694 (p0) cc_final: 0.8386 (p0) REVERT: B 420 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7464 (mm-30) REVERT: B 487 ASN cc_start: 0.9236 (m-40) cc_final: 0.8748 (m110) REVERT: B 577 MET cc_start: 0.8097 (tpp) cc_final: 0.7819 (tpt) REVERT: B 590 LYS cc_start: 0.8311 (mttp) cc_final: 0.7375 (tmtt) REVERT: C 343 ASP cc_start: 0.8678 (p0) cc_final: 0.8366 (p0) REVERT: C 348 ASP cc_start: 0.7681 (p0) cc_final: 0.7394 (p0) REVERT: C 390 MET cc_start: 0.8152 (ttp) cc_final: 0.7865 (ttp) REVERT: C 412 THR cc_start: 0.7631 (p) cc_final: 0.7427 (p) REVERT: C 439 PHE cc_start: 0.8275 (t80) cc_final: 0.7515 (t80) REVERT: C 442 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7932 (mm-30) REVERT: C 448 CYS cc_start: 0.6731 (t) cc_final: 0.6420 (t) REVERT: D 464 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7676 (tm-30) REVERT: D 466 LEU cc_start: 0.9242 (tp) cc_final: 0.8862 (tp) REVERT: D 516 LEU cc_start: 0.9288 (pp) cc_final: 0.8422 (tt) REVERT: D 536 GLN cc_start: 0.7705 (tp40) cc_final: 0.7268 (tm-30) REVERT: D 537 LEU cc_start: 0.9231 (tp) cc_final: 0.8555 (tp) REVERT: D 561 ILE cc_start: 0.8692 (mm) cc_final: 0.8448 (mm) REVERT: D 604 TYR cc_start: 0.8672 (m-10) cc_final: 0.8405 (m-10) REVERT: D 606 ARG cc_start: 0.8136 (ttp-110) cc_final: 0.7677 (ttp-110) REVERT: E 390 MET cc_start: 0.8225 (tpt) cc_final: 0.7973 (tpt) REVERT: E 434 GLN cc_start: 0.8841 (pp30) cc_final: 0.8629 (pp30) REVERT: E 488 ARG cc_start: 0.8655 (mpt-90) cc_final: 0.8067 (mpp80) REVERT: E 536 GLN cc_start: 0.6360 (mt0) cc_final: 0.5995 (pp30) REVERT: E 599 GLN cc_start: 0.6761 (tp40) cc_final: 0.6227 (pm20) REVERT: E 600 THR cc_start: 0.6853 (p) cc_final: 0.6456 (p) REVERT: E 604 TYR cc_start: 0.5605 (m-80) cc_final: 0.5120 (m-10) outliers start: 2 outliers final: 0 residues processed: 317 average time/residue: 0.2210 time to fit residues: 98.5521 Evaluate side-chains 245 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 HIS ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.122344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102784 restraints weight = 25916.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105445 restraints weight = 16231.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107265 restraints weight = 11410.793| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11255 Z= 0.155 Angle : 0.689 8.145 15197 Z= 0.319 Chirality : 0.044 0.290 1753 Planarity : 0.005 0.062 1960 Dihedral : 12.775 176.024 1578 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1387 helix: 0.02 (0.18), residues: 771 sheet: -1.18 (0.41), residues: 138 loop : -1.78 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 607 HIS 0.002 0.001 HIS B 455 PHE 0.014 0.002 PHE B 465 TYR 0.026 0.001 TYR E 604 ARG 0.008 0.001 ARG C 498 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 513) hydrogen bonds : angle 4.82231 ( 1500) covalent geometry : bond 0.00352 (11251) covalent geometry : angle 0.68928 (15197) Misc. bond : bond 0.00115 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.319 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 372 ARG cc_start: 0.6385 (ptp90) cc_final: 0.5604 (mmt90) REVERT: A 442 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8166 (mm-30) REVERT: A 487 ASN cc_start: 0.8124 (m-40) cc_final: 0.7017 (m110) REVERT: B 347 GLN cc_start: 0.8608 (mp10) cc_final: 0.7993 (mp10) REVERT: B 348 ASP cc_start: 0.8355 (p0) cc_final: 0.8084 (p0) REVERT: B 420 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7929 (mm-30) REVERT: B 487 ASN cc_start: 0.9145 (m-40) cc_final: 0.8938 (m110) REVERT: B 516 LEU cc_start: 0.9111 (mp) cc_final: 0.8878 (mt) REVERT: B 590 LYS cc_start: 0.8336 (mttp) cc_final: 0.7531 (tmtt) REVERT: C 348 ASP cc_start: 0.7504 (p0) cc_final: 0.7225 (p0) REVERT: C 390 MET cc_start: 0.8015 (ttp) cc_final: 0.7814 (ttp) REVERT: C 412 THR cc_start: 0.7000 (p) cc_final: 0.6779 (p) REVERT: C 439 PHE cc_start: 0.8032 (t80) cc_final: 0.7373 (t80) REVERT: C 461 LEU cc_start: 0.8711 (mt) cc_final: 0.8506 (mt) REVERT: C 607 TRP cc_start: 0.8604 (t-100) cc_final: 0.8030 (t-100) REVERT: D 390 MET cc_start: 0.7967 (ptt) cc_final: 0.7608 (ptm) REVERT: D 420 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8927 (mm-30) REVERT: D 456 ASP cc_start: 0.7914 (m-30) cc_final: 0.7685 (m-30) REVERT: D 466 LEU cc_start: 0.9202 (tp) cc_final: 0.8858 (tp) REVERT: D 468 GLU cc_start: 0.7804 (tp30) cc_final: 0.7407 (tp30) REVERT: D 516 LEU cc_start: 0.9293 (pp) cc_final: 0.8433 (tt) REVERT: D 561 ILE cc_start: 0.8566 (mm) cc_final: 0.8198 (mm) REVERT: E 390 MET cc_start: 0.8103 (tpt) cc_final: 0.7802 (tpt) REVERT: E 487 ASN cc_start: 0.8462 (t0) cc_final: 0.7668 (m110) REVERT: E 488 ARG cc_start: 0.8475 (mpt-90) cc_final: 0.8177 (mpp80) REVERT: E 536 GLN cc_start: 0.6367 (mt0) cc_final: 0.5999 (pp30) REVERT: E 599 GLN cc_start: 0.6840 (tp40) cc_final: 0.6300 (pm20) REVERT: E 600 THR cc_start: 0.7034 (p) cc_final: 0.6574 (p) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2715 time to fit residues: 123.3503 Evaluate side-chains 238 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 18 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 HIS ** B 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN E 347 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.118553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.099137 restraints weight = 26272.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.101550 restraints weight = 16939.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.103290 restraints weight = 12269.303| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11255 Z= 0.223 Angle : 0.756 8.117 15197 Z= 0.354 Chirality : 0.045 0.309 1753 Planarity : 0.005 0.064 1960 Dihedral : 12.406 167.303 1578 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1387 helix: 0.09 (0.19), residues: 773 sheet: -1.09 (0.41), residues: 148 loop : -1.65 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 607 HIS 0.003 0.001 HIS D 455 PHE 0.024 0.002 PHE C 403 TYR 0.010 0.001 TYR C 544 ARG 0.006 0.001 ARG D 606 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 513) hydrogen bonds : angle 4.88219 ( 1500) covalent geometry : bond 0.00500 (11251) covalent geometry : angle 0.75647 (15197) Misc. bond : bond 0.00284 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.293 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 372 ARG cc_start: 0.6863 (ptp90) cc_final: 0.6051 (mmt90) REVERT: A 439 PHE cc_start: 0.8795 (t80) cc_final: 0.8473 (t80) REVERT: A 494 GLU cc_start: 0.8280 (mp0) cc_final: 0.8026 (mp0) REVERT: B 347 GLN cc_start: 0.8571 (mp10) cc_final: 0.8300 (mp10) REVERT: B 348 ASP cc_start: 0.8463 (p0) cc_final: 0.8186 (p0) REVERT: B 354 LEU cc_start: 0.9002 (tp) cc_final: 0.8789 (tp) REVERT: B 410 SER cc_start: 0.9140 (p) cc_final: 0.8700 (t) REVERT: B 420 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8013 (mm-30) REVERT: C 348 ASP cc_start: 0.7453 (p0) cc_final: 0.7221 (p0) REVERT: C 439 PHE cc_start: 0.8066 (t80) cc_final: 0.7328 (t80) REVERT: C 461 LEU cc_start: 0.8915 (mt) cc_final: 0.8626 (mt) REVERT: C 592 ILE cc_start: 0.8730 (mm) cc_final: 0.8460 (mt) REVERT: D 352 GLN cc_start: 0.9136 (pp30) cc_final: 0.8910 (pp30) REVERT: D 420 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8919 (mm-30) REVERT: D 456 ASP cc_start: 0.7999 (m-30) cc_final: 0.7715 (m-30) REVERT: D 464 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6984 (tm-30) REVERT: D 468 GLU cc_start: 0.8160 (tp30) cc_final: 0.7911 (tp30) REVERT: D 516 LEU cc_start: 0.9260 (pp) cc_final: 0.8430 (tt) REVERT: D 561 ILE cc_start: 0.8642 (mm) cc_final: 0.8425 (mm) REVERT: E 454 GLU cc_start: 0.5419 (tp30) cc_final: 0.5105 (tp30) REVERT: E 487 ASN cc_start: 0.8577 (t0) cc_final: 0.7948 (m110) REVERT: E 488 ARG cc_start: 0.8558 (mpt-90) cc_final: 0.8162 (mpp80) REVERT: E 505 TYR cc_start: 0.7579 (t80) cc_final: 0.7348 (t80) REVERT: E 523 CYS cc_start: 0.4331 (p) cc_final: 0.3563 (m) REVERT: E 536 GLN cc_start: 0.6640 (mt0) cc_final: 0.5960 (pp30) REVERT: E 599 GLN cc_start: 0.6905 (tp40) cc_final: 0.6430 (pm20) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2508 time to fit residues: 107.0323 Evaluate side-chains 237 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 3 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 98 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 HIS ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101994 restraints weight = 25736.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.104806 restraints weight = 15751.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106765 restraints weight = 10941.646| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11255 Z= 0.131 Angle : 0.683 8.300 15197 Z= 0.316 Chirality : 0.043 0.317 1753 Planarity : 0.005 0.096 1960 Dihedral : 12.209 164.422 1578 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1387 helix: 0.30 (0.19), residues: 772 sheet: -0.91 (0.41), residues: 145 loop : -1.52 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 607 HIS 0.002 0.001 HIS A 455 PHE 0.015 0.002 PHE D 465 TYR 0.014 0.001 TYR E 505 ARG 0.011 0.001 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 513) hydrogen bonds : angle 4.71270 ( 1500) covalent geometry : bond 0.00294 (11251) covalent geometry : angle 0.68261 (15197) Misc. bond : bond 0.00073 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.713 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 372 ARG cc_start: 0.6674 (ptp90) cc_final: 0.5814 (mmt90) REVERT: A 439 PHE cc_start: 0.8778 (t80) cc_final: 0.8512 (t80) REVERT: A 442 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8177 (mm-30) REVERT: A 487 ASN cc_start: 0.8018 (m-40) cc_final: 0.6802 (m110) REVERT: A 494 GLU cc_start: 0.8231 (mp0) cc_final: 0.7962 (mp0) REVERT: B 347 GLN cc_start: 0.8441 (mp10) cc_final: 0.8157 (mp10) REVERT: B 348 ASP cc_start: 0.8437 (p0) cc_final: 0.8202 (p0) REVERT: B 420 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7911 (mm-30) REVERT: B 478 ASP cc_start: 0.6481 (p0) cc_final: 0.6220 (m-30) REVERT: B 487 ASN cc_start: 0.9365 (m110) cc_final: 0.9130 (m110) REVERT: B 558 LEU cc_start: 0.8275 (mt) cc_final: 0.7996 (mp) REVERT: B 602 GLU cc_start: 0.7165 (tp30) cc_final: 0.6885 (tp30) REVERT: C 347 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7051 (pt0) REVERT: C 348 ASP cc_start: 0.7522 (p0) cc_final: 0.7214 (p0) REVERT: C 439 PHE cc_start: 0.7888 (t80) cc_final: 0.7312 (t80) REVERT: C 442 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7724 (mm-30) REVERT: C 461 LEU cc_start: 0.8830 (mt) cc_final: 0.8497 (mt) REVERT: C 464 GLU cc_start: 0.8105 (tp30) cc_final: 0.7883 (tp30) REVERT: C 468 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8098 (mm-30) REVERT: C 592 ILE cc_start: 0.8685 (mm) cc_final: 0.8398 (mt) REVERT: C 607 TRP cc_start: 0.8589 (t-100) cc_final: 0.8103 (t-100) REVERT: D 431 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.8052 (mtm-85) REVERT: D 456 ASP cc_start: 0.7927 (m-30) cc_final: 0.7710 (m-30) REVERT: D 465 PHE cc_start: 0.9243 (t80) cc_final: 0.8999 (t80) REVERT: D 466 LEU cc_start: 0.9150 (tp) cc_final: 0.8940 (tt) REVERT: D 516 LEU cc_start: 0.9220 (pp) cc_final: 0.8458 (tt) REVERT: D 536 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7080 (tm-30) REVERT: E 487 ASN cc_start: 0.8574 (t0) cc_final: 0.8053 (m110) REVERT: E 488 ARG cc_start: 0.8540 (mpt-90) cc_final: 0.8253 (mpp80) REVERT: E 536 GLN cc_start: 0.6664 (mt0) cc_final: 0.6148 (pp30) REVERT: E 599 GLN cc_start: 0.6888 (tp40) cc_final: 0.6363 (pm20) REVERT: E 600 THR cc_start: 0.6939 (p) cc_final: 0.6716 (p) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.2742 time to fit residues: 122.3511 Evaluate side-chains 242 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 73 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 127 optimal weight: 0.0980 chunk 94 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 119 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 HIS B 386 ASN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.120749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101805 restraints weight = 25851.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104327 restraints weight = 16338.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106112 restraints weight = 11632.121| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11255 Z= 0.123 Angle : 0.667 6.877 15197 Z= 0.307 Chirality : 0.042 0.324 1753 Planarity : 0.005 0.060 1960 Dihedral : 11.896 163.835 1578 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.54 (0.22), residues: 1387 helix: 0.43 (0.19), residues: 773 sheet: -0.86 (0.42), residues: 144 loop : -1.40 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 607 HIS 0.001 0.000 HIS A 455 PHE 0.028 0.002 PHE B 341 TYR 0.016 0.001 TYR E 505 ARG 0.006 0.000 ARG C 499 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 513) hydrogen bonds : angle 4.61987 ( 1500) covalent geometry : bond 0.00274 (11251) covalent geometry : angle 0.66718 (15197) Misc. bond : bond 0.00070 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ARG cc_start: 0.6719 (ptp90) cc_final: 0.6060 (mmt90) REVERT: A 439 PHE cc_start: 0.8796 (t80) cc_final: 0.8506 (t80) REVERT: A 442 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8137 (mm-30) REVERT: A 487 ASN cc_start: 0.8043 (m-40) cc_final: 0.6760 (m110) REVERT: A 494 GLU cc_start: 0.8206 (mp0) cc_final: 0.7906 (mp0) REVERT: B 347 GLN cc_start: 0.8365 (mp10) cc_final: 0.8095 (mp10) REVERT: B 558 LEU cc_start: 0.8278 (mt) cc_final: 0.8011 (mp) REVERT: B 572 MET cc_start: 0.8304 (tmm) cc_final: 0.7555 (tpt) REVERT: B 602 GLU cc_start: 0.7098 (tp30) cc_final: 0.6813 (tp30) REVERT: C 347 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7104 (pm20) REVERT: C 348 ASP cc_start: 0.7539 (p0) cc_final: 0.7230 (p0) REVERT: C 420 GLU cc_start: 0.8318 (mp0) cc_final: 0.8056 (mp0) REVERT: C 439 PHE cc_start: 0.7739 (t80) cc_final: 0.7083 (t80) REVERT: C 442 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7202 (mm-30) REVERT: C 444 ASP cc_start: 0.8869 (p0) cc_final: 0.8460 (p0) REVERT: C 461 LEU cc_start: 0.8816 (mt) cc_final: 0.8470 (mt) REVERT: C 592 ILE cc_start: 0.8679 (mm) cc_final: 0.8361 (mt) REVERT: D 456 ASP cc_start: 0.8018 (m-30) cc_final: 0.7652 (m-30) REVERT: D 465 PHE cc_start: 0.9201 (t80) cc_final: 0.8863 (t80) REVERT: D 468 GLU cc_start: 0.7996 (tp30) cc_final: 0.7552 (tp30) REVERT: D 516 LEU cc_start: 0.9164 (pp) cc_final: 0.8432 (tt) REVERT: D 536 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7241 (tm-30) REVERT: E 487 ASN cc_start: 0.8593 (t0) cc_final: 0.8060 (m110) REVERT: E 488 ARG cc_start: 0.8524 (mpt-90) cc_final: 0.8212 (mpp80) REVERT: E 536 GLN cc_start: 0.6718 (mt0) cc_final: 0.6245 (pp30) REVERT: E 599 GLN cc_start: 0.6889 (tp40) cc_final: 0.6376 (pm20) REVERT: E 600 THR cc_start: 0.6908 (p) cc_final: 0.6693 (p) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2815 time to fit residues: 126.0123 Evaluate side-chains 245 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 104 optimal weight: 0.0370 chunk 52 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 89 optimal weight: 0.1980 chunk 106 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 HIS ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.118199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098873 restraints weight = 26590.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101643 restraints weight = 16192.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103545 restraints weight = 11174.453| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11255 Z= 0.191 Angle : 0.731 7.171 15197 Z= 0.343 Chirality : 0.044 0.320 1753 Planarity : 0.006 0.105 1960 Dihedral : 11.719 160.796 1578 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.46 (0.22), residues: 1387 helix: 0.44 (0.19), residues: 763 sheet: -0.75 (0.43), residues: 145 loop : -1.24 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 607 HIS 0.003 0.001 HIS E 455 PHE 0.018 0.002 PHE D 585 TYR 0.007 0.001 TYR E 415 ARG 0.008 0.001 ARG D 606 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 513) hydrogen bonds : angle 4.69230 ( 1500) covalent geometry : bond 0.00436 (11251) covalent geometry : angle 0.73138 (15197) Misc. bond : bond 0.00192 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 PHE cc_start: 0.6652 (m-80) cc_final: 0.6450 (m-10) REVERT: A 372 ARG cc_start: 0.6754 (ptp90) cc_final: 0.6225 (mmt90) REVERT: A 494 GLU cc_start: 0.8339 (mp0) cc_final: 0.8035 (mp0) REVERT: B 347 GLN cc_start: 0.8326 (mp10) cc_final: 0.8055 (mp10) REVERT: B 348 ASP cc_start: 0.8433 (p0) cc_final: 0.8221 (p0) REVERT: B 390 MET cc_start: 0.8125 (ttp) cc_final: 0.7910 (ttp) REVERT: B 420 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7377 (mm-30) REVERT: B 464 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7721 (tm-30) REVERT: B 558 LEU cc_start: 0.8338 (mt) cc_final: 0.8104 (mp) REVERT: B 601 LEU cc_start: 0.8486 (pp) cc_final: 0.8256 (pp) REVERT: C 347 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7212 (pm20) REVERT: C 348 ASP cc_start: 0.7741 (p0) cc_final: 0.7448 (p0) REVERT: C 439 PHE cc_start: 0.8017 (t80) cc_final: 0.7338 (t80) REVERT: C 442 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7636 (mm-30) REVERT: C 448 CYS cc_start: 0.6966 (t) cc_final: 0.6674 (t) REVERT: C 461 LEU cc_start: 0.8926 (mt) cc_final: 0.8538 (mt) REVERT: C 572 MET cc_start: 0.7773 (ptp) cc_final: 0.7527 (ptt) REVERT: C 592 ILE cc_start: 0.8751 (mm) cc_final: 0.8439 (mt) REVERT: D 456 ASP cc_start: 0.8068 (m-30) cc_final: 0.7737 (m-30) REVERT: D 516 LEU cc_start: 0.9202 (pp) cc_final: 0.8403 (tt) REVERT: D 536 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7541 (tm-30) REVERT: E 390 MET cc_start: 0.8126 (tpt) cc_final: 0.7814 (tpt) REVERT: E 454 GLU cc_start: 0.5607 (tp30) cc_final: 0.5352 (mm-30) REVERT: E 487 ASN cc_start: 0.8696 (t0) cc_final: 0.8300 (m110) REVERT: E 488 ARG cc_start: 0.8560 (mpt-90) cc_final: 0.8207 (mpp80) REVERT: E 523 CYS cc_start: 0.4635 (p) cc_final: 0.4159 (m) REVERT: E 536 GLN cc_start: 0.6774 (mt0) cc_final: 0.6140 (pp30) REVERT: E 599 GLN cc_start: 0.6911 (tp40) cc_final: 0.6411 (pm20) REVERT: E 600 THR cc_start: 0.6917 (p) cc_final: 0.6687 (p) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2881 time to fit residues: 131.5452 Evaluate side-chains 241 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 83 optimal weight: 0.0570 chunk 66 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 HIS B 386 ASN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.120914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.102110 restraints weight = 26094.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104664 restraints weight = 16722.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.106455 restraints weight = 11995.759| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11255 Z= 0.130 Angle : 0.684 6.933 15197 Z= 0.315 Chirality : 0.043 0.347 1753 Planarity : 0.005 0.062 1960 Dihedral : 11.568 159.053 1578 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: 1387 helix: 0.57 (0.19), residues: 767 sheet: -0.68 (0.43), residues: 140 loop : -1.22 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 607 HIS 0.002 0.001 HIS A 455 PHE 0.032 0.002 PHE A 439 TYR 0.012 0.001 TYR G 8 ARG 0.008 0.000 ARG C 499 Details of bonding type rmsd hydrogen bonds : bond 0.03135 ( 513) hydrogen bonds : angle 4.62318 ( 1500) covalent geometry : bond 0.00298 (11251) covalent geometry : angle 0.68353 (15197) Misc. bond : bond 0.00067 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.196 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 368 PHE cc_start: 0.6577 (m-80) cc_final: 0.6339 (m-10) REVERT: A 372 ARG cc_start: 0.6753 (ptp90) cc_final: 0.6012 (mmt90) REVERT: A 487 ASN cc_start: 0.8309 (m-40) cc_final: 0.7681 (m-40) REVERT: A 494 GLU cc_start: 0.8205 (mp0) cc_final: 0.7901 (mp0) REVERT: B 347 GLN cc_start: 0.8221 (mp10) cc_final: 0.8003 (mp10) REVERT: B 420 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7361 (mm-30) REVERT: B 558 LEU cc_start: 0.8343 (mt) cc_final: 0.8040 (mp) REVERT: B 572 MET cc_start: 0.8138 (tmm) cc_final: 0.7377 (tmm) REVERT: B 586 THR cc_start: 0.9181 (p) cc_final: 0.8923 (t) REVERT: B 599 GLN cc_start: 0.8061 (mp10) cc_final: 0.7671 (mt0) REVERT: B 601 LEU cc_start: 0.8312 (pp) cc_final: 0.8083 (pp) REVERT: C 348 ASP cc_start: 0.7578 (p0) cc_final: 0.7294 (p0) REVERT: C 420 GLU cc_start: 0.8231 (mp0) cc_final: 0.8007 (mp0) REVERT: C 439 PHE cc_start: 0.7700 (t80) cc_final: 0.6998 (t80) REVERT: C 442 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7622 (mm-30) REVERT: C 448 CYS cc_start: 0.6891 (t) cc_final: 0.6617 (t) REVERT: C 461 LEU cc_start: 0.8873 (mt) cc_final: 0.8461 (mt) REVERT: C 592 ILE cc_start: 0.8723 (mm) cc_final: 0.8388 (mt) REVERT: D 390 MET cc_start: 0.8209 (ptt) cc_final: 0.7884 (ptm) REVERT: D 420 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8967 (mm-30) REVERT: D 456 ASP cc_start: 0.8031 (m-30) cc_final: 0.7612 (m-30) REVERT: D 516 LEU cc_start: 0.9151 (pp) cc_final: 0.8417 (tt) REVERT: D 536 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7584 (tm-30) REVERT: D 572 MET cc_start: 0.4975 (ptp) cc_final: 0.4735 (tmm) REVERT: E 390 MET cc_start: 0.8079 (tpt) cc_final: 0.7794 (tpt) REVERT: E 454 GLU cc_start: 0.5444 (tp30) cc_final: 0.5242 (mm-30) REVERT: E 487 ASN cc_start: 0.8664 (t0) cc_final: 0.8247 (m110) REVERT: E 488 ARG cc_start: 0.8562 (mpt-90) cc_final: 0.8293 (mpp80) REVERT: E 523 CYS cc_start: 0.4560 (p) cc_final: 0.4071 (m) REVERT: E 536 GLN cc_start: 0.6684 (mt0) cc_final: 0.6133 (pp30) REVERT: E 599 GLN cc_start: 0.6925 (tp40) cc_final: 0.6402 (pm20) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2034 time to fit residues: 89.9480 Evaluate side-chains 249 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 63 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 0.0010 chunk 99 optimal weight: 0.0870 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101999 restraints weight = 26135.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104824 restraints weight = 16057.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.106777 restraints weight = 11179.974| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11255 Z= 0.127 Angle : 0.692 7.765 15197 Z= 0.318 Chirality : 0.043 0.370 1753 Planarity : 0.005 0.060 1960 Dihedral : 11.399 158.102 1578 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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 (0.23), residues: 1387 helix: 0.62 (0.19), residues: 765 sheet: -0.62 (0.44), residues: 140 loop : -1.21 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 607 HIS 0.001 0.000 HIS A 455 PHE 0.016 0.002 PHE E 465 TYR 0.009 0.001 TYR G 8 ARG 0.008 0.001 ARG D 606 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 513) hydrogen bonds : angle 4.65554 ( 1500) covalent geometry : bond 0.00289 (11251) covalent geometry : angle 0.69245 (15197) Misc. bond : bond 0.00055 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 PHE cc_start: 0.6440 (m-80) cc_final: 0.6160 (m-10) REVERT: A 372 ARG cc_start: 0.6621 (ptp90) cc_final: 0.5973 (mmt90) REVERT: A 439 PHE cc_start: 0.8698 (t80) cc_final: 0.8412 (t80) REVERT: A 494 GLU cc_start: 0.8208 (mp0) cc_final: 0.7912 (mp0) REVERT: B 347 GLN cc_start: 0.8232 (mp10) cc_final: 0.7820 (mp10) REVERT: B 420 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7372 (mm-30) REVERT: B 558 LEU cc_start: 0.8226 (mt) cc_final: 0.8024 (mp) REVERT: B 586 THR cc_start: 0.9180 (p) cc_final: 0.8923 (t) REVERT: C 344 ILE cc_start: 0.8357 (mm) cc_final: 0.8060 (mm) REVERT: C 348 ASP cc_start: 0.7652 (p0) cc_final: 0.7393 (p0) REVERT: C 390 MET cc_start: 0.7559 (ttp) cc_final: 0.7189 (ttp) REVERT: C 412 THR cc_start: 0.6842 (p) cc_final: 0.6630 (p) REVERT: C 439 PHE cc_start: 0.7764 (t80) cc_final: 0.7172 (t80) REVERT: C 442 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7207 (mm-30) REVERT: C 448 CYS cc_start: 0.6786 (t) cc_final: 0.6573 (t) REVERT: C 461 LEU cc_start: 0.8815 (mt) cc_final: 0.8497 (mt) REVERT: C 499 ARG cc_start: 0.8686 (mmt-90) cc_final: 0.8156 (mmt-90) REVERT: C 572 MET cc_start: 0.8148 (ptp) cc_final: 0.7865 (ptt) REVERT: C 592 ILE cc_start: 0.8736 (mm) cc_final: 0.8373 (mt) REVERT: D 390 MET cc_start: 0.8224 (ptt) cc_final: 0.7822 (ptm) REVERT: D 456 ASP cc_start: 0.7939 (m-30) cc_final: 0.7591 (m-30) REVERT: D 516 LEU cc_start: 0.9154 (pp) cc_final: 0.8426 (tt) REVERT: D 536 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7663 (tm-30) REVERT: D 572 MET cc_start: 0.4992 (ptp) cc_final: 0.4755 (tmm) REVERT: E 390 MET cc_start: 0.8046 (tpt) cc_final: 0.7793 (tpt) REVERT: E 488 ARG cc_start: 0.8543 (mpt-90) cc_final: 0.8177 (mpp80) REVERT: E 523 CYS cc_start: 0.4557 (p) cc_final: 0.4086 (m) REVERT: E 536 GLN cc_start: 0.6706 (mt0) cc_final: 0.6286 (pp30) REVERT: E 599 GLN cc_start: 0.6930 (tp40) cc_final: 0.6394 (pm20) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1988 time to fit residues: 88.9385 Evaluate side-chains 243 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.1980 chunk 84 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.119623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101439 restraints weight = 25792.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103990 restraints weight = 16242.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.105729 restraints weight = 11455.413| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11255 Z= 0.138 Angle : 0.706 8.195 15197 Z= 0.327 Chirality : 0.044 0.380 1753 Planarity : 0.005 0.057 1960 Dihedral : 11.304 156.843 1578 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.08 % Allowed : 0.34 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.22 (0.23), residues: 1387 helix: 0.61 (0.19), residues: 765 sheet: -0.50 (0.44), residues: 140 loop : -1.16 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 607 HIS 0.005 0.001 HIS A 455 PHE 0.015 0.002 PHE E 465 TYR 0.010 0.001 TYR E 505 ARG 0.007 0.000 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 513) hydrogen bonds : angle 4.62253 ( 1500) covalent geometry : bond 0.00315 (11251) covalent geometry : angle 0.70561 (15197) Misc. bond : bond 0.00077 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.6451 (tpt) cc_final: 0.5825 (ttp) REVERT: A 368 PHE cc_start: 0.6546 (m-80) cc_final: 0.6302 (m-10) REVERT: A 372 ARG cc_start: 0.6714 (ptp90) cc_final: 0.6126 (mmt90) REVERT: A 487 ASN cc_start: 0.8615 (m-40) cc_final: 0.7495 (m110) REVERT: A 494 GLU cc_start: 0.8222 (mp0) cc_final: 0.7928 (mp0) REVERT: B 347 GLN cc_start: 0.8218 (mp10) cc_final: 0.7736 (mp10) REVERT: B 599 GLN cc_start: 0.8161 (mp10) cc_final: 0.7765 (mt0) REVERT: B 601 LEU cc_start: 0.8391 (pp) cc_final: 0.8120 (pp) REVERT: C 348 ASP cc_start: 0.7730 (p0) cc_final: 0.7417 (p0) REVERT: C 390 MET cc_start: 0.7872 (ttp) cc_final: 0.7603 (ttp) REVERT: C 412 THR cc_start: 0.6934 (p) cc_final: 0.6709 (p) REVERT: C 420 GLU cc_start: 0.8267 (mp0) cc_final: 0.8048 (mp0) REVERT: C 439 PHE cc_start: 0.7674 (t80) cc_final: 0.7252 (t80) REVERT: C 442 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7267 (mm-30) REVERT: C 461 LEU cc_start: 0.8840 (mt) cc_final: 0.8488 (mt) REVERT: C 469 PHE cc_start: 0.8535 (t80) cc_final: 0.8319 (t80) REVERT: C 499 ARG cc_start: 0.8677 (mmt-90) cc_final: 0.8207 (mmt-90) REVERT: C 592 ILE cc_start: 0.8696 (mm) cc_final: 0.8317 (mt) REVERT: D 390 MET cc_start: 0.8349 (ptt) cc_final: 0.7928 (ptm) REVERT: D 420 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8678 (mm-30) REVERT: D 454 GLU cc_start: 0.8078 (pm20) cc_final: 0.7833 (pm20) REVERT: D 456 ASP cc_start: 0.8090 (m-30) cc_final: 0.7714 (m-30) REVERT: D 516 LEU cc_start: 0.9172 (pp) cc_final: 0.8414 (tt) REVERT: D 536 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7711 (tm-30) REVERT: D 572 MET cc_start: 0.5002 (ptp) cc_final: 0.4766 (tmm) REVERT: E 488 ARG cc_start: 0.8727 (mpt-90) cc_final: 0.8041 (mpp80) REVERT: E 523 CYS cc_start: 0.4633 (p) cc_final: 0.4190 (m) REVERT: E 536 GLN cc_start: 0.6708 (mt0) cc_final: 0.6306 (pp30) REVERT: E 599 GLN cc_start: 0.6915 (tp40) cc_final: 0.6360 (pm20) outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.1985 time to fit residues: 88.8663 Evaluate side-chains 237 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 134 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 HIS ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.115464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.097095 restraints weight = 26059.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.099451 restraints weight = 16790.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101041 restraints weight = 12135.684| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11255 Z= 0.223 Angle : 0.783 8.073 15197 Z= 0.368 Chirality : 0.046 0.314 1753 Planarity : 0.006 0.074 1960 Dihedral : 11.305 152.267 1578 Min Nonbonded Distance : 1.197 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.08 % Allowed : 0.34 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.40 (0.22), residues: 1387 helix: 0.41 (0.19), residues: 766 sheet: -0.52 (0.44), residues: 145 loop : -1.16 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 607 HIS 0.003 0.001 HIS E 455 PHE 0.030 0.002 PHE A 439 TYR 0.016 0.002 TYR G 8 ARG 0.009 0.001 ARG D 606 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 513) hydrogen bonds : angle 4.83232 ( 1500) covalent geometry : bond 0.00509 (11251) covalent geometry : angle 0.78347 (15197) Misc. bond : bond 0.00149 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3946.95 seconds wall clock time: 73 minutes 27.54 seconds (4407.54 seconds total)