Starting phenix.real_space_refine on Wed Sep 17 20:44:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pek_20327/09_2025/6pek_20327.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pek_20327/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6pek_20327/09_2025/6pek_20327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pek_20327/09_2025/6pek_20327.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pek_20327/09_2025/6pek_20327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pek_20327/09_2025/6pek_20327.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.65, per 1000 atoms: 0.24 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: 0.96 Conformation dependent library (CDL) restraints added in 498.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.40 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: 1.63 Time building geometry restraints manager: 1.26 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 703)) selection = (chain 'C' and (resid 323 through 472 or resid 478 through 703)) selection = (chain 'D' and (resid 323 through 472 or resid 478 through 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: 0.970 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.640 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- 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 : 4.37 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG B 503 TYR 0.003 0.000 TYR C 604 PHE 0.004 0.000 PHE D 465 TRP 0.002 0.000 TRP D 607 HIS 0.001 0.000 HIS E 455 Details of bonding type rmsd covalent geometry : bond 0.00459 (11251) covalent geometry : angle 0.73118 (15197) hydrogen bonds : bond 0.16155 ( 513) hydrogen bonds : angle 5.58379 ( 1500) 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 : 0.349 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: 0.1244 time to fit residues: 74.0921 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 ASN D 434 GLN E 400 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.129037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.110167 restraints weight = 25792.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.112876 restraints weight = 16456.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.114736 restraints weight = 11653.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.115963 restraints weight = 9010.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.116920 restraints weight = 7434.737| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11255 Z= 0.155 Angle : 0.712 7.893 15197 Z= 0.331 Chirality : 0.044 0.238 1753 Planarity : 0.005 0.055 1960 Dihedral : 12.977 168.278 1578 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.08 % Allowed : 3.21 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.22), residues: 1387 helix: -0.16 (0.18), residues: 773 sheet: -1.38 (0.44), residues: 123 loop : -2.02 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 594 TYR 0.028 0.001 TYR E 604 PHE 0.028 0.002 PHE A 341 TRP 0.009 0.001 TRP A 607 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00355 (11251) covalent geometry : angle 0.71182 (15197) hydrogen bonds : bond 0.03529 ( 513) hydrogen bonds : angle 4.87480 ( 1500) Misc. bond : bond 0.00485 ( 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 344 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 0.417 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: 0.5748 (ptp90) cc_final: 0.5261 (mmt90) REVERT: A 442 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8025 (mm-30) REVERT: A 487 ASN cc_start: 0.7707 (m110) cc_final: 0.6805 (m110) REVERT: A 568 GLN cc_start: 0.8348 (tp-100) cc_final: 0.7887 (tp40) REVERT: B 335 ASN cc_start: 0.7295 (p0) cc_final: 0.7014 (p0) REVERT: B 347 GLN cc_start: 0.8659 (mp10) cc_final: 0.8122 (mp10) REVERT: B 348 ASP cc_start: 0.8412 (p0) cc_final: 0.8148 (p0) REVERT: B 420 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7688 (mm-30) REVERT: B 456 ASP cc_start: 0.8062 (t70) cc_final: 0.7820 (t70) REVERT: B 487 ASN cc_start: 0.8506 (m110) cc_final: 0.8122 (m110) REVERT: B 577 MET cc_start: 0.7765 (tpp) cc_final: 0.7464 (tpt) REVERT: B 586 THR cc_start: 0.8882 (p) cc_final: 0.8569 (t) REVERT: C 343 ASP cc_start: 0.8338 (p0) cc_final: 0.8096 (p0) REVERT: C 347 GLN cc_start: 0.7258 (mm-40) cc_final: 0.7018 (pt0) REVERT: C 348 ASP cc_start: 0.7535 (p0) cc_final: 0.7186 (p0) REVERT: C 390 MET cc_start: 0.7674 (ttp) cc_final: 0.7272 (ttp) REVERT: C 404 PHE cc_start: 0.8101 (m-10) cc_final: 0.7888 (m-10) REVERT: C 439 PHE cc_start: 0.8009 (t80) cc_final: 0.7404 (t80) REVERT: C 442 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7461 (mm-30) REVERT: D 465 PHE cc_start: 0.9138 (t80) cc_final: 0.8888 (t80) REVERT: D 466 LEU cc_start: 0.9094 (tp) cc_final: 0.8521 (tp) REVERT: D 516 LEU cc_start: 0.9190 (pp) cc_final: 0.8321 (tt) REVERT: D 537 LEU cc_start: 0.9031 (tp) cc_final: 0.8633 (tp) REVERT: D 561 ILE cc_start: 0.8555 (mm) cc_final: 0.8282 (mm) REVERT: D 585 PHE cc_start: 0.8266 (m-80) cc_final: 0.7923 (m-80) REVERT: D 606 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7477 (ttp-110) REVERT: E 342 ASP cc_start: 0.8075 (p0) cc_final: 0.7868 (p0) REVERT: E 390 MET cc_start: 0.7994 (tpt) cc_final: 0.7747 (tpt) REVERT: E 488 ARG cc_start: 0.8533 (mpt-90) cc_final: 0.7954 (mpp80) REVERT: E 599 GLN cc_start: 0.6843 (tp40) cc_final: 0.6348 (pm20) REVERT: E 600 THR cc_start: 0.6887 (p) cc_final: 0.6299 (p) REVERT: E 604 TYR cc_start: 0.5630 (m-80) cc_final: 0.5333 (m-10) outliers start: 1 outliers final: 0 residues processed: 344 average time/residue: 0.0941 time to fit residues: 46.9649 Evaluate side-chains 246 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 E 455 HIS E 510 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.127338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107756 restraints weight = 25949.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110522 restraints weight = 16357.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.112445 restraints weight = 11580.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113740 restraints weight = 8903.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.114742 restraints weight = 7341.837| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11255 Z= 0.134 Angle : 0.669 7.130 15197 Z= 0.308 Chirality : 0.043 0.276 1753 Planarity : 0.005 0.059 1960 Dihedral : 12.823 177.800 1578 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.22), residues: 1387 helix: 0.15 (0.19), residues: 780 sheet: -1.18 (0.41), residues: 145 loop : -1.84 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 376 TYR 0.026 0.001 TYR E 604 PHE 0.025 0.002 PHE E 427 TRP 0.010 0.002 TRP B 607 HIS 0.002 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00302 (11251) covalent geometry : angle 0.66881 (15197) hydrogen bonds : bond 0.03210 ( 513) hydrogen bonds : angle 4.68841 ( 1500) Misc. bond : bond 0.00121 ( 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 313 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.415 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: 0.5947 (ptp90) cc_final: 0.5413 (mmt90) REVERT: A 442 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8033 (mm-30) REVERT: A 487 ASN cc_start: 0.7743 (m110) cc_final: 0.6807 (m110) REVERT: A 568 GLN cc_start: 0.8303 (tp-100) cc_final: 0.8033 (tp40) REVERT: B 347 GLN cc_start: 0.8566 (mp10) cc_final: 0.8044 (mp10) REVERT: B 348 ASP cc_start: 0.8300 (p0) cc_final: 0.8051 (p0) REVERT: B 420 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 456 ASP cc_start: 0.8041 (t70) cc_final: 0.7835 (t70) REVERT: B 487 ASN cc_start: 0.8491 (m110) cc_final: 0.8283 (m110) REVERT: C 343 ASP cc_start: 0.8342 (p0) cc_final: 0.8133 (p0) REVERT: C 348 ASP cc_start: 0.7525 (p0) cc_final: 0.7215 (p0) REVERT: C 390 MET cc_start: 0.7706 (ttp) cc_final: 0.7462 (ttp) REVERT: C 439 PHE cc_start: 0.7879 (t80) cc_final: 0.7299 (t80) REVERT: C 461 LEU cc_start: 0.8732 (mt) cc_final: 0.8466 (mt) REVERT: C 498 ARG cc_start: 0.8616 (tmm160) cc_final: 0.7876 (ttp80) REVERT: D 466 LEU cc_start: 0.9079 (tp) cc_final: 0.8550 (tp) REVERT: D 516 LEU cc_start: 0.9160 (pp) cc_final: 0.8287 (tt) REVERT: D 537 LEU cc_start: 0.9013 (tp) cc_final: 0.8736 (tp) REVERT: D 585 PHE cc_start: 0.8237 (m-80) cc_final: 0.7959 (m-80) REVERT: E 488 ARG cc_start: 0.8566 (mpt-90) cc_final: 0.7901 (mpp80) REVERT: E 599 GLN cc_start: 0.6835 (tp40) cc_final: 0.6278 (pm20) REVERT: E 600 THR cc_start: 0.6923 (p) cc_final: 0.6534 (p) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.0951 time to fit residues: 43.0067 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 : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 60 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 E 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.126476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.107357 restraints weight = 25973.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.110004 restraints weight = 16658.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.111836 restraints weight = 11878.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.112970 restraints weight = 9209.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113907 restraints weight = 7708.403| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11255 Z= 0.133 Angle : 0.666 7.172 15197 Z= 0.308 Chirality : 0.043 0.302 1753 Planarity : 0.005 0.059 1960 Dihedral : 12.496 170.380 1578 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.22), residues: 1387 helix: 0.52 (0.19), residues: 772 sheet: -0.90 (0.42), residues: 145 loop : -1.73 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 606 TYR 0.012 0.001 TYR E 505 PHE 0.055 0.002 PHE A 341 TRP 0.013 0.002 TRP C 607 HIS 0.002 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00298 (11251) covalent geometry : angle 0.66612 (15197) hydrogen bonds : bond 0.03049 ( 513) hydrogen bonds : angle 4.65116 ( 1500) Misc. bond : bond 0.00125 ( 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 317 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.478 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: 0.6251 (ptp90) cc_final: 0.5662 (mmt90) REVERT: A 494 GLU cc_start: 0.8159 (mp0) cc_final: 0.7862 (mp0) REVERT: A 568 GLN cc_start: 0.8365 (tp-100) cc_final: 0.8127 (tp40) REVERT: A 607 TRP cc_start: 0.7562 (t-100) cc_final: 0.7313 (t-100) REVERT: B 347 GLN cc_start: 0.8584 (mp10) cc_final: 0.8137 (mp10) REVERT: B 348 ASP cc_start: 0.8260 (p0) cc_final: 0.8023 (p0) REVERT: B 354 LEU cc_start: 0.8957 (tp) cc_final: 0.8698 (tp) REVERT: B 420 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 456 ASP cc_start: 0.8090 (t70) cc_final: 0.7718 (t70) REVERT: C 348 ASP cc_start: 0.7594 (p0) cc_final: 0.7270 (p0) REVERT: C 390 MET cc_start: 0.7904 (ttp) cc_final: 0.7689 (ttp) REVERT: C 439 PHE cc_start: 0.7817 (t80) cc_final: 0.7214 (t80) REVERT: C 461 LEU cc_start: 0.8767 (mt) cc_final: 0.8492 (mt) REVERT: D 464 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6767 (tm-30) REVERT: D 466 LEU cc_start: 0.9052 (tp) cc_final: 0.8809 (tp) REVERT: D 516 LEU cc_start: 0.9143 (pp) cc_final: 0.8348 (tt) REVERT: D 561 ILE cc_start: 0.8538 (mm) cc_final: 0.8293 (mm) REVERT: D 585 PHE cc_start: 0.8333 (m-80) cc_final: 0.7975 (m-80) REVERT: E 390 MET cc_start: 0.8290 (tpt) cc_final: 0.7943 (tpt) REVERT: E 488 ARG cc_start: 0.8479 (mpt-90) cc_final: 0.7870 (mpp80) REVERT: E 599 GLN cc_start: 0.6910 (tp40) cc_final: 0.6379 (pm20) REVERT: E 600 THR cc_start: 0.6911 (p) cc_final: 0.6679 (p) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.0981 time to fit residues: 45.0647 Evaluate side-chains 236 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 130 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 105 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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** E 455 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.107642 restraints weight = 25835.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110286 restraints weight = 16552.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112096 restraints weight = 11750.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113375 restraints weight = 9092.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114174 restraints weight = 7511.229| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11255 Z= 0.132 Angle : 0.674 7.639 15197 Z= 0.311 Chirality : 0.043 0.327 1753 Planarity : 0.005 0.057 1960 Dihedral : 12.170 169.295 1578 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.23), residues: 1387 helix: 0.61 (0.19), residues: 768 sheet: -0.79 (0.42), residues: 150 loop : -1.57 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 594 TYR 0.014 0.001 TYR A 544 PHE 0.028 0.002 PHE A 341 TRP 0.008 0.001 TRP D 607 HIS 0.002 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00298 (11251) covalent geometry : angle 0.67406 (15197) hydrogen bonds : bond 0.03021 ( 513) hydrogen bonds : angle 4.58491 ( 1500) Misc. bond : bond 0.00105 ( 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 308 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.450 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: 0.6160 (ptp90) cc_final: 0.5912 (mmt90) REVERT: A 494 GLU cc_start: 0.8135 (mp0) cc_final: 0.7859 (mp0) REVERT: A 498 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7621 (mmm-85) REVERT: A 568 GLN cc_start: 0.8349 (tp-100) cc_final: 0.7987 (tp40) REVERT: B 347 GLN cc_start: 0.8520 (mp10) cc_final: 0.8080 (mp10) REVERT: B 348 ASP cc_start: 0.8267 (p0) cc_final: 0.8018 (p0) REVERT: B 390 MET cc_start: 0.7755 (ttp) cc_final: 0.7521 (ttp) REVERT: C 348 ASP cc_start: 0.7516 (p0) cc_final: 0.7188 (p0) REVERT: C 390 MET cc_start: 0.7995 (ttp) cc_final: 0.7684 (ttp) REVERT: C 412 THR cc_start: 0.6913 (p) cc_final: 0.6702 (p) REVERT: C 439 PHE cc_start: 0.7813 (t80) cc_final: 0.7207 (t80) REVERT: C 461 LEU cc_start: 0.8692 (mt) cc_final: 0.8433 (mt) REVERT: C 503 ARG cc_start: 0.7863 (mpp-170) cc_final: 0.7134 (mtm110) REVERT: D 358 VAL cc_start: 0.8832 (t) cc_final: 0.8574 (p) REVERT: D 466 LEU cc_start: 0.8985 (tp) cc_final: 0.8719 (tp) REVERT: D 516 LEU cc_start: 0.9133 (pp) cc_final: 0.8356 (tt) REVERT: D 561 ILE cc_start: 0.8525 (mm) cc_final: 0.8266 (mm) REVERT: D 585 PHE cc_start: 0.8353 (m-80) cc_final: 0.7918 (m-80) REVERT: E 487 ASN cc_start: 0.8562 (t0) cc_final: 0.7569 (m-40) REVERT: E 488 ARG cc_start: 0.8457 (mpt-90) cc_final: 0.7966 (mpp80) REVERT: E 505 TYR cc_start: 0.7544 (t80) cc_final: 0.7262 (t80) REVERT: E 523 CYS cc_start: 0.3832 (p) cc_final: 0.3523 (m) REVERT: E 599 GLN cc_start: 0.6922 (tp40) cc_final: 0.6332 (pm20) REVERT: E 600 THR cc_start: 0.6973 (p) cc_final: 0.6406 (p) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.0965 time to fit residues: 42.7360 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 : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 30 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 78 optimal weight: 0.0470 chunk 106 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0884 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.124633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105519 restraints weight = 25932.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.108249 restraints weight = 16190.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110177 restraints weight = 11360.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111491 restraints weight = 8657.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112486 restraints weight = 7057.853| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11255 Z= 0.156 Angle : 0.688 9.422 15197 Z= 0.317 Chirality : 0.043 0.308 1753 Planarity : 0.005 0.055 1960 Dihedral : 11.882 167.874 1578 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.23), residues: 1387 helix: 0.72 (0.19), residues: 766 sheet: -0.54 (0.44), residues: 140 loop : -1.48 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 606 TYR 0.011 0.001 TYR G 8 PHE 0.029 0.002 PHE E 427 TRP 0.013 0.002 TRP A 607 HIS 0.002 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00353 (11251) covalent geometry : angle 0.68756 (15197) hydrogen bonds : bond 0.02993 ( 513) hydrogen bonds : angle 4.58941 ( 1500) Misc. bond : bond 0.00126 ( 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 311 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.452 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: 0.6200 (ptp90) cc_final: 0.5795 (mmt90) REVERT: A 494 GLU cc_start: 0.8168 (mp0) cc_final: 0.7880 (mp0) REVERT: A 568 GLN cc_start: 0.8401 (tp-100) cc_final: 0.8120 (tp40) REVERT: B 347 GLN cc_start: 0.8499 (mp10) cc_final: 0.8048 (mp10) REVERT: B 348 ASP cc_start: 0.8315 (p0) cc_final: 0.8080 (p0) REVERT: B 420 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 590 LYS cc_start: 0.8231 (mttp) cc_final: 0.7488 (tmtt) REVERT: C 348 ASP cc_start: 0.7575 (p0) cc_final: 0.7266 (p0) REVERT: C 390 MET cc_start: 0.8085 (ttp) cc_final: 0.7868 (ttp) REVERT: C 437 ILE cc_start: 0.9272 (tp) cc_final: 0.9070 (tp) REVERT: C 439 PHE cc_start: 0.7793 (t80) cc_final: 0.7258 (t80) REVERT: C 442 GLU cc_start: 0.8094 (mm-30) cc_final: 0.6988 (mm-30) REVERT: C 444 ASP cc_start: 0.8745 (p0) cc_final: 0.8315 (p0) REVERT: C 461 LEU cc_start: 0.8789 (mt) cc_final: 0.8541 (mt) REVERT: C 464 GLU cc_start: 0.8120 (tp30) cc_final: 0.7837 (tp30) REVERT: C 594 ARG cc_start: 0.7492 (ptm160) cc_final: 0.7012 (ptm160) REVERT: D 358 VAL cc_start: 0.8857 (t) cc_final: 0.8533 (p) REVERT: D 516 LEU cc_start: 0.9110 (pp) cc_final: 0.8364 (tt) REVERT: D 537 LEU cc_start: 0.8996 (tp) cc_final: 0.7964 (tp) REVERT: D 585 PHE cc_start: 0.8434 (m-80) cc_final: 0.7924 (m-80) REVERT: E 487 ASN cc_start: 0.8495 (t0) cc_final: 0.8269 (t0) REVERT: E 488 ARG cc_start: 0.8539 (mpt-90) cc_final: 0.8155 (mpp80) REVERT: E 505 TYR cc_start: 0.7532 (t80) cc_final: 0.7330 (t80) REVERT: E 523 CYS cc_start: 0.3957 (p) cc_final: 0.3652 (m) REVERT: E 599 GLN cc_start: 0.6950 (tp40) cc_final: 0.6429 (pm20) REVERT: E 600 THR cc_start: 0.6916 (p) cc_final: 0.6454 (p) REVERT: E 604 TYR cc_start: 0.5014 (m-10) cc_final: 0.4780 (m-10) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.1034 time to fit residues: 46.1740 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 : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 0.0050 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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** B 487 ASN C 347 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.125793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107023 restraints weight = 25526.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109711 restraints weight = 16269.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111597 restraints weight = 11543.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.112843 restraints weight = 8851.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.113566 restraints weight = 7297.079| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11255 Z= 0.128 Angle : 0.691 7.691 15197 Z= 0.318 Chirality : 0.043 0.348 1753 Planarity : 0.006 0.130 1960 Dihedral : 11.641 161.948 1578 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.08 % Allowed : 1.18 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.23), residues: 1387 helix: 0.67 (0.19), residues: 769 sheet: -0.57 (0.43), residues: 149 loop : -1.44 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 459 TYR 0.012 0.001 TYR E 505 PHE 0.031 0.002 PHE B 341 TRP 0.012 0.001 TRP D 607 HIS 0.002 0.000 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00287 (11251) covalent geometry : angle 0.69103 (15197) hydrogen bonds : bond 0.02961 ( 513) hydrogen bonds : angle 4.57349 ( 1500) Misc. bond : bond 0.00056 ( 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 320 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 0.376 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: 0.6381 (ptp90) cc_final: 0.6051 (mmt90) REVERT: A 459 ARG cc_start: 0.6876 (mmt90) cc_final: 0.6649 (tpp80) REVERT: A 494 GLU cc_start: 0.8131 (mp0) cc_final: 0.7818 (mp0) REVERT: A 568 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8091 (tp40) REVERT: B 347 GLN cc_start: 0.8362 (mp10) cc_final: 0.8001 (mp10) REVERT: B 420 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7177 (mm-30) REVERT: B 558 LEU cc_start: 0.8301 (mt) cc_final: 0.8088 (mp) REVERT: C 348 ASP cc_start: 0.7513 (p0) cc_final: 0.7158 (p0) REVERT: C 439 PHE cc_start: 0.7565 (t80) cc_final: 0.6950 (t80) REVERT: C 442 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7151 (mm-30) REVERT: C 461 LEU cc_start: 0.8828 (mt) cc_final: 0.8531 (mt) REVERT: D 358 VAL cc_start: 0.8820 (t) cc_final: 0.8587 (p) REVERT: D 420 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8758 (mm-30) REVERT: D 516 LEU cc_start: 0.9085 (pp) cc_final: 0.8339 (tt) REVERT: D 537 LEU cc_start: 0.9035 (tp) cc_final: 0.8539 (tp) REVERT: D 572 MET cc_start: 0.4604 (ptt) cc_final: 0.4397 (tmm) REVERT: D 585 PHE cc_start: 0.8410 (m-80) cc_final: 0.7919 (m-80) REVERT: D 607 TRP cc_start: 0.8293 (t60) cc_final: 0.7856 (t-100) REVERT: E 487 ASN cc_start: 0.8528 (t0) cc_final: 0.8142 (t0) REVERT: E 488 ARG cc_start: 0.8531 (mpt-90) cc_final: 0.8013 (mpp80) REVERT: E 523 CYS cc_start: 0.4027 (p) cc_final: 0.3641 (m) REVERT: E 599 GLN cc_start: 0.6950 (tp40) cc_final: 0.6402 (pm20) REVERT: E 600 THR cc_start: 0.6906 (p) cc_final: 0.6399 (p) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.0970 time to fit residues: 45.0604 Evaluate side-chains 244 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 112 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 GLN ** D 531 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 = 0.3731 r_free = 0.3731 target = 0.124401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105720 restraints weight = 25965.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108372 restraints weight = 16579.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.110232 restraints weight = 11748.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111513 restraints weight = 9019.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112402 restraints weight = 7402.776| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11255 Z= 0.144 Angle : 0.691 7.745 15197 Z= 0.320 Chirality : 0.043 0.315 1753 Planarity : 0.005 0.074 1960 Dihedral : 11.457 162.250 1578 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.08 % Allowed : 1.18 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.23), residues: 1387 helix: 0.70 (0.19), residues: 767 sheet: -0.55 (0.43), residues: 150 loop : -1.36 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 499 TYR 0.037 0.001 TYR E 604 PHE 0.024 0.002 PHE A 439 TRP 0.019 0.002 TRP A 607 HIS 0.002 0.001 HIS E 455 Details of bonding type rmsd covalent geometry : bond 0.00328 (11251) covalent geometry : angle 0.69136 (15197) hydrogen bonds : bond 0.03075 ( 513) hydrogen bonds : angle 4.56632 ( 1500) Misc. bond : bond 0.00107 ( 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: 1 poor density : 303 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ARG cc_start: 0.6477 (ptp90) cc_final: 0.6120 (mmt90) REVERT: A 494 GLU cc_start: 0.8086 (mp0) cc_final: 0.7815 (mp0) REVERT: B 347 GLN cc_start: 0.8379 (mp10) cc_final: 0.7994 (mp10) REVERT: B 348 ASP cc_start: 0.8232 (p0) cc_final: 0.8029 (p0) REVERT: B 487 ASN cc_start: 0.8929 (m-40) cc_final: 0.8686 (m110) REVERT: B 558 LEU cc_start: 0.8194 (mt) cc_final: 0.7984 (mp) REVERT: B 590 LYS cc_start: 0.8166 (mttp) cc_final: 0.7357 (tmtt) REVERT: C 348 ASP cc_start: 0.7449 (p0) cc_final: 0.7050 (p0) REVERT: C 439 PHE cc_start: 0.7766 (t80) cc_final: 0.7199 (t80) REVERT: C 442 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7092 (mm-30) REVERT: C 461 LEU cc_start: 0.8778 (mt) cc_final: 0.8527 (mt) REVERT: C 464 GLU cc_start: 0.8135 (tp30) cc_final: 0.7930 (tp30) REVERT: D 358 VAL cc_start: 0.8868 (t) cc_final: 0.8629 (p) REVERT: D 494 GLU cc_start: 0.7669 (tp30) cc_final: 0.7242 (tp30) REVERT: D 516 LEU cc_start: 0.9077 (pp) cc_final: 0.8336 (tt) REVERT: D 572 MET cc_start: 0.4653 (ptt) cc_final: 0.4405 (tmm) REVERT: D 585 PHE cc_start: 0.8475 (m-80) cc_final: 0.7979 (m-80) REVERT: E 487 ASN cc_start: 0.8507 (t0) cc_final: 0.7705 (t0) REVERT: E 488 ARG cc_start: 0.8349 (mpt-90) cc_final: 0.8035 (mpp80) REVERT: E 523 CYS cc_start: 0.4311 (p) cc_final: 0.3919 (m) REVERT: E 599 GLN cc_start: 0.7025 (tp40) cc_final: 0.6407 (pm20) REVERT: E 600 THR cc_start: 0.6818 (p) cc_final: 0.6500 (p) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.0952 time to fit residues: 42.2851 Evaluate side-chains 234 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 77 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.103309 restraints weight = 25323.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105720 restraints weight = 16188.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107516 restraints weight = 11583.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108635 restraints weight = 8910.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109595 restraints weight = 7354.802| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11255 Z= 0.157 Angle : 0.715 8.740 15197 Z= 0.336 Chirality : 0.044 0.358 1753 Planarity : 0.005 0.062 1960 Dihedral : 11.297 157.196 1578 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.08 % Allowed : 0.59 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.23), residues: 1387 helix: 0.66 (0.19), residues: 769 sheet: -0.40 (0.44), residues: 140 loop : -1.24 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 499 TYR 0.031 0.001 TYR E 604 PHE 0.022 0.002 PHE E 427 TRP 0.013 0.002 TRP D 607 HIS 0.002 0.001 HIS C 455 Details of bonding type rmsd covalent geometry : bond 0.00357 (11251) covalent geometry : angle 0.71510 (15197) hydrogen bonds : bond 0.03207 ( 513) hydrogen bonds : angle 4.59836 ( 1500) Misc. bond : bond 0.00119 ( 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 298 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 PHE cc_start: 0.6477 (m-80) cc_final: 0.6233 (m-10) REVERT: A 372 ARG cc_start: 0.6465 (ptp90) cc_final: 0.6066 (mmt90) REVERT: A 494 GLU cc_start: 0.8138 (mp0) cc_final: 0.7855 (mp0) REVERT: B 347 GLN cc_start: 0.8412 (mp10) cc_final: 0.8060 (mp10) REVERT: B 558 LEU cc_start: 0.8225 (mt) cc_final: 0.8007 (mp) REVERT: B 590 LYS cc_start: 0.8188 (mttp) cc_final: 0.7418 (tmtt) REVERT: B 599 GLN cc_start: 0.8551 (mp10) cc_final: 0.8331 (mp10) REVERT: C 348 ASP cc_start: 0.7553 (p0) cc_final: 0.7206 (p0) REVERT: C 390 MET cc_start: 0.8062 (ttp) cc_final: 0.7736 (ttp) REVERT: C 439 PHE cc_start: 0.7740 (t80) cc_final: 0.7231 (t80) REVERT: C 442 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7131 (mm-30) REVERT: C 444 ASP cc_start: 0.8712 (p0) cc_final: 0.8458 (p0) REVERT: C 461 LEU cc_start: 0.8766 (mt) cc_final: 0.8490 (mt) REVERT: C 464 GLU cc_start: 0.8172 (tp30) cc_final: 0.7927 (tp30) REVERT: D 494 GLU cc_start: 0.7750 (tp30) cc_final: 0.7349 (tp30) REVERT: D 516 LEU cc_start: 0.9104 (pp) cc_final: 0.8410 (tt) REVERT: D 572 MET cc_start: 0.4668 (ptt) cc_final: 0.4433 (tmm) REVERT: D 585 PHE cc_start: 0.8490 (m-80) cc_final: 0.8034 (m-80) REVERT: E 487 ASN cc_start: 0.8478 (t0) cc_final: 0.7414 (t0) REVERT: E 488 ARG cc_start: 0.8391 (mpt-90) cc_final: 0.7792 (mpp80) REVERT: E 523 CYS cc_start: 0.4390 (p) cc_final: 0.4026 (m) REVERT: E 599 GLN cc_start: 0.7046 (tp40) cc_final: 0.6406 (pm20) REVERT: E 600 THR cc_start: 0.6727 (p) cc_final: 0.6411 (p) outliers start: 1 outliers final: 1 residues processed: 298 average time/residue: 0.0947 time to fit residues: 41.6883 Evaluate side-chains 233 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 68 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 45 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.122870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104615 restraints weight = 25432.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107153 restraints weight = 16124.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.108960 restraints weight = 11434.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110221 restraints weight = 8742.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.111050 restraints weight = 7108.442| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11255 Z= 0.128 Angle : 0.703 7.469 15197 Z= 0.326 Chirality : 0.043 0.328 1753 Planarity : 0.005 0.070 1960 Dihedral : 11.096 151.924 1578 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.23), residues: 1387 helix: 0.73 (0.19), residues: 763 sheet: -0.35 (0.44), residues: 140 loop : -1.21 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 499 TYR 0.014 0.001 TYR G 8 PHE 0.027 0.002 PHE A 439 TRP 0.015 0.002 TRP D 607 HIS 0.001 0.000 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00292 (11251) covalent geometry : angle 0.70336 (15197) hydrogen bonds : bond 0.03037 ( 513) hydrogen bonds : angle 4.60305 ( 1500) Misc. bond : bond 0.00052 ( 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 306 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ARG cc_start: 0.6502 (ptp90) cc_final: 0.6097 (mmt90) REVERT: A 494 GLU cc_start: 0.8089 (mp0) cc_final: 0.7801 (mp0) REVERT: B 558 LEU cc_start: 0.8214 (mt) cc_final: 0.7995 (mp) REVERT: C 348 ASP cc_start: 0.7481 (p0) cc_final: 0.7128 (p0) REVERT: C 390 MET cc_start: 0.7992 (ttp) cc_final: 0.7676 (ttp) REVERT: C 412 THR cc_start: 0.7003 (p) cc_final: 0.6776 (p) REVERT: C 439 PHE cc_start: 0.7653 (t80) cc_final: 0.7220 (t80) REVERT: C 442 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7064 (mm-30) REVERT: C 461 LEU cc_start: 0.8783 (mt) cc_final: 0.8536 (mt) REVERT: C 468 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8423 (mm-30) REVERT: D 494 GLU cc_start: 0.7689 (tp30) cc_final: 0.7301 (tp30) REVERT: D 516 LEU cc_start: 0.9103 (pp) cc_final: 0.8409 (tt) REVERT: D 585 PHE cc_start: 0.8369 (m-80) cc_final: 0.7973 (m-80) REVERT: D 607 TRP cc_start: 0.8415 (t60) cc_final: 0.7952 (t-100) REVERT: E 390 MET cc_start: 0.7798 (tpt) cc_final: 0.7492 (tpt) REVERT: E 487 ASN cc_start: 0.8477 (t0) cc_final: 0.7820 (t0) REVERT: E 488 ARG cc_start: 0.8466 (mpt-90) cc_final: 0.7852 (mpp80) REVERT: E 523 CYS cc_start: 0.4271 (p) cc_final: 0.3930 (m) REVERT: E 599 GLN cc_start: 0.6951 (tp40) cc_final: 0.6343 (pm20) REVERT: E 600 THR cc_start: 0.7118 (p) cc_final: 0.6653 (p) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.0948 time to fit residues: 43.0305 Evaluate side-chains 240 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 83 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.0570 chunk 73 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 25 optimal weight: 0.0020 overall best weight: 0.4306 ------------------------------------------------------------------------------- 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** B 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105432 restraints weight = 25183.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108048 restraints weight = 15928.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.109879 restraints weight = 11175.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111169 restraints weight = 8476.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.111947 restraints weight = 6863.043| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11255 Z= 0.124 Angle : 0.715 8.626 15197 Z= 0.333 Chirality : 0.044 0.348 1753 Planarity : 0.005 0.056 1960 Dihedral : 10.889 149.683 1578 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.22), residues: 1387 helix: 0.72 (0.19), residues: 762 sheet: -0.34 (0.44), residues: 140 loop : -1.19 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 499 TYR 0.010 0.001 TYR D 415 PHE 0.019 0.001 PHE E 427 TRP 0.015 0.002 TRP D 607 HIS 0.005 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00279 (11251) covalent geometry : angle 0.71472 (15197) hydrogen bonds : bond 0.03072 ( 513) hydrogen bonds : angle 4.62305 ( 1500) Misc. bond : bond 0.00036 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.57 seconds wall clock time: 32 minutes 37.46 seconds (1957.46 seconds total)