Starting phenix.real_space_refine on Sat Jul 4 05:27:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7x_44327/07_2026/9b7x_44327.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7x_44327/07_2026/9b7x_44327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b7x_44327/07_2026/9b7x_44327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7x_44327/07_2026/9b7x_44327.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b7x_44327/07_2026/9b7x_44327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7x_44327/07_2026/9b7x_44327.map" } resolution = 2.76 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 ------------------------------------------------------------------------------- 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= 1.000 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 67 5.16 5 C 12037 2.51 5 N 3311 2.21 5 O 3687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19103 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3166 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 369} Chain breaks: 2 Chain: "B" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1548 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 185} Chain breaks: 2 Chain: "C" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4039 Classifications: {'peptide': 506} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 472} Chain breaks: 1 Chain: "D" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3166 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 369} Chain breaks: 2 Chain: "E" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1333 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 160} Chain breaks: 1 Chain: "F" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4039 Classifications: {'peptide': 506} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 472} Chain breaks: 1 Chain: "H" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 806 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 4.06, per 1000 atoms: 0.21 Number of scatterers: 19103 At special positions: 0 Unit cell: (157.25, 135.975, 103.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 67 16.00 O 3687 8.00 N 3311 7.00 C 12037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " distance=2.05 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 110 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 978.3 milliseconds 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4442 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 51 sheets defined 7.9% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.641A pdb=" N LEU A 435 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.920A pdb=" N LEU B 435 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 569 removed outlier: 4.367A pdb=" N THR B 568 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.515A pdb=" N CYS C 291 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.550A pdb=" N ASN C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 removed outlier: 3.633A pdb=" N SER C 358 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 359 " --> pdb=" O LEU C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 359' Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 431 through 435 removed outlier: 4.096A pdb=" N LEU C 435 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 540 removed outlier: 4.064A pdb=" N SER C 540 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 569 removed outlier: 4.435A pdb=" N THR C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 431 through 435 removed outlier: 3.641A pdb=" N LEU D 435 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 567 Processing helix chain 'E' and resid 431 through 435 removed outlier: 3.920A pdb=" N LEU E 435 " --> pdb=" O LEU E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 569 removed outlier: 4.366A pdb=" N THR E 568 " --> pdb=" O GLU E 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 288 through 292 Processing helix chain 'F' and resid 294 through 304 removed outlier: 3.550A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 removed outlier: 3.582A pdb=" N SER F 358 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA F 359 " --> pdb=" O LEU F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 359' Processing helix chain 'F' and resid 396 through 400 Processing helix chain 'F' and resid 431 through 435 removed outlier: 4.096A pdb=" N LEU F 435 " --> pdb=" O LEU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 563 through 569 removed outlier: 4.293A pdb=" N THR F 568 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 250 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 240 through 250 current: chain 'A' and resid 331 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA3, first strand: chain 'A' and resid 479 through 480 removed outlier: 6.488A pdb=" N ILE A 479 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET A 605 " --> pdb=" O PHE B 629 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 490 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 511 Processing sheet with id=AA7, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AA8, first strand: chain 'A' and resid 551 through 553 removed outlier: 7.069A pdb=" N ASP A 551 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL C 465 " --> pdb=" O ASP A 551 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 593 through 596 removed outlier: 4.022A pdb=" N GLY A 578 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 619 through 621 removed outlier: 6.235A pdb=" N ALA A 620 " --> pdb=" O MET A 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 627 through 629 removed outlier: 3.947A pdb=" N MET C 605 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 451 removed outlier: 5.487A pdb=" N LEU B 447 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER B 464 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE B 451 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR B 460 " --> pdb=" O ILE B 451 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.262A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET B 605 " --> pdb=" O PHE C 629 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 483 through 484 Processing sheet with id=AB6, first strand: chain 'B' and resid 488 through 490 Processing sheet with id=AB7, first strand: chain 'B' and resid 593 through 596 removed outlier: 4.046A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 238 through 249 current: chain 'C' and resid 331 through 336 Processing sheet with id=AB9, first strand: chain 'C' and resid 258 through 261 Processing sheet with id=AC1, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.243A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AC3, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC4, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AC5, first strand: chain 'C' and resid 578 through 581 removed outlier: 3.941A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 619 through 621 removed outlier: 6.059A pdb=" N ALA C 620 " --> pdb=" O MET C 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 240 through 249 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 240 through 249 current: chain 'D' and resid 331 through 336 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 258 through 261 Processing sheet with id=AC9, first strand: chain 'D' and resid 479 through 480 removed outlier: 6.487A pdb=" N ILE D 479 " --> pdb=" O VAL D 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 483 through 484 Processing sheet with id=AD2, first strand: chain 'D' and resid 488 through 490 Processing sheet with id=AD3, first strand: chain 'D' and resid 514 through 517 removed outlier: 3.941A pdb=" N GLY F 578 " --> pdb=" O VAL F 596 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 542 through 544 Processing sheet with id=AD5, first strand: chain 'D' and resid 551 through 554 removed outlier: 7.053A pdb=" N ASP D 551 " --> pdb=" O VAL F 465 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL F 465 " --> pdb=" O ASP D 551 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 593 through 596 removed outlier: 4.023A pdb=" N GLY D 578 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 619 through 621 removed outlier: 6.235A pdb=" N ALA D 620 " --> pdb=" O MET D 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 627 through 629 removed outlier: 3.974A pdb=" N MET F 605 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 445 through 451 removed outlier: 5.487A pdb=" N LEU E 447 " --> pdb=" O SER E 464 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER E 464 " --> pdb=" O LEU E 447 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE E 451 " --> pdb=" O THR E 460 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR E 460 " --> pdb=" O ILE E 451 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 479 through 480 removed outlier: 6.261A pdb=" N ILE E 479 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET E 605 " --> pdb=" O PHE F 629 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 483 through 484 Processing sheet with id=AE3, first strand: chain 'E' and resid 488 through 490 Processing sheet with id=AE4, first strand: chain 'E' and resid 593 through 596 removed outlier: 4.047A pdb=" N GLY E 578 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 238 through 249 current: chain 'F' and resid 331 through 336 Processing sheet with id=AE6, first strand: chain 'F' and resid 258 through 261 Processing sheet with id=AE7, first strand: chain 'F' and resid 427 through 428 removed outlier: 6.236A pdb=" N ALA F 427 " --> pdb=" O ARG F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'F' and resid 483 through 484 Processing sheet with id=AE9, first strand: chain 'F' and resid 488 through 490 Processing sheet with id=AF1, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AF2, first strand: chain 'F' and resid 619 through 621 removed outlier: 6.058A pdb=" N ALA F 620 " --> pdb=" O MET F 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AF4, first strand: chain 'H' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 30 through 31 current: chain 'H' and resid 65 through 70 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 76 through 78 current: chain 'H' and resid 133 through 136 Processing sheet with id=AF5, first strand: chain 'L' and resid 29 through 32 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 29 through 32 current: chain 'L' and resid 67 through 70 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 67 through 70 current: chain 'L' and resid 119 through 121 No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'L' and resid 38 through 43 239 hydrogen bonds defined for protein. 453 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: 3.37 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5868 1.33 - 1.45: 3593 1.45 - 1.57: 10077 1.57 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 19654 Sorted by residual: bond pdb=" C TYR D 399 " pdb=" N PHE D 400 " ideal model delta sigma weight residual 1.331 1.264 0.067 2.07e-02 2.33e+03 1.03e+01 bond pdb=" C TYR A 399 " pdb=" N PHE A 400 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.07e-02 2.33e+03 1.01e+01 bond pdb=" C PRO C 365 " pdb=" O PRO C 365 " ideal model delta sigma weight residual 1.246 1.226 0.020 8.50e-03 1.38e+04 5.28e+00 bond pdb=" C GLU C 723 " pdb=" O GLU C 723 " ideal model delta sigma weight residual 1.246 1.226 0.020 9.20e-03 1.18e+04 4.94e+00 bond pdb=" CB VAL F 239 " pdb=" CG2 VAL F 239 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.81e+00 ... (remaining 19649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 26246 2.79 - 5.58: 453 5.58 - 8.38: 52 8.38 - 11.17: 17 11.17 - 13.96: 1 Bond angle restraints: 26769 Sorted by residual: angle pdb=" N ASP L 48 " pdb=" CA ASP L 48 " pdb=" C ASP L 48 " ideal model delta sigma weight residual 111.14 122.25 -11.11 1.08e+00 8.57e-01 1.06e+02 angle pdb=" N TYR H 131 " pdb=" CA TYR H 131 " pdb=" C TYR H 131 " ideal model delta sigma weight residual 108.41 122.37 -13.96 1.61e+00 3.86e-01 7.52e+01 angle pdb=" N GLU H 124 " pdb=" CA GLU H 124 " pdb=" C GLU H 124 " ideal model delta sigma weight residual 111.28 119.67 -8.39 1.09e+00 8.42e-01 5.92e+01 angle pdb=" N SER A 269 " pdb=" CA SER A 269 " pdb=" C SER A 269 " ideal model delta sigma weight residual 110.28 120.82 -10.54 1.48e+00 4.57e-01 5.07e+01 angle pdb=" N THR A 264 " pdb=" CA THR A 264 " pdb=" C THR A 264 " ideal model delta sigma weight residual 111.07 103.72 7.35 1.07e+00 8.73e-01 4.71e+01 ... (remaining 26764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 11026 17.77 - 35.53: 381 35.53 - 53.30: 59 53.30 - 71.07: 14 71.07 - 88.83: 17 Dihedral angle restraints: 11497 sinusoidal: 4528 harmonic: 6969 Sorted by residual: dihedral pdb=" N SER D 268 " pdb=" C SER D 268 " pdb=" CA SER D 268 " pdb=" CB SER D 268 " ideal model delta harmonic sigma weight residual 122.80 136.10 -13.30 0 2.50e+00 1.60e-01 2.83e+01 dihedral pdb=" N ASP L 48 " pdb=" C ASP L 48 " pdb=" CA ASP L 48 " pdb=" CB ASP L 48 " ideal model delta harmonic sigma weight residual 122.80 135.42 -12.62 0 2.50e+00 1.60e-01 2.55e+01 dihedral pdb=" C ASN A 253 " pdb=" N ASN A 253 " pdb=" CA ASN A 253 " pdb=" CB ASN A 253 " ideal model delta harmonic sigma weight residual -122.60 -135.11 12.51 0 2.50e+00 1.60e-01 2.50e+01 ... (remaining 11494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 2596 0.116 - 0.233: 162 0.233 - 0.349: 14 0.349 - 0.466: 0 0.466 - 0.582: 3 Chirality restraints: 2775 Sorted by residual: chirality pdb=" CA SER D 268 " pdb=" N SER D 268 " pdb=" C SER D 268 " pdb=" CB SER D 268 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.48e+00 chirality pdb=" CA ASP L 48 " pdb=" N ASP L 48 " pdb=" C ASP L 48 " pdb=" CB ASP L 48 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.30e+00 chirality pdb=" CA ASN A 253 " pdb=" N ASN A 253 " pdb=" C ASN A 253 " pdb=" CB ASN A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.17e+00 ... (remaining 2772 not shown) Planarity restraints: 3558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 69 " -0.018 2.00e-02 2.50e+03 1.59e-02 5.04e+00 pdb=" CG TYR H 69 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR H 69 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR H 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 69 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR H 69 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR H 69 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 69 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 367 " 0.015 2.00e-02 2.50e+03 1.56e-02 4.25e+00 pdb=" CG PHE F 367 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE F 367 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE F 367 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE F 367 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 367 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE F 367 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 228 " -0.011 2.00e-02 2.50e+03 1.26e-02 3.96e+00 pdb=" CG TRP C 228 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP C 228 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 228 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 228 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 228 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 228 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 228 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 228 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 228 " 0.003 2.00e-02 2.50e+03 ... (remaining 3555 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 187 2.56 - 3.15: 15875 3.15 - 3.73: 29903 3.73 - 4.32: 45181 4.32 - 4.90: 74106 Nonbonded interactions: 165252 Sorted by model distance: nonbonded pdb=" OE2 GLU C 563 " pdb=" OH TYR C 613 " model vdw 1.980 3.040 nonbonded pdb=" O SER D 358 " pdb=" NE2 GLN F 442 " model vdw 2.052 3.120 nonbonded pdb=" OG SER A 265 " pdb=" OH TYR A 274 " model vdw 2.108 3.040 nonbonded pdb=" OE2 GLU C 712 " pdb=" NH2 ARG C 725 " model vdw 2.119 3.120 nonbonded pdb=" NH2 ARG A 485 " pdb=" OG SER A 576 " model vdw 2.200 3.120 ... (remaining 165247 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 'D' } ncs_group { reference = (chain 'B' and resid 420 through 608) selection = chain 'E' } ncs_group { reference = (chain 'C' and resid 219 through 736) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 18.130 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.009 0.072 19656 Z= 0.429 Angle : 0.942 13.962 26773 Z= 0.582 Chirality : 0.065 0.582 2775 Planarity : 0.005 0.037 3558 Dihedral : 10.411 88.834 7049 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.81 % Allowed : 2.34 % Favored : 96.85 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.70 % 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 are not related in a simple way. whole: -1.09 (0.14), residues: 2390 helix: -4.06 (0.30), residues: 92 sheet: -0.33 (0.17), residues: 626 loop : -0.67 (0.12), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG C 296 TYR 0.039 0.003 TYR H 69 PHE 0.036 0.003 PHE F 367 TRP 0.033 0.004 TRP H 136 HIS 0.017 0.003 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00925 / 0.43 (19654) covalent geometry : angle 0.94231 / 0.58 (26769) SS BOND : bond 0.01041 / 0.54 ( 2) SS BOND : angle 0.91082 / 0.50 ( 4) hydrogen bonds : bond 0.23122 / 15.54 ( 239) hydrogen bonds : angle 8.37310 / 5.96 ( 453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 433 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 367 PHE cc_start: 0.7406 (t80) cc_final: 0.6077 (m-10) REVERT: A 565 GLU cc_start: 0.7087 (mp0) cc_final: 0.6436 (mt-10) REVERT: A 651 ASN cc_start: 0.7717 (m110) cc_final: 0.7424 (m110) REVERT: B 485 ARG cc_start: 0.6932 (ttm170) cc_final: 0.6575 (ttp-170) REVERT: B 514 ARG cc_start: 0.8103 (mtm180) cc_final: 0.6748 (mmt180) REVERT: C 259 GLN cc_start: 0.7064 (tt0) cc_final: 0.5636 (pm20) REVERT: C 495 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: C 676 THR cc_start: 0.7705 (t) cc_final: 0.7440 (p) REVERT: D 367 PHE cc_start: 0.6544 (t80) cc_final: 0.5958 (m-10) REVERT: D 528 LYS cc_start: 0.7193 (mtmt) cc_final: 0.6959 (mtpp) REVERT: E 514 ARG cc_start: 0.7488 (mtm180) cc_final: 0.5528 (tpt170) REVERT: H 91 ASP cc_start: 0.7881 (t0) cc_final: 0.7679 (t0) REVERT: H 124 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6350 (mp0) outliers start: 17 outliers final: 9 residues processed: 447 average time/residue: 0.5540 time to fit residues: 280.3821 Evaluate side-chains 250 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 239 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 131 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 272 ASN A 292 HIS A 430 GLN A 608 GLN A 646 GLN A 651 ASN B 430 GLN B 452 ASN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 HIS B 630 HIS C 253 ASN C 410 ASN C 452 ASN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 519 ASN C 585 GLN C 646 GLN C 651 ASN C 673 GLN C 700 GLN D 253 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 GLN D 624 HIS D 646 GLN D 651 ASN E 428 HIS ** E 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN E 515 ASN E 585 GLN F 253 ASN F 272 ASN F 343 GLN F 452 ASN F 495 GLN F 546 GLN F 585 GLN F 608 GLN F 646 GLN F 651 ASN F 673 GLN F 700 GLN F 704 ASN H 71 HIS H 117 GLN H 138 GLN ** L 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 ASN L 101 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101462 restraints weight = 32469.688| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.22 r_work: 0.3257 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19656 Z= 0.125 Angle : 0.589 8.837 26773 Z= 0.311 Chirality : 0.044 0.207 2775 Planarity : 0.004 0.051 3558 Dihedral : 5.949 82.281 2636 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.38 % Allowed : 10.06 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 are not related in a simple way. whole: -0.41 (0.15), residues: 2390 helix: -3.04 (0.41), residues: 92 sheet: 0.13 (0.18), residues: 611 loop : -0.22 (0.13), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 485 TYR 0.017 0.002 TYR D 674 PHE 0.018 0.001 PHE L 84 TRP 0.016 0.001 TRP C 228 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (19654) covalent geometry : angle 0.58861 / 0.31 (26769) SS BOND : bond 0.00439 / 0.22 ( 2) SS BOND : angle 1.67607 / 0.91 ( 4) hydrogen bonds : bond 0.03609 / 2.46 ( 239) hydrogen bonds : angle 6.36406 / 4.46 ( 453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 279 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 367 PHE cc_start: 0.7470 (t80) cc_final: 0.5863 (m-10) REVERT: A 518 MET cc_start: 0.8032 (tpp) cc_final: 0.7687 (ttp) REVERT: A 524 MET cc_start: 0.7291 (mtm) cc_final: 0.6997 (mtm) REVERT: A 651 ASN cc_start: 0.7923 (m-40) cc_final: 0.7428 (m110) REVERT: B 514 ARG cc_start: 0.7930 (mtm180) cc_final: 0.6285 (mmt180) REVERT: C 238 ARG cc_start: 0.8592 (ptp-170) cc_final: 0.8112 (ptt180) REVERT: C 259 GLN cc_start: 0.7298 (tt0) cc_final: 0.5471 (pm20) REVERT: C 626 ASP cc_start: 0.7810 (m-30) cc_final: 0.7390 (m-30) REVERT: D 367 PHE cc_start: 0.6376 (t80) cc_final: 0.5639 (m-10) REVERT: D 373 MET cc_start: 0.6856 (ttt) cc_final: 0.6639 (ttp) REVERT: D 641 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8458 (mttm) REVERT: E 514 ARG cc_start: 0.6969 (mtm180) cc_final: 0.4799 (tpt170) REVERT: E 531 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7772 (mp0) REVERT: E 566 ILE cc_start: 0.8284 (pt) cc_final: 0.8084 (pp) REVERT: F 316 LYS cc_start: 0.8084 (mttt) cc_final: 0.7634 (mmtt) REVERT: F 691 ASN cc_start: 0.8296 (t0) cc_final: 0.8035 (t0) REVERT: H 25 GLU cc_start: 0.8811 (mp0) cc_final: 0.8575 (mp0) outliers start: 50 outliers final: 18 residues processed: 309 average time/residue: 0.5325 time to fit residues: 186.8555 Evaluate side-chains 243 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain D residue 641 LYS Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 76 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 227 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 overall best weight: 7.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 486 GLN A 646 GLN A 678 GLN B 512 ASN B 608 GLN C 253 ASN C 262 ASN C 343 GLN C 376 GLN C 410 ASN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN F 253 ASN F 272 ASN F 321 GLN F 410 ASN F 428 HIS ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 GLN F 599 GLN ** F 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** L 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.094886 restraints weight = 33148.129| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.19 r_work: 0.3162 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 19656 Z= 0.292 Angle : 0.658 8.144 26773 Z= 0.350 Chirality : 0.047 0.199 2775 Planarity : 0.005 0.043 3558 Dihedral : 5.457 51.072 2618 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.10 % Allowed : 11.25 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 are not related in a simple way. whole: -0.54 (0.16), residues: 2390 helix: -2.99 (0.46), residues: 92 sheet: 0.22 (0.20), residues: 558 loop : -0.39 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 238 TYR 0.022 0.002 TYR C 701 PHE 0.028 0.002 PHE L 84 TRP 0.017 0.002 TRP F 228 HIS 0.016 0.002 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.29 (19654) covalent geometry : angle 0.65732 / 0.35 (26769) SS BOND : bond 0.00712 / 0.37 ( 2) SS BOND : angle 1.65936 / 0.92 ( 4) hydrogen bonds : bond 0.03934 / 2.71 ( 239) hydrogen bonds : angle 6.24986 / 4.38 ( 453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 605 MET cc_start: 0.8428 (mtt) cc_final: 0.7997 (mtt) REVERT: A 640 MET cc_start: 0.8716 (mtp) cc_final: 0.8478 (ttt) REVERT: B 514 ARG cc_start: 0.7938 (mtm180) cc_final: 0.6262 (mmt180) REVERT: C 259 GLN cc_start: 0.7723 (tt0) cc_final: 0.5662 (pm20) REVERT: C 377 TYR cc_start: 0.8497 (t80) cc_final: 0.8209 (t80) REVERT: E 486 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: E 514 ARG cc_start: 0.7155 (mtm180) cc_final: 0.4665 (tpt170) REVERT: E 542 ILE cc_start: 0.3128 (pp) cc_final: 0.2826 (mt) REVERT: F 316 LYS cc_start: 0.8352 (mttt) cc_final: 0.7969 (mmtt) REVERT: F 410 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.7102 (p0) REVERT: F 691 ASN cc_start: 0.8252 (t0) cc_final: 0.7999 (t0) REVERT: H 25 GLU cc_start: 0.8777 (mp0) cc_final: 0.8563 (mp0) outliers start: 65 outliers final: 35 residues processed: 276 average time/residue: 0.5114 time to fit residues: 160.9731 Evaluate side-chains 244 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 410 ASN Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 649 ILE Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 41 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 GLN C 410 ASN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 HIS L 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.121072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097245 restraints weight = 32665.397| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.17 r_work: 0.3193 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19656 Z= 0.138 Angle : 0.551 7.176 26773 Z= 0.289 Chirality : 0.042 0.183 2775 Planarity : 0.004 0.053 3558 Dihedral : 4.953 46.100 2618 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.81 % Allowed : 12.97 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 are not related in a simple way. whole: -0.40 (0.16), residues: 2390 helix: -2.88 (0.47), residues: 92 sheet: 0.23 (0.20), residues: 580 loop : -0.25 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 610 TYR 0.020 0.002 TYR D 674 PHE 0.013 0.001 PHE L 84 TRP 0.013 0.001 TRP H 136 HIS 0.006 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19654) covalent geometry : angle 0.55093 / 0.29 (26769) SS BOND : bond 0.00405 / 0.21 ( 2) SS BOND : angle 1.46482 / 0.81 ( 4) hydrogen bonds : bond 0.03083 / 2.11 ( 239) hydrogen bonds : angle 5.90611 / 4.14 ( 453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 240 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 253 ASN cc_start: 0.6999 (OUTLIER) cc_final: 0.6768 (p0) REVERT: A 367 PHE cc_start: 0.7465 (t80) cc_final: 0.5720 (m-10) REVERT: A 585 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6764 (pm20) REVERT: A 640 MET cc_start: 0.8656 (mtp) cc_final: 0.8367 (ttt) REVERT: B 514 ARG cc_start: 0.7946 (mtm180) cc_final: 0.6260 (mmt180) REVERT: C 231 ASP cc_start: 0.7331 (p0) cc_final: 0.7049 (p0) REVERT: C 238 ARG cc_start: 0.8558 (ptp-170) cc_final: 0.8105 (ptt180) REVERT: C 259 GLN cc_start: 0.7688 (tt0) cc_final: 0.5635 (pm20) REVERT: C 377 TYR cc_start: 0.8371 (t80) cc_final: 0.8128 (t80) REVERT: D 367 PHE cc_start: 0.6362 (t80) cc_final: 0.5612 (m-10) REVERT: E 486 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: E 514 ARG cc_start: 0.7147 (mtm180) cc_final: 0.4714 (tpt170) REVERT: E 542 ILE cc_start: 0.3114 (pp) cc_final: 0.2848 (mt) REVERT: E 564 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6525 (pp20) REVERT: E 567 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8416 (ttpp) REVERT: F 316 LYS cc_start: 0.8377 (mttt) cc_final: 0.7981 (mmtt) REVERT: F 691 ASN cc_start: 0.8089 (t0) cc_final: 0.7835 (t0) REVERT: H 25 GLU cc_start: 0.8685 (mp0) cc_final: 0.8423 (mp0) REVERT: H 138 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8595 (mp10) outliers start: 59 outliers final: 22 residues processed: 273 average time/residue: 0.5462 time to fit residues: 169.0192 Evaluate side-chains 246 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 564 GLU Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 98 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 98 optimal weight: 10.0000 chunk 186 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 ASN C 410 ASN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN D 319 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN L 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.095756 restraints weight = 32653.892| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.18 r_work: 0.3172 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19656 Z= 0.196 Angle : 0.577 7.945 26773 Z= 0.302 Chirality : 0.044 0.173 2775 Planarity : 0.004 0.052 3558 Dihedral : 4.971 44.994 2618 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.96 % Allowed : 13.45 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 are not related in a simple way. whole: -0.46 (0.16), residues: 2390 helix: -2.94 (0.46), residues: 92 sheet: 0.21 (0.20), residues: 572 loop : -0.30 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 610 TYR 0.021 0.002 TYR D 674 PHE 0.017 0.002 PHE A 535 TRP 0.012 0.002 TRP A 509 HIS 0.009 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (19654) covalent geometry : angle 0.57667 / 0.30 (26769) SS BOND : bond 0.00561 / 0.29 ( 2) SS BOND : angle 1.33029 / 0.74 ( 4) hydrogen bonds : bond 0.03272 / 2.25 ( 239) hydrogen bonds : angle 5.89135 / 4.12 ( 453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 223 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 253 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6721 (p0) REVERT: A 585 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: B 514 ARG cc_start: 0.7947 (mtm180) cc_final: 0.6251 (mmt180) REVERT: C 231 ASP cc_start: 0.7340 (p0) cc_final: 0.7111 (p0) REVERT: C 238 ARG cc_start: 0.8577 (ptp-170) cc_final: 0.8157 (ptt180) REVERT: C 259 GLN cc_start: 0.7746 (tt0) cc_final: 0.5712 (pm20) REVERT: D 367 PHE cc_start: 0.6339 (t80) cc_final: 0.5611 (m-10) REVERT: E 436 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7463 (ptp) REVERT: E 486 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: E 514 ARG cc_start: 0.7201 (mtm180) cc_final: 0.4629 (tpt170) REVERT: E 564 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6496 (pp20) REVERT: F 316 LYS cc_start: 0.8384 (mttt) cc_final: 0.8150 (mmmt) REVERT: F 691 ASN cc_start: 0.8084 (t0) cc_final: 0.7808 (t0) outliers start: 62 outliers final: 35 residues processed: 260 average time/residue: 0.5369 time to fit residues: 158.8791 Evaluate side-chains 240 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 564 GLU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 77 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 0.0000 chunk 122 optimal weight: 0.8980 chunk 191 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 overall best weight: 4.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN F 430 GLN ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 GLN H 138 GLN L 21 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.119448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.095609 restraints weight = 32720.501| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.17 r_work: 0.3172 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19656 Z= 0.198 Angle : 0.578 7.814 26773 Z= 0.302 Chirality : 0.044 0.161 2775 Planarity : 0.004 0.055 3558 Dihedral : 4.941 42.810 2618 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.20 % Allowed : 13.40 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 are not related in a simple way. whole: -0.51 (0.16), residues: 2390 helix: -2.94 (0.46), residues: 92 sheet: 0.15 (0.20), residues: 592 loop : -0.34 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 610 TYR 0.023 0.002 TYR C 377 PHE 0.013 0.002 PHE C 535 TRP 0.012 0.002 TRP A 509 HIS 0.007 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (19654) covalent geometry : angle 0.57808 / 0.30 (26769) SS BOND : bond 0.00529 / 0.28 ( 2) SS BOND : angle 1.28520 / 0.71 ( 4) hydrogen bonds : bond 0.03253 / 2.23 ( 239) hydrogen bonds : angle 5.83389 / 4.07 ( 453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 223 time to evaluate : 0.804 Fit side-chains REVERT: A 253 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6742 (p0) REVERT: A 367 PHE cc_start: 0.7409 (t80) cc_final: 0.5717 (m-10) REVERT: A 585 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: A 605 MET cc_start: 0.8386 (mtt) cc_final: 0.7845 (mtt) REVERT: A 640 MET cc_start: 0.8674 (mtp) cc_final: 0.8463 (ttt) REVERT: B 514 ARG cc_start: 0.7931 (mtm180) cc_final: 0.6181 (mmt180) REVERT: C 238 ARG cc_start: 0.8585 (ptp-170) cc_final: 0.8175 (ptt180) REVERT: C 259 GLN cc_start: 0.7775 (tt0) cc_final: 0.5722 (pm20) REVERT: D 367 PHE cc_start: 0.6379 (t80) cc_final: 0.5587 (m-10) REVERT: D 590 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: E 436 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7506 (ptp) REVERT: E 486 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: E 514 ARG cc_start: 0.7244 (mtm180) cc_final: 0.4617 (tpt170) REVERT: E 564 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6544 (pp20) REVERT: F 691 ASN cc_start: 0.8040 (t0) cc_final: 0.7776 (t0) outliers start: 67 outliers final: 40 residues processed: 263 average time/residue: 0.5459 time to fit residues: 163.1381 Evaluate side-chains 251 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 641 LYS Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 564 GLU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 649 ILE Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain L residue 21 GLN Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 129 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 230 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN C 430 GLN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN ** F 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN L 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.119900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096170 restraints weight = 32727.165| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.18 r_work: 0.3181 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19656 Z= 0.166 Angle : 0.560 7.523 26773 Z= 0.291 Chirality : 0.043 0.151 2775 Planarity : 0.004 0.058 3558 Dihedral : 4.813 40.767 2618 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.10 % Allowed : 13.73 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 are not related in a simple way. whole: -0.49 (0.16), residues: 2390 helix: -2.87 (0.47), residues: 92 sheet: 0.16 (0.20), residues: 592 loop : -0.33 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 610 TYR 0.022 0.002 TYR D 674 PHE 0.013 0.002 PHE C 535 TRP 0.011 0.001 TRP A 509 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (19654) covalent geometry : angle 0.56016 / 0.29 (26769) SS BOND : bond 0.00471 / 0.25 ( 2) SS BOND : angle 1.25652 / 0.69 ( 4) hydrogen bonds : bond 0.03092 / 2.11 ( 239) hydrogen bonds : angle 5.74424 / 3.99 ( 453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 210 time to evaluate : 0.532 Fit side-chains REVERT: A 253 ASN cc_start: 0.6974 (OUTLIER) cc_final: 0.6770 (p0) REVERT: A 367 PHE cc_start: 0.7405 (t80) cc_final: 0.5718 (m-10) REVERT: A 585 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: B 514 ARG cc_start: 0.7879 (mtm180) cc_final: 0.6093 (mmt180) REVERT: C 238 ARG cc_start: 0.8578 (ptp-170) cc_final: 0.8080 (ptt180) REVERT: C 259 GLN cc_start: 0.7743 (tt0) cc_final: 0.5723 (pm20) REVERT: C 403 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.6921 (mp10) REVERT: D 590 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: E 436 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7464 (ptp) REVERT: E 486 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: E 514 ARG cc_start: 0.7309 (mtm180) cc_final: 0.4735 (tpt170) REVERT: E 564 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6514 (pp20) REVERT: F 691 ASN cc_start: 0.8011 (t0) cc_final: 0.7768 (t0) outliers start: 65 outliers final: 42 residues processed: 252 average time/residue: 0.5392 time to fit residues: 154.7531 Evaluate side-chains 249 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 641 LYS Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 564 GLU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 649 ILE Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain L residue 21 GLN Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 98 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 97 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 210 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN L 21 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.119355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.095572 restraints weight = 32636.359| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.18 r_work: 0.3171 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19656 Z= 0.192 Angle : 0.584 7.702 26773 Z= 0.304 Chirality : 0.044 0.197 2775 Planarity : 0.004 0.056 3558 Dihedral : 4.860 40.858 2618 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.15 % Allowed : 14.26 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 are not related in a simple way. whole: -0.56 (0.16), residues: 2390 helix: -2.93 (0.46), residues: 92 sheet: 0.12 (0.20), residues: 592 loop : -0.38 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 610 TYR 0.022 0.002 TYR D 674 PHE 0.015 0.002 PHE A 662 TRP 0.012 0.001 TRP A 509 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (19654) covalent geometry : angle 0.58402 / 0.30 (26769) SS BOND : bond 0.00522 / 0.27 ( 2) SS BOND : angle 1.23783 / 0.69 ( 4) hydrogen bonds : bond 0.03185 / 2.18 ( 239) hydrogen bonds : angle 5.76462 / 4.00 ( 453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 0.673 Fit side-chains REVERT: A 253 ASN cc_start: 0.6982 (OUTLIER) cc_final: 0.6730 (p0) REVERT: A 367 PHE cc_start: 0.7379 (t80) cc_final: 0.5663 (m-10) REVERT: A 585 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6915 (pm20) REVERT: B 425 SER cc_start: 0.7620 (p) cc_final: 0.7330 (t) REVERT: B 514 ARG cc_start: 0.7891 (mtm180) cc_final: 0.6094 (mmt180) REVERT: C 259 GLN cc_start: 0.7777 (tt0) cc_final: 0.5759 (pm20) REVERT: C 403 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: E 436 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7512 (ptp) REVERT: E 486 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: E 514 ARG cc_start: 0.7311 (mtm180) cc_final: 0.4634 (tpt170) REVERT: E 564 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6538 (pp20) REVERT: F 691 ASN cc_start: 0.8041 (t0) cc_final: 0.7626 (t0) outliers start: 66 outliers final: 48 residues processed: 257 average time/residue: 0.5444 time to fit residues: 158.9932 Evaluate side-chains 256 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 641 LYS Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 564 GLU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 649 ILE Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain L residue 21 GLN Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 41 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 225 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 109 optimal weight: 0.5980 chunk 162 optimal weight: 20.0000 chunk 227 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 overall best weight: 3.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS C 410 ASN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN ** F 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** L 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.119829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096269 restraints weight = 32584.040| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.18 r_work: 0.3178 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19656 Z= 0.164 Angle : 0.569 7.677 26773 Z= 0.295 Chirality : 0.043 0.154 2775 Planarity : 0.004 0.058 3558 Dihedral : 4.782 39.437 2618 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.91 % Allowed : 14.74 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 are not related in a simple way. whole: -0.54 (0.16), residues: 2390 helix: -2.84 (0.45), residues: 98 sheet: 0.15 (0.21), residues: 591 loop : -0.36 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 514 TYR 0.023 0.002 TYR D 674 PHE 0.017 0.002 PHE B 535 TRP 0.011 0.001 TRP D 509 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (19654) covalent geometry : angle 0.56902 / 0.29 (26769) SS BOND : bond 0.00455 / 0.24 ( 2) SS BOND : angle 1.20788 / 0.67 ( 4) hydrogen bonds : bond 0.03079 / 2.10 ( 239) hydrogen bonds : angle 5.71576 / 3.97 ( 453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 0.715 Fit side-chains REVERT: A 367 PHE cc_start: 0.7373 (t80) cc_final: 0.5684 (m-10) REVERT: A 585 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6935 (pm20) REVERT: B 425 SER cc_start: 0.7620 (p) cc_final: 0.7288 (t) REVERT: B 514 ARG cc_start: 0.7889 (mtm180) cc_final: 0.6085 (mmt180) REVERT: C 238 ARG cc_start: 0.8587 (ptp90) cc_final: 0.8103 (ptt180) REVERT: C 259 GLN cc_start: 0.7751 (tt0) cc_final: 0.5755 (pm20) REVERT: C 403 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.6928 (mp10) REVERT: D 550 ARG cc_start: 0.7064 (ttp80) cc_final: 0.6608 (ttt-90) REVERT: E 436 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7472 (ptp) REVERT: E 486 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: E 514 ARG cc_start: 0.7336 (mtm180) cc_final: 0.4721 (tpt170) REVERT: E 564 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6473 (pp20) outliers start: 61 outliers final: 44 residues processed: 251 average time/residue: 0.5097 time to fit residues: 146.4852 Evaluate side-chains 250 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 641 LYS Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 564 GLU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 649 ILE Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 76 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 ASN A 646 GLN C 410 ASN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN L 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095838 restraints weight = 32648.946| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.18 r_work: 0.3175 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19656 Z= 0.180 Angle : 0.587 9.419 26773 Z= 0.303 Chirality : 0.043 0.156 2775 Planarity : 0.004 0.056 3558 Dihedral : 4.742 21.188 2616 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.77 % Allowed : 15.21 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 are not related in a simple way. whole: -0.57 (0.16), residues: 2390 helix: -2.87 (0.45), residues: 98 sheet: 0.13 (0.21), residues: 591 loop : -0.39 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 514 TYR 0.032 0.002 TYR B 484 PHE 0.017 0.002 PHE A 662 TRP 0.012 0.001 TRP B 509 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (19654) covalent geometry : angle 0.58647 / 0.30 (26769) SS BOND : bond 0.00490 / 0.26 ( 2) SS BOND : angle 1.20896 / 0.67 ( 4) hydrogen bonds : bond 0.03146 / 2.14 ( 239) hydrogen bonds : angle 5.73760 / 3.99 ( 453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 207 time to evaluate : 0.728 Fit side-chains REVERT: A 367 PHE cc_start: 0.7380 (t80) cc_final: 0.5658 (m-10) REVERT: A 585 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: B 425 SER cc_start: 0.7761 (p) cc_final: 0.7411 (t) REVERT: B 514 ARG cc_start: 0.7890 (mtm180) cc_final: 0.6116 (mmt180) REVERT: B 519 ASN cc_start: 0.7762 (t0) cc_final: 0.7086 (p0) REVERT: C 238 ARG cc_start: 0.8593 (ptp90) cc_final: 0.8109 (ptt180) REVERT: C 259 GLN cc_start: 0.7767 (tt0) cc_final: 0.5765 (pm20) REVERT: C 403 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.6893 (mp10) REVERT: D 550 ARG cc_start: 0.7091 (ttp80) cc_final: 0.6630 (ttt-90) REVERT: E 436 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7493 (ptp) REVERT: E 486 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7763 (mt0) REVERT: E 514 ARG cc_start: 0.7350 (mtm180) cc_final: 0.4691 (tpt170) REVERT: E 564 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6419 (pp20) outliers start: 58 outliers final: 45 residues processed: 243 average time/residue: 0.5215 time to fit residues: 144.4727 Evaluate side-chains 249 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 641 LYS Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 564 GLU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 640 MET Chi-restraints excluded: chain F residue 649 ILE Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 93 optimal weight: 0.0570 chunk 14 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 113 optimal weight: 0.0670 chunk 144 optimal weight: 0.5980 chunk 177 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 486 GLN B 630 HIS C 477 ASN C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN L 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.121644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098160 restraints weight = 32516.462| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.19 r_work: 0.3210 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19656 Z= 0.107 Angle : 0.540 7.288 26773 Z= 0.277 Chirality : 0.042 0.146 2775 Planarity : 0.004 0.057 3558 Dihedral : 4.431 20.015 2616 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.72 % Allowed : 16.12 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 are not related in a simple way. whole: -0.43 (0.16), residues: 2390 helix: -2.67 (0.48), residues: 98 sheet: 0.21 (0.21), residues: 592 loop : -0.28 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 514 TYR 0.025 0.001 TYR B 484 PHE 0.016 0.001 PHE A 662 TRP 0.011 0.001 TRP C 228 HIS 0.003 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (19654) covalent geometry : angle 0.53987 / 0.28 (26769) SS BOND : bond 0.00320 / 0.16 ( 2) SS BOND : angle 1.15996 / 0.63 ( 4) hydrogen bonds : bond 0.02739 / 1.86 ( 239) hydrogen bonds : angle 5.50440 / 3.82 ( 453) =============================================================================== Job complete usr+sys time: 6443.58 seconds wall clock time: 110 minutes 47.16 seconds (6647.16 seconds total)