Starting phenix.real_space_refine on Thu Sep 18 17:17:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7x_44327/09_2025/9b7x_44327.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7x_44327/09_2025/9b7x_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_44327/09_2025/9b7x_44327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7x_44327/09_2025/9b7x_44327.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b7x_44327/09_2025/9b7x_44327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7x_44327/09_2025/9b7x_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-2.0-5805/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.64, per 1000 atoms: 0.24 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: 1.78 Conformation dependent library (CDL) restraints added in 833.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.65 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: 2.84 Time building geometry restraints manager: 2.25 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.120 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 aren 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 covalent geometry : bond 0.00925 (19654) covalent geometry : angle 0.94231 (26769) SS BOND : bond 0.01041 ( 2) SS BOND : angle 0.91082 ( 4) hydrogen bonds : bond 0.23122 ( 239) hydrogen bonds : angle 8.37310 ( 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 : 0.791 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: 0.6843 (mtpp) REVERT: E 514 ARG cc_start: 0.7488 (mtm180) cc_final: 0.5526 (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: 0.6007 time to fit residues: 302.9854 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 : 0.749 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 430 GLN A 608 GLN A 646 GLN A 651 ASN B 430 GLN B 452 ASN B 608 GLN 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 D 253 ASN 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 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: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101699 restraints weight = 32419.272| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.22 r_work: 0.3260 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19656 Z= 0.128 Angle : 0.583 8.734 26773 Z= 0.308 Chirality : 0.044 0.201 2775 Planarity : 0.004 0.049 3558 Dihedral : 5.880 84.626 2636 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.43 % Allowed : 9.92 % Favored : 87.65 % 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 aren not related in a simple way. whole: -0.38 (0.15), residues: 2390 helix: -2.97 (0.42), residues: 92 sheet: 0.18 (0.19), residues: 592 loop : -0.21 (0.13), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 485 TYR 0.018 0.002 TYR D 674 PHE 0.019 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 covalent geometry : bond 0.00278 (19654) covalent geometry : angle 0.58255 (26769) SS BOND : bond 0.00385 ( 2) SS BOND : angle 1.63232 ( 4) hydrogen bonds : bond 0.03503 ( 239) hydrogen bonds : angle 6.30033 ( 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 333 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 367 PHE cc_start: 0.7426 (t80) cc_final: 0.5820 (m-10) REVERT: A 518 MET cc_start: 0.7993 (tpp) cc_final: 0.7761 (ttp) REVERT: A 524 MET cc_start: 0.7293 (mtm) cc_final: 0.6997 (mtm) REVERT: A 585 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6286 (pm20) REVERT: A 651 ASN cc_start: 0.7898 (m-40) cc_final: 0.7441 (m110) REVERT: B 514 ARG cc_start: 0.7921 (mtm180) cc_final: 0.6283 (mmt180) REVERT: C 238 ARG cc_start: 0.8591 (ptp-170) cc_final: 0.8098 (ptt180) REVERT: C 259 GLN cc_start: 0.7312 (tt0) cc_final: 0.5441 (pm20) REVERT: C 377 TYR cc_start: 0.8230 (t80) cc_final: 0.7812 (t80) REVERT: C 626 ASP cc_start: 0.7781 (m-30) cc_final: 0.7441 (m-30) REVERT: D 367 PHE cc_start: 0.6368 (t80) cc_final: 0.5632 (m-10) REVERT: D 373 MET cc_start: 0.6830 (ttt) cc_final: 0.6608 (ttp) REVERT: D 641 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8513 (mttm) REVERT: E 514 ARG cc_start: 0.7083 (mtm180) cc_final: 0.4872 (tpt170) REVERT: E 531 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7790 (mp0) REVERT: F 316 LYS cc_start: 0.8113 (mttt) cc_final: 0.7676 (mmtt) REVERT: F 412 GLN cc_start: 0.7875 (pt0) cc_final: 0.7620 (pt0) REVERT: F 691 ASN cc_start: 0.8256 (t0) cc_final: 0.7987 (t0) REVERT: H 25 GLU cc_start: 0.8801 (mp0) cc_final: 0.8566 (mp0) outliers start: 51 outliers final: 19 residues processed: 313 average time/residue: 0.6039 time to fit residues: 213.8491 Evaluate side-chains 241 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 540 SER Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN 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: 20.0000 chunk 234 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 428 HIS A 646 GLN A 678 GLN B 512 ASN 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 C 700 GLN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN F 253 ASN F 272 ASN F 321 GLN 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** ** L 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.117988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094145 restraints weight = 33276.623| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.18 r_work: 0.3148 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 19656 Z= 0.340 Angle : 0.694 8.436 26773 Z= 0.370 Chirality : 0.049 0.204 2775 Planarity : 0.005 0.044 3558 Dihedral : 5.555 51.456 2618 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.15 % Allowed : 11.40 % Favored : 85.46 % 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 aren not related in a simple way. whole: -0.63 (0.16), residues: 2390 helix: -3.11 (0.46), residues: 92 sheet: 0.18 (0.20), residues: 568 loop : -0.46 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 238 TYR 0.024 0.003 TYR F 257 PHE 0.029 0.003 PHE L 84 TRP 0.018 0.002 TRP F 228 HIS 0.018 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00799 (19654) covalent geometry : angle 0.69381 (26769) SS BOND : bond 0.00815 ( 2) SS BOND : angle 1.71814 ( 4) hydrogen bonds : bond 0.04187 ( 239) hydrogen bonds : angle 6.31185 ( 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 299 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 233 time to evaluate : 0.789 Fit side-chains REVERT: B 514 ARG cc_start: 0.7955 (mtm180) cc_final: 0.6275 (mmt180) REVERT: C 259 GLN cc_start: 0.7767 (tt0) cc_final: 0.5672 (pm20) REVERT: E 486 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7904 (mt0) REVERT: E 514 ARG cc_start: 0.7170 (mtm180) cc_final: 0.4663 (tpt170) REVERT: E 542 ILE cc_start: 0.3172 (pp) cc_final: 0.2867 (mt) REVERT: F 316 LYS cc_start: 0.8350 (mttt) cc_final: 0.7985 (mmtt) REVERT: F 691 ASN cc_start: 0.8281 (t0) cc_final: 0.8045 (t0) outliers start: 66 outliers final: 36 residues processed: 279 average time/residue: 0.5942 time to fit residues: 188.1425 Evaluate side-chains 239 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 569 THR Chi-restraints excluded: chain A residue 660 THR 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 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 569 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 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 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: 2.9990 chunk 80 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 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 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 HIS 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 = 0.3613 r_free = 0.3613 target = 0.120192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.096486 restraints weight = 32720.336| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.19 r_work: 0.3184 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19656 Z= 0.165 Angle : 0.564 7.424 26773 Z= 0.296 Chirality : 0.043 0.184 2775 Planarity : 0.004 0.052 3558 Dihedral : 5.012 46.724 2618 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.15 % Allowed : 12.97 % Favored : 83.88 % 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 aren not related in a simple way. whole: -0.51 (0.16), residues: 2390 helix: -2.95 (0.47), residues: 92 sheet: 0.18 (0.20), residues: 580 loop : -0.34 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 610 TYR 0.019 0.002 TYR D 674 PHE 0.012 0.002 PHE C 535 TRP 0.014 0.001 TRP F 228 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00382 (19654) covalent geometry : angle 0.56396 (26769) SS BOND : bond 0.00443 ( 2) SS BOND : angle 1.50973 ( 4) hydrogen bonds : bond 0.03167 ( 239) hydrogen bonds : angle 5.91961 ( 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 303 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 237 time to evaluate : 0.782 Fit side-chains REVERT: A 253 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6795 (p0) REVERT: A 367 PHE cc_start: 0.7493 (t80) cc_final: 0.5784 (m-10) REVERT: B 514 ARG cc_start: 0.7944 (mtm180) cc_final: 0.6261 (mmt180) REVERT: C 238 ARG cc_start: 0.8558 (ptp-170) cc_final: 0.8111 (ptt180) REVERT: C 259 GLN cc_start: 0.7708 (tt0) cc_final: 0.5667 (pm20) REVERT: C 377 TYR cc_start: 0.8267 (t80) cc_final: 0.7768 (t80) REVERT: D 367 PHE cc_start: 0.6340 (t80) cc_final: 0.5592 (m-10) REVERT: D 641 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8530 (mttm) REVERT: E 514 ARG cc_start: 0.7228 (mtm180) cc_final: 0.4643 (tpt170) REVERT: E 542 ILE cc_start: 0.3174 (pp) cc_final: 0.2903 (mt) REVERT: E 564 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6527 (pp20) REVERT: E 567 LYS cc_start: 0.8702 (ttpp) cc_final: 0.8421 (ttpp) REVERT: F 316 LYS cc_start: 0.8395 (mttt) cc_final: 0.8003 (mmtt) REVERT: F 691 ASN cc_start: 0.8139 (t0) cc_final: 0.7897 (t0) outliers start: 66 outliers final: 27 residues processed: 275 average time/residue: 0.5781 time to fit residues: 180.4431 Evaluate side-chains 245 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 569 THR 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 537 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 641 LYS Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 512 ASN 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 412 GLN Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain L residue 30 VAL 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 82 ASN 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: 3.9990 chunk 138 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 673 GLN ** 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 = 0.3604 r_free = 0.3604 target = 0.119434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.095626 restraints weight = 32740.383| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.20 r_work: 0.3168 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19656 Z= 0.193 Angle : 0.574 7.682 26773 Z= 0.300 Chirality : 0.044 0.173 2775 Planarity : 0.004 0.052 3558 Dihedral : 4.963 44.666 2618 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.05 % Allowed : 13.45 % Favored : 83.50 % 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 aren not related in a simple way. whole: -0.53 (0.16), residues: 2390 helix: -2.95 (0.47), residues: 92 sheet: 0.20 (0.20), residues: 576 loop : -0.38 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 610 TYR 0.019 0.002 TYR C 377 PHE 0.018 0.002 PHE A 535 TRP 0.012 0.002 TRP A 509 HIS 0.007 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00450 (19654) covalent geometry : angle 0.57334 (26769) SS BOND : bond 0.00540 ( 2) SS BOND : angle 1.45906 ( 4) hydrogen bonds : bond 0.03223 ( 239) hydrogen bonds : angle 5.84865 ( 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 289 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 225 time to evaluate : 0.641 Fit side-chains REVERT: A 253 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.6776 (p0) REVERT: A 605 MET cc_start: 0.8357 (mtt) cc_final: 0.7812 (mtt) REVERT: B 425 SER cc_start: 0.7797 (p) cc_final: 0.7462 (t) REVERT: B 514 ARG cc_start: 0.7943 (mtm180) cc_final: 0.6231 (mmt180) REVERT: C 238 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8142 (ptt180) REVERT: C 259 GLN cc_start: 0.7785 (tt0) cc_final: 0.5777 (pm20) REVERT: C 514 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8380 (mtm-85) REVERT: D 367 PHE cc_start: 0.6342 (t80) cc_final: 0.5604 (m-10) REVERT: D 574 THR cc_start: 0.8504 (m) cc_final: 0.8291 (m) REVERT: D 590 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7215 (mp10) REVERT: E 436 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7362 (ptp) REVERT: E 514 ARG cc_start: 0.7254 (mtm180) cc_final: 0.4638 (tpt170) REVERT: E 564 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6493 (pp20) REVERT: E 608 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7312 (mm-40) REVERT: F 316 LYS cc_start: 0.8407 (mttt) cc_final: 0.8036 (mmtt) REVERT: F 691 ASN cc_start: 0.8107 (t0) cc_final: 0.7831 (t0) outliers start: 64 outliers final: 40 residues processed: 260 average time/residue: 0.6002 time to fit residues: 176.9131 Evaluate side-chains 251 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 528 LYS Chi-restraints excluded: chain A residue 569 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 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 465 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 235 LEU Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 412 GLN Chi-restraints excluded: chain F residue 529 GLU 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 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 82 ASN Chi-restraints excluded: chain L residue 98 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 77 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 136 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 224 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 157 optimal weight: 0.5980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 343 GLN F 430 GLN F 512 ASN H 138 GLN L 21 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.120346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.096780 restraints weight = 32588.250| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.18 r_work: 0.3186 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19656 Z= 0.148 Angle : 0.542 7.135 26773 Z= 0.281 Chirality : 0.042 0.158 2775 Planarity : 0.004 0.057 3558 Dihedral : 4.754 41.241 2618 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.86 % Allowed : 13.83 % Favored : 83.31 % 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 aren not related in a simple way. whole: -0.48 (0.16), residues: 2390 helix: -2.84 (0.48), residues: 92 sheet: 0.16 (0.20), residues: 594 loop : -0.32 (0.14), residues: 1704 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 0.012 0.001 PHE C 535 TRP 0.011 0.001 TRP F 228 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00342 (19654) covalent geometry : angle 0.54176 (26769) SS BOND : bond 0.00413 ( 2) SS BOND : angle 1.36581 ( 4) hydrogen bonds : bond 0.02954 ( 239) hydrogen bonds : angle 5.66625 ( 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 283 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 0.703 Fit side-chains REVERT: A 367 PHE cc_start: 0.7436 (t80) cc_final: 0.5772 (m-10) REVERT: B 425 SER cc_start: 0.7800 (p) cc_final: 0.7505 (t) REVERT: B 514 ARG cc_start: 0.7935 (mtm180) cc_final: 0.6239 (mmt180) REVERT: C 238 ARG cc_start: 0.8540 (ptp-170) cc_final: 0.8039 (ptt180) REVERT: C 259 GLN cc_start: 0.7727 (tt0) cc_final: 0.5662 (pm20) REVERT: C 377 TYR cc_start: 0.8179 (t80) cc_final: 0.7696 (t80) REVERT: C 403 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: C 514 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.8414 (mtm-85) REVERT: D 367 PHE cc_start: 0.6325 (t80) cc_final: 0.5537 (m-10) REVERT: D 574 THR cc_start: 0.8487 (m) cc_final: 0.8273 (m) REVERT: D 590 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: E 514 ARG cc_start: 0.7232 (mtm180) cc_final: 0.4668 (tpt170) REVERT: E 564 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6455 (pp20) REVERT: E 608 GLN cc_start: 0.7464 (mm-40) cc_final: 0.7232 (mm-40) REVERT: F 316 LYS cc_start: 0.8388 (mttt) cc_final: 0.8018 (mmtt) REVERT: F 691 ASN cc_start: 0.8030 (t0) cc_final: 0.7793 (t0) outliers start: 60 outliers final: 37 residues processed: 259 average time/residue: 0.5660 time to fit residues: 166.5307 Evaluate side-chains 253 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 569 THR 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 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 454 SER Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 512 ASN 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 404 MET Chi-restraints excluded: chain F residue 412 GLN Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain L residue 21 GLN Chi-restraints excluded: chain L residue 22 SER 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 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: 20.0000 chunk 225 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 chunk 230 optimal weight: 2.9990 chunk 158 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 497 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.120604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.096904 restraints weight = 32730.137| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.20 r_work: 0.3190 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19656 Z= 0.140 Angle : 0.540 7.106 26773 Z= 0.280 Chirality : 0.042 0.161 2775 Planarity : 0.004 0.052 3558 Dihedral : 4.584 20.494 2616 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.91 % Allowed : 14.45 % Favored : 82.64 % 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 aren not related in a simple way. whole: -0.43 (0.16), residues: 2390 helix: -2.78 (0.49), residues: 92 sheet: 0.17 (0.20), residues: 594 loop : -0.27 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 610 TYR 0.020 0.001 TYR D 674 PHE 0.014 0.001 PHE B 535 TRP 0.010 0.001 TRP D 509 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00325 (19654) covalent geometry : angle 0.53972 (26769) SS BOND : bond 0.00413 ( 2) SS BOND : angle 1.34439 ( 4) hydrogen bonds : bond 0.02918 ( 239) hydrogen bonds : angle 5.59548 ( 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 279 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 0.768 Fit side-chains REVERT: A 367 PHE cc_start: 0.7397 (t80) cc_final: 0.5714 (m-10) REVERT: A 585 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: B 425 SER cc_start: 0.7798 (p) cc_final: 0.7509 (t) REVERT: B 514 ARG cc_start: 0.7856 (mtm180) cc_final: 0.6127 (mmt180) REVERT: B 533 ARG cc_start: 0.7315 (ptt-90) cc_final: 0.6933 (ptt180) REVERT: C 238 ARG cc_start: 0.8571 (ptp-170) cc_final: 0.8074 (ptt180) REVERT: C 259 GLN cc_start: 0.7703 (tt0) cc_final: 0.5679 (pm20) REVERT: C 377 TYR cc_start: 0.8156 (t80) cc_final: 0.7616 (t80) REVERT: C 403 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: C 514 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8406 (mtm-85) REVERT: D 367 PHE cc_start: 0.6396 (t80) cc_final: 0.5556 (m-10) REVERT: D 550 ARG cc_start: 0.6942 (ttp80) cc_final: 0.6537 (ttt-90) REVERT: D 574 THR cc_start: 0.8505 (m) cc_final: 0.8279 (m) REVERT: E 436 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7381 (ptp) REVERT: E 514 ARG cc_start: 0.7261 (mtm180) cc_final: 0.4732 (tpt170) REVERT: E 564 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6461 (pp20) REVERT: F 285 ASP cc_start: 0.7433 (t0) cc_final: 0.7232 (t0) REVERT: F 316 LYS cc_start: 0.8387 (mttt) cc_final: 0.8063 (mmtt) REVERT: F 691 ASN cc_start: 0.8012 (t0) cc_final: 0.7622 (t0) outliers start: 61 outliers final: 38 residues processed: 251 average time/residue: 0.5830 time to fit residues: 166.0871 Evaluate side-chains 247 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 403 GLN 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 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 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 30 LEU Chi-restraints excluded: chain H residue 127 THR 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 82 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 97 optimal weight: 0.0010 chunk 204 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 111 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.120266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.096538 restraints weight = 32547.208| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.20 r_work: 0.3184 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 0.039 19656 Z= 0.159 Angle : 0.548 7.244 26773 Z= 0.284 Chirality : 0.043 0.147 2775 Planarity : 0.004 0.056 3558 Dihedral : 4.592 20.692 2616 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.91 % Allowed : 14.83 % Favored : 82.26 % 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 aren not related in a simple way. whole: -0.44 (0.16), residues: 2390 helix: -2.84 (0.48), residues: 92 sheet: 0.16 (0.20), residues: 594 loop : -0.28 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 610 TYR 0.019 0.002 TYR D 674 PHE 0.015 0.002 PHE A 662 TRP 0.011 0.001 TRP D 509 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00371 (19654) covalent geometry : angle 0.54790 (26769) SS BOND : bond 0.00457 ( 2) SS BOND : angle 1.31206 ( 4) hydrogen bonds : bond 0.02978 ( 239) hydrogen bonds : angle 5.59263 ( 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 276 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 215 time to evaluate : 0.814 Fit side-chains REVERT: A 367 PHE cc_start: 0.7415 (t80) cc_final: 0.5715 (m-10) REVERT: A 585 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: B 425 SER cc_start: 0.7621 (p) cc_final: 0.7336 (t) REVERT: B 514 ARG cc_start: 0.7838 (mtm180) cc_final: 0.6078 (mmt180) REVERT: B 533 ARG cc_start: 0.7352 (ptt-90) cc_final: 0.7033 (ptt180) REVERT: C 238 ARG cc_start: 0.8583 (ptp-170) cc_final: 0.8085 (ptt180) REVERT: C 259 GLN cc_start: 0.7694 (tt0) cc_final: 0.5701 (pm20) REVERT: C 377 TYR cc_start: 0.8168 (t80) cc_final: 0.7714 (t80) REVERT: C 403 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.6909 (mp10) REVERT: C 514 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8396 (mtm-85) REVERT: D 550 ARG cc_start: 0.7005 (ttp80) cc_final: 0.6587 (ttt-90) REVERT: D 574 THR cc_start: 0.8540 (m) cc_final: 0.8303 (m) REVERT: E 436 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7392 (ptp) REVERT: E 514 ARG cc_start: 0.7282 (mtm180) cc_final: 0.4647 (tpt170) REVERT: E 564 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6463 (pp20) REVERT: F 316 LYS cc_start: 0.8402 (mttt) cc_final: 0.8156 (mttt) REVERT: F 512 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8644 (t0) REVERT: F 691 ASN cc_start: 0.7976 (t0) cc_final: 0.7601 (t0) outliers start: 61 outliers final: 43 residues processed: 250 average time/residue: 0.5577 time to fit residues: 158.6668 Evaluate side-chains 251 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 493 VAL Chi-restraints excluded: chain A residue 494 THR 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 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 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 425 SER Chi-restraints excluded: chain F residue 512 ASN 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 55 VAL Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 82 ASN 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: 3.9990 chunk 225 optimal weight: 9.9990 chunk 199 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 109 optimal weight: 0.9990 chunk 162 optimal weight: 20.0000 chunk 227 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN A 646 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 HIS C 410 ASN C 477 ASN C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN F 552 ASN ** F 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN L 21 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.096723 restraints weight = 32588.240| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.20 r_work: 0.3189 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19656 Z= 0.149 Angle : 0.544 7.184 26773 Z= 0.282 Chirality : 0.042 0.146 2775 Planarity : 0.004 0.053 3558 Dihedral : 4.555 20.538 2616 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.77 % Allowed : 15.12 % Favored : 82.12 % 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 aren not related in a simple way. whole: -0.44 (0.16), residues: 2390 helix: -2.81 (0.49), residues: 92 sheet: 0.16 (0.20), residues: 594 loop : -0.28 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 610 TYR 0.019 0.002 TYR D 674 PHE 0.017 0.001 PHE A 662 TRP 0.011 0.001 TRP D 509 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00347 (19654) covalent geometry : angle 0.54332 (26769) SS BOND : bond 0.00434 ( 2) SS BOND : angle 1.31990 ( 4) hydrogen bonds : bond 0.02927 ( 239) hydrogen bonds : angle 5.57356 ( 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 277 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 0.787 Fit side-chains REVERT: A 367 PHE cc_start: 0.7402 (t80) cc_final: 0.5711 (m-10) REVERT: A 585 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: B 425 SER cc_start: 0.7594 (p) cc_final: 0.7297 (t) REVERT: B 514 ARG cc_start: 0.7846 (mtm180) cc_final: 0.6052 (mmt180) REVERT: C 238 ARG cc_start: 0.8580 (ptp-170) cc_final: 0.8081 (ptt180) REVERT: C 259 GLN cc_start: 0.7679 (tt0) cc_final: 0.5705 (pm20) REVERT: C 347 ASP cc_start: 0.8717 (t0) cc_final: 0.8514 (t0) REVERT: C 377 TYR cc_start: 0.8169 (t80) cc_final: 0.7698 (t80) REVERT: C 514 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.8400 (mtm-85) REVERT: D 550 ARG cc_start: 0.7070 (ttp80) cc_final: 0.6651 (ttt-90) REVERT: D 574 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8293 (m) REVERT: E 436 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7366 (ptp) REVERT: E 514 ARG cc_start: 0.7271 (mtm180) cc_final: 0.4657 (tpt170) REVERT: E 564 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6441 (pp20) REVERT: F 316 LYS cc_start: 0.8432 (mttt) cc_final: 0.8213 (mttt) REVERT: F 691 ASN cc_start: 0.7972 (t0) cc_final: 0.7605 (t0) outliers start: 58 outliers final: 43 residues processed: 256 average time/residue: 0.5670 time to fit residues: 164.9413 Evaluate side-chains 255 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 493 VAL Chi-restraints excluded: chain A residue 494 THR 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 537 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 574 THR 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 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 412 GLN Chi-restraints excluded: chain F residue 425 SER 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 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 55 VAL Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 82 ASN 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: 8.9990 chunk 206 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.097552 restraints weight = 32402.671| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.16 r_work: 0.3205 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19656 Z= 0.126 Angle : 0.538 7.179 26773 Z= 0.277 Chirality : 0.042 0.172 2775 Planarity : 0.004 0.054 3558 Dihedral : 4.444 20.040 2616 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.24 % Allowed : 15.93 % Favored : 81.83 % 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 aren not related in a simple way. whole: -0.39 (0.16), residues: 2390 helix: -2.71 (0.50), residues: 92 sheet: 0.20 (0.21), residues: 593 loop : -0.25 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 610 TYR 0.020 0.001 TYR D 674 PHE 0.026 0.001 PHE A 662 TRP 0.010 0.001 TRP C 228 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00292 (19654) covalent geometry : angle 0.53734 (26769) SS BOND : bond 0.00379 ( 2) SS BOND : angle 1.29865 ( 4) hydrogen bonds : bond 0.02804 ( 239) hydrogen bonds : angle 5.47953 ( 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 263 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.669 Fit side-chains REVERT: A 367 PHE cc_start: 0.7379 (t80) cc_final: 0.5683 (m-10) REVERT: A 585 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: B 425 SER cc_start: 0.7636 (p) cc_final: 0.7285 (t) REVERT: B 514 ARG cc_start: 0.7863 (mtm180) cc_final: 0.6127 (mmt180) REVERT: C 238 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8051 (ptt180) REVERT: C 259 GLN cc_start: 0.7707 (tt0) cc_final: 0.5740 (pm20) REVERT: C 347 ASP cc_start: 0.8608 (t0) cc_final: 0.8399 (t0) REVERT: C 377 TYR cc_start: 0.8093 (t80) cc_final: 0.7663 (t80) REVERT: C 514 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8400 (mtm-85) REVERT: C 734 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8686 (ttt180) REVERT: D 550 ARG cc_start: 0.7023 (ttp80) cc_final: 0.6623 (ttt-90) REVERT: D 574 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8294 (m) REVERT: E 436 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7255 (ptp) REVERT: E 514 ARG cc_start: 0.7311 (mtm180) cc_final: 0.4718 (tpt170) REVERT: E 564 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6412 (pp20) REVERT: F 316 LYS cc_start: 0.8417 (mttt) cc_final: 0.8181 (mttt) REVERT: F 691 ASN cc_start: 0.8003 (t0) cc_final: 0.7625 (t0) outliers start: 47 outliers final: 32 residues processed: 243 average time/residue: 0.5514 time to fit residues: 152.2585 Evaluate side-chains 241 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 569 THR Chi-restraints excluded: chain A residue 585 GLN 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 574 THR Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 564 GLU 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 425 SER 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 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 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 93 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 177 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 512 ASN ** F 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN L 21 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.096029 restraints weight = 32723.475| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.18 r_work: 0.3182 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19656 Z= 0.186 Angle : 0.568 7.522 26773 Z= 0.295 Chirality : 0.043 0.156 2775 Planarity : 0.004 0.055 3558 Dihedral : 4.611 20.687 2616 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.48 % Allowed : 15.45 % Favored : 82.07 % 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 aren not related in a simple way. whole: -0.47 (0.16), residues: 2390 helix: -2.89 (0.48), residues: 92 sheet: 0.15 (0.21), residues: 574 loop : -0.29 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 610 TYR 0.019 0.002 TYR H 69 PHE 0.020 0.002 PHE A 662 TRP 0.013 0.001 TRP F 509 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00436 (19654) covalent geometry : angle 0.56793 (26769) SS BOND : bond 0.00534 ( 2) SS BOND : angle 1.24946 ( 4) hydrogen bonds : bond 0.03095 ( 239) hydrogen bonds : angle 5.62815 ( 453) =============================================================================== Job complete usr+sys time: 7188.86 seconds wall clock time: 123 minutes 10.06 seconds (7390.06 seconds total)