Starting phenix.real_space_refine on Mon Jun 16 12:51:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7x_44327/06_2025/9b7x_44327.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7x_44327/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7x_44327/06_2025/9b7x_44327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7x_44327/06_2025/9b7x_44327.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7x_44327/06_2025/9b7x_44327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7x_44327/06_2025/9b7x_44327.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.83, per 1000 atoms: 0.57 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: 4.81 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.13 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: 6.26 Time building geometry restraints manager: 5.73 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: 0.480 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 44.410 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.070 ------------------------------------------------------------------------------- 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 : 13.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (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 TRP 0.033 0.004 TRP H 136 HIS 0.017 0.003 HIS C 290 PHE 0.036 0.003 PHE F 367 TYR 0.039 0.003 TYR H 69 ARG 0.011 0.002 ARG C 296 Details of bonding type rmsd hydrogen bonds : bond 0.23122 ( 239) hydrogen bonds : angle 8.37310 ( 453) SS BOND : bond 0.01041 ( 2) SS BOND : angle 0.91082 ( 4) covalent geometry : bond 0.00925 (19654) covalent geometry : angle 0.94231 (26769) *********************** 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 : 2.072 Fit side-chains revert: symmetry clash REVERT: A 367 PHE cc_start: 0.7406 (t80) cc_final: 0.6077 (m-10) REVERT: A 565 GLU cc_start: 0.7087 (mp0) cc_final: 0.6436 (mt-10) REVERT: A 651 ASN cc_start: 0.7717 (m110) cc_final: 0.7424 (m110) REVERT: B 485 ARG cc_start: 0.6932 (ttm170) cc_final: 0.6575 (ttp-170) REVERT: B 514 ARG cc_start: 0.8103 (mtm180) cc_final: 0.6748 (mmt180) REVERT: C 259 GLN cc_start: 0.7064 (tt0) cc_final: 0.5636 (pm20) REVERT: C 495 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: C 676 THR cc_start: 0.7705 (t) cc_final: 0.7440 (p) REVERT: D 367 PHE cc_start: 0.6544 (t80) cc_final: 0.5958 (m-10) REVERT: D 528 LYS cc_start: 0.7193 (mtmt) cc_final: 0.6959 (mtpp) REVERT: E 514 ARG cc_start: 0.7488 (mtm180) cc_final: 0.5528 (tpt170) REVERT: H 91 ASP cc_start: 0.7881 (t0) cc_final: 0.7679 (t0) REVERT: H 124 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6350 (mp0) outliers start: 17 outliers final: 9 residues processed: 447 average time/residue: 1.2497 time to fit residues: 632.2175 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 : 2.041 ------------------------------------------------------------------------------- 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 202 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 188 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 292 HIS A 430 GLN A 608 GLN A 646 GLN A 651 ASN A 678 GLN B 430 GLN B 452 ASN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 HIS B 630 HIS C 410 ASN C 452 ASN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 519 ASN C 585 GLN C 646 GLN C 651 ASN C 673 GLN C 700 GLN D 253 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 GLN D 624 HIS D 646 GLN D 651 ASN E 428 HIS ** E 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN E 515 ASN E 585 GLN F 272 ASN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.099336 restraints weight = 32535.639| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.21 r_work: 0.3222 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19656 Z= 0.167 Angle : 0.613 8.979 26773 Z= 0.324 Chirality : 0.045 0.215 2775 Planarity : 0.004 0.051 3558 Dihedral : 6.086 87.421 2636 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.58 % Allowed : 9.87 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 2390 helix: -3.06 (0.42), residues: 92 sheet: 0.12 (0.19), residues: 602 loop : -0.29 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 228 HIS 0.011 0.001 HIS F 290 PHE 0.022 0.002 PHE L 84 TYR 0.018 0.002 TYR H 69 ARG 0.006 0.001 ARG F 296 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 239) hydrogen bonds : angle 6.36122 ( 453) SS BOND : bond 0.00502 ( 2) SS BOND : angle 1.65480 ( 4) covalent geometry : bond 0.00382 (19654) covalent geometry : angle 0.61313 (26769) *********************** 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 319 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 2.159 Fit side-chains revert: symmetry clash REVERT: A 253 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.6948 (p0) REVERT: A 367 PHE cc_start: 0.7454 (t80) cc_final: 0.5820 (m-10) REVERT: A 518 MET cc_start: 0.8027 (tpp) cc_final: 0.7730 (ttp) REVERT: A 524 MET cc_start: 0.7326 (mtm) cc_final: 0.7059 (mtm) REVERT: A 585 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6443 (pm20) REVERT: B 514 ARG cc_start: 0.7932 (mtm180) cc_final: 0.6280 (mmt180) REVERT: C 259 GLN cc_start: 0.7398 (tt0) cc_final: 0.5499 (pm20) REVERT: C 377 TYR cc_start: 0.8305 (t80) cc_final: 0.7974 (t80) REVERT: C 412 GLN cc_start: 0.7744 (pp30) cc_final: 0.7521 (pp30) REVERT: C 626 ASP cc_start: 0.7948 (m-30) cc_final: 0.7583 (m-30) REVERT: D 367 PHE cc_start: 0.6406 (t80) cc_final: 0.5715 (m-10) REVERT: D 373 MET cc_start: 0.7034 (ttt) cc_final: 0.6828 (ttp) REVERT: D 641 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8483 (mttm) REVERT: E 514 ARG cc_start: 0.7042 (mtm180) cc_final: 0.4809 (tpt170) REVERT: F 316 LYS cc_start: 0.8148 (mttt) cc_final: 0.7732 (mmtt) REVERT: F 691 ASN cc_start: 0.8287 (t0) cc_final: 0.8015 (t0) REVERT: H 25 GLU cc_start: 0.8804 (mp0) cc_final: 0.8577 (mp0) outliers start: 54 outliers final: 19 residues processed: 297 average time/residue: 1.2385 time to fit residues: 417.9067 Evaluate side-chains 246 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain 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 F residue 717 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 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 19 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 512 ASN B 608 GLN C 262 ASN C 343 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** E 430 GLN E 585 GLN F 272 ASN F 321 GLN F 428 HIS F 585 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.094427 restraints weight = 32917.939| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.17 r_work: 0.3153 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 19656 Z= 0.309 Angle : 0.680 8.507 26773 Z= 0.361 Chirality : 0.048 0.202 2775 Planarity : 0.005 0.046 3558 Dihedral : 5.575 51.230 2619 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.34 % Allowed : 11.92 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2390 helix: -3.07 (0.46), residues: 92 sheet: 0.22 (0.21), residues: 524 loop : -0.50 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 228 HIS 0.015 0.002 HIS F 290 PHE 0.029 0.003 PHE L 84 TYR 0.023 0.002 TYR F 257 ARG 0.009 0.001 ARG F 238 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 239) hydrogen bonds : angle 6.25507 ( 453) SS BOND : bond 0.00731 ( 2) SS BOND : angle 1.62711 ( 4) covalent geometry : bond 0.00728 (19654) covalent geometry : angle 0.67989 (26769) *********************** 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 306 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 236 time to evaluate : 2.265 Fit side-chains revert: symmetry clash REVERT: A 533 ARG cc_start: 0.6984 (ptt-90) cc_final: 0.6750 (ptt-90) REVERT: B 514 ARG cc_start: 0.7886 (mtm180) cc_final: 0.6209 (mmt180) REVERT: C 238 ARG cc_start: 0.8670 (ptp90) cc_final: 0.8266 (ptt180) REVERT: C 259 GLN cc_start: 0.7747 (tt0) cc_final: 0.5717 (pm20) REVERT: C 377 TYR cc_start: 0.8543 (t80) cc_final: 0.8341 (t80) REVERT: D 688 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: E 514 ARG cc_start: 0.7158 (mtm180) cc_final: 0.4656 (tpt170) REVERT: E 542 ILE cc_start: 0.3151 (pp) cc_final: 0.2815 (mt) REVERT: F 316 LYS cc_start: 0.8409 (mttt) cc_final: 0.8020 (mmtt) REVERT: F 691 ASN cc_start: 0.8265 (t0) cc_final: 0.8016 (t0) REVERT: H 25 GLU cc_start: 0.8791 (mp0) cc_final: 0.8583 (mp0) outliers start: 70 outliers final: 38 residues processed: 283 average time/residue: 1.3132 time to fit residues: 420.7867 Evaluate side-chains 240 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 2.094 ------------------------------------------------------------------------------- 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 493 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 688 GLN 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 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 469 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 F residue 736 LEU 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 0 optimal weight: 20.0000 chunk 173 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 223 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 HIS 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 = 0.3634 r_free = 0.3634 target = 0.121649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097882 restraints weight = 32557.595| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.18 r_work: 0.3208 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19656 Z= 0.115 Angle : 0.538 6.803 26773 Z= 0.281 Chirality : 0.042 0.177 2775 Planarity : 0.004 0.055 3558 Dihedral : 4.873 44.318 2619 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.38 % Allowed : 13.69 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2390 helix: -2.81 (0.48), residues: 92 sheet: 0.20 (0.20), residues: 580 loop : -0.26 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 228 HIS 0.004 0.001 HIS F 290 PHE 0.011 0.001 PHE C 629 TYR 0.020 0.001 TYR D 674 ARG 0.009 0.000 ARG B 610 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 239) hydrogen bonds : angle 5.79410 ( 453) SS BOND : bond 0.00310 ( 2) SS BOND : angle 1.39246 ( 4) covalent geometry : bond 0.00258 (19654) covalent geometry : angle 0.53742 (26769) *********************** 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 290 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 2.216 Fit side-chains revert: symmetry clash REVERT: A 367 PHE cc_start: 0.7466 (t80) cc_final: 0.5774 (m-10) REVERT: A 533 ARG cc_start: 0.6969 (ptt-90) cc_final: 0.6743 (ptt-90) REVERT: B 514 ARG cc_start: 0.7914 (mtm180) cc_final: 0.6252 (mmt180) REVERT: C 231 ASP cc_start: 0.7260 (p0) cc_final: 0.6959 (p0) REVERT: C 238 ARG cc_start: 0.8593 (ptp-170) cc_final: 0.8069 (ptt180) REVERT: C 259 GLN cc_start: 0.7643 (tt0) cc_final: 0.5666 (pm20) REVERT: C 412 GLN cc_start: 0.7792 (pp30) cc_final: 0.7439 (pp30) REVERT: D 367 PHE cc_start: 0.6389 (t80) cc_final: 0.5663 (m-10) REVERT: D 641 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8512 (mttm) REVERT: E 486 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: E 514 ARG cc_start: 0.7226 (mtm180) cc_final: 0.4801 (tpt170) REVERT: E 542 ILE cc_start: 0.3074 (pp) cc_final: 0.2826 (mt) REVERT: E 567 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8296 (ttpp) REVERT: F 316 LYS cc_start: 0.8353 (mttt) cc_final: 0.7981 (mmtt) REVERT: F 691 ASN cc_start: 0.8063 (t0) cc_final: 0.7797 (t0) REVERT: H 25 GLU cc_start: 0.8731 (mp0) cc_final: 0.8491 (mp0) outliers start: 50 outliers final: 18 residues processed: 267 average time/residue: 1.3257 time to fit residues: 407.8277 Evaluate side-chains 238 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 528 LYS 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 261 SER Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 641 LYS Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 82 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 15 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 68 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 608 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 GLN C 410 ASN C 519 ASN C 552 ASN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 HIS ** F 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3573 r_free = 0.3573 target = 0.117257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.093570 restraints weight = 33152.479| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.15 r_work: 0.3140 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 19656 Z= 0.331 Angle : 0.668 8.635 26773 Z= 0.353 Chirality : 0.048 0.188 2775 Planarity : 0.005 0.048 3558 Dihedral : 5.306 22.100 2616 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.43 % Allowed : 13.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 2390 helix: -3.16 (0.44), residues: 92 sheet: 0.21 (0.21), residues: 524 loop : -0.56 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 509 HIS 0.010 0.002 HIS C 290 PHE 0.018 0.002 PHE C 411 TYR 0.024 0.003 TYR F 257 ARG 0.007 0.001 ARG B 610 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 239) hydrogen bonds : angle 6.12509 ( 453) SS BOND : bond 0.00753 ( 2) SS BOND : angle 1.43465 ( 4) covalent geometry : bond 0.00772 (19654) covalent geometry : angle 0.66764 (26769) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 213 time to evaluate : 2.497 Fit side-chains REVERT: A 533 ARG cc_start: 0.7039 (ptt-90) cc_final: 0.6765 (ptt-90) REVERT: B 514 ARG cc_start: 0.7938 (mtm180) cc_final: 0.6205 (mmt180) REVERT: C 259 GLN cc_start: 0.7822 (tt0) cc_final: 0.5752 (pm20) REVERT: C 403 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.6701 (mp10) REVERT: C 412 GLN cc_start: 0.7927 (pp30) cc_final: 0.7467 (pp30) REVERT: D 590 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: E 514 ARG cc_start: 0.7320 (mtm180) cc_final: 0.4705 (tpt170) REVERT: E 542 ILE cc_start: 0.3551 (pp) cc_final: 0.3058 (mm) REVERT: F 316 LYS cc_start: 0.8420 (mttt) cc_final: 0.8025 (mmtt) REVERT: F 691 ASN cc_start: 0.8172 (t0) cc_final: 0.7885 (t0) outliers start: 72 outliers final: 42 residues processed: 258 average time/residue: 1.5590 time to fit residues: 455.4901 Evaluate side-chains 242 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 4.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 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 660 THR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 569 THR 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 676 THR Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain H residue 138 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 64 LYS Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 49 optimal weight: 0.0170 chunk 150 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 228 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 ASN C 410 ASN C 430 GLN C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN F 430 GLN F 673 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 = 0.3626 r_free = 0.3626 target = 0.121047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.097450 restraints weight = 32621.287| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.18 r_work: 0.3200 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19656 Z= 0.112 Angle : 0.530 6.682 26773 Z= 0.275 Chirality : 0.042 0.154 2775 Planarity : 0.004 0.057 3558 Dihedral : 4.658 20.248 2616 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.15 % Allowed : 14.93 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2390 helix: -2.84 (0.47), residues: 92 sheet: 0.12 (0.20), residues: 591 loop : -0.34 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 228 HIS 0.003 0.001 HIS A 290 PHE 0.011 0.001 PHE C 629 TYR 0.021 0.001 TYR D 674 ARG 0.009 0.000 ARG B 610 Details of bonding type rmsd hydrogen bonds : bond 0.02842 ( 239) hydrogen bonds : angle 5.65547 ( 453) SS BOND : bond 0.00325 ( 2) SS BOND : angle 1.18605 ( 4) covalent geometry : bond 0.00255 (19654) covalent geometry : angle 0.52951 (26769) *********************** 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 277 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 2.115 Fit side-chains REVERT: A 367 PHE cc_start: 0.7402 (t80) cc_final: 0.5737 (m-10) REVERT: A 533 ARG cc_start: 0.6955 (ptt-90) cc_final: 0.6700 (ptt-90) REVERT: A 585 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: B 514 ARG cc_start: 0.7882 (mtm180) cc_final: 0.6174 (mmt180) REVERT: C 238 ARG cc_start: 0.8577 (ptp90) cc_final: 0.8074 (ptt180) REVERT: C 259 GLN cc_start: 0.7683 (tt0) cc_final: 0.5704 (pm20) REVERT: C 412 GLN cc_start: 0.7898 (pp30) cc_final: 0.7481 (pp30) REVERT: D 367 PHE cc_start: 0.6329 (t80) cc_final: 0.5540 (m-10) REVERT: D 590 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7215 (mp10) REVERT: E 514 ARG cc_start: 0.7250 (mtm180) cc_final: 0.4787 (tpt170) REVERT: E 518 MET cc_start: 0.7267 (ttm) cc_final: 0.6793 (ttp) REVERT: E 542 ILE cc_start: 0.3340 (pp) cc_final: 0.2838 (mm) REVERT: E 564 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6486 (pp20) REVERT: F 316 LYS cc_start: 0.8319 (mttt) cc_final: 0.7985 (mmtt) REVERT: F 691 ASN cc_start: 0.8002 (t0) cc_final: 0.7784 (t0) REVERT: H 25 GLU cc_start: 0.8678 (mp0) cc_final: 0.8439 (mp0) outliers start: 45 outliers final: 18 residues processed: 258 average time/residue: 1.2295 time to fit residues: 360.7852 Evaluate side-chains 234 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 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 322 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 640 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 469 SER Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain L residue 21 GLN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 114 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 167 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 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 = 0.3579 r_free = 0.3579 target = 0.117676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.094107 restraints weight = 32876.083| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.15 r_work: 0.3141 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19656 Z= 0.287 Angle : 0.630 8.641 26773 Z= 0.331 Chirality : 0.046 0.195 2775 Planarity : 0.005 0.050 3558 Dihedral : 5.044 21.697 2616 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.62 % Allowed : 14.97 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2390 helix: -3.18 (0.43), residues: 92 sheet: 0.10 (0.21), residues: 574 loop : -0.49 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 509 HIS 0.009 0.001 HIS D 290 PHE 0.019 0.002 PHE A 535 TYR 0.022 0.002 TYR C 701 ARG 0.009 0.001 ARG B 610 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 239) hydrogen bonds : angle 5.92826 ( 453) SS BOND : bond 0.00710 ( 2) SS BOND : angle 1.38943 ( 4) covalent geometry : bond 0.00673 (19654) covalent geometry : angle 0.62978 (26769) *********************** 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 260 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 205 time to evaluate : 2.081 Fit side-chains REVERT: A 533 ARG cc_start: 0.7047 (ptt-90) cc_final: 0.6775 (ptt-90) REVERT: B 425 SER cc_start: 0.7634 (p) cc_final: 0.7337 (t) REVERT: B 514 ARG cc_start: 0.7860 (mtm180) cc_final: 0.6095 (mmt180) REVERT: C 259 GLN cc_start: 0.7815 (tt0) cc_final: 0.5787 (pm20) REVERT: C 384 ASP cc_start: 0.7520 (t70) cc_final: 0.7303 (t70) REVERT: C 412 GLN cc_start: 0.7972 (pp30) cc_final: 0.7471 (pp30) REVERT: E 514 ARG cc_start: 0.7368 (mtm180) cc_final: 0.4716 (tpt170) REVERT: E 518 MET cc_start: 0.7476 (ttm) cc_final: 0.6862 (ttp) REVERT: E 564 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6467 (pp20) REVERT: F 316 LYS cc_start: 0.8411 (mttt) cc_final: 0.8148 (mttt) REVERT: F 678 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7017 (mp10) REVERT: F 691 ASN cc_start: 0.8088 (t0) cc_final: 0.7838 (t0) outliers start: 55 outliers final: 35 residues processed: 242 average time/residue: 1.2961 time to fit residues: 354.8138 Evaluate side-chains 238 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 564 GLU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 101 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 51 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 214 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 137 optimal weight: 0.1980 chunk 172 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 199 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 630 HIS 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** 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 = 0.3616 r_free = 0.3616 target = 0.120374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096542 restraints weight = 32702.881| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.21 r_work: 0.3185 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3402 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= 0.134 Angle : 0.550 8.478 26773 Z= 0.285 Chirality : 0.042 0.146 2775 Planarity : 0.004 0.053 3558 Dihedral : 4.688 20.522 2616 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.10 % Allowed : 15.45 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2390 helix: -2.90 (0.46), residues: 92 sheet: 0.06 (0.20), residues: 591 loop : -0.39 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 228 HIS 0.004 0.001 HIS C 290 PHE 0.015 0.001 PHE A 662 TYR 0.022 0.001 TYR B 484 ARG 0.009 0.000 ARG B 610 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 239) hydrogen bonds : angle 5.67476 ( 453) SS BOND : bond 0.00344 ( 2) SS BOND : angle 1.10097 ( 4) covalent geometry : bond 0.00310 (19654) covalent geometry : angle 0.55012 (26769) *********************** 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 259 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 2.390 Fit side-chains REVERT: A 367 PHE cc_start: 0.7414 (t80) cc_final: 0.5732 (m-10) REVERT: A 533 ARG cc_start: 0.6971 (ptt-90) cc_final: 0.6695 (ptt-90) REVERT: A 585 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: B 425 SER cc_start: 0.7588 (p) cc_final: 0.7253 (t) REVERT: B 514 ARG cc_start: 0.7818 (mtm180) cc_final: 0.6070 (mmt180) REVERT: C 238 ARG cc_start: 0.8586 (ptp90) cc_final: 0.8103 (ptt180) REVERT: C 259 GLN cc_start: 0.7730 (tt0) cc_final: 0.5763 (pm20) REVERT: C 412 GLN cc_start: 0.7854 (pp30) cc_final: 0.7342 (pp30) REVERT: D 550 ARG cc_start: 0.7067 (ttp80) cc_final: 0.6646 (ttt-90) REVERT: E 514 ARG cc_start: 0.7329 (mtm180) cc_final: 0.4766 (tpt170) REVERT: E 518 MET cc_start: 0.7438 (ttm) cc_final: 0.6855 (ttp) REVERT: E 564 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6368 (pp20) REVERT: F 316 LYS cc_start: 0.8385 (mttt) cc_final: 0.8118 (mttt) REVERT: F 691 ASN cc_start: 0.7979 (t0) cc_final: 0.7598 (t0) outliers start: 44 outliers final: 26 residues processed: 240 average time/residue: 1.2358 time to fit residues: 337.2179 Evaluate side-chains 234 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain 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 333 THR Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 564 GLU Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 640 MET Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 736 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 82 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 102 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 161 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN F 552 ASN ** F 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095870 restraints weight = 32573.550| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.18 r_work: 0.3179 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19656 Z= 0.179 Angle : 0.575 8.204 26773 Z= 0.298 Chirality : 0.043 0.152 2775 Planarity : 0.004 0.059 3558 Dihedral : 4.736 20.995 2616 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.15 % Allowed : 15.88 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2390 helix: -2.94 (0.46), residues: 92 sheet: 0.05 (0.20), residues: 592 loop : -0.39 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 509 HIS 0.006 0.001 HIS C 290 PHE 0.016 0.002 PHE A 662 TYR 0.034 0.002 TYR B 484 ARG 0.011 0.001 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 239) hydrogen bonds : angle 5.68335 ( 453) SS BOND : bond 0.00495 ( 2) SS BOND : angle 1.20687 ( 4) covalent geometry : bond 0.00418 (19654) covalent geometry : angle 0.57489 (26769) *********************** 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 255 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 2.133 Fit side-chains REVERT: A 367 PHE cc_start: 0.7391 (t80) cc_final: 0.5668 (m-10) REVERT: A 533 ARG cc_start: 0.7038 (ptt-90) cc_final: 0.6753 (ptt-90) REVERT: A 585 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6859 (pm20) REVERT: B 425 SER cc_start: 0.7696 (p) cc_final: 0.7359 (t) REVERT: B 514 ARG cc_start: 0.7840 (mtm180) cc_final: 0.6074 (mmt180) REVERT: B 519 ASN cc_start: 0.7749 (t0) cc_final: 0.7050 (p0) REVERT: C 238 ARG cc_start: 0.8607 (ptp90) cc_final: 0.8134 (ptt180) REVERT: C 259 GLN cc_start: 0.7765 (tt0) cc_final: 0.5777 (pm20) REVERT: C 412 GLN cc_start: 0.7882 (pp30) cc_final: 0.7445 (pp30) REVERT: D 550 ARG cc_start: 0.7095 (ttp80) cc_final: 0.6668 (ttt-90) REVERT: E 514 ARG cc_start: 0.7418 (mtm180) cc_final: 0.4817 (tpt170) REVERT: E 564 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6406 (pp20) REVERT: F 316 LYS cc_start: 0.8402 (mttt) cc_final: 0.8171 (mmtt) REVERT: F 691 ASN cc_start: 0.8008 (t0) cc_final: 0.7627 (t0) REVERT: H 138 GLN cc_start: 0.8843 (mp-120) cc_final: 0.8630 (mp10) outliers start: 45 outliers final: 34 residues processed: 239 average time/residue: 1.2613 time to fit residues: 341.7447 Evaluate side-chains 238 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 333 THR 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 640 MET Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 564 GLU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 640 MET Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain L residue 21 GLN Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 98 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 197 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 71 optimal weight: 0.0570 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- 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 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** L 21 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096221 restraints weight = 32589.945| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.16 r_work: 0.3185 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19656 Z= 0.181 Angle : 0.578 8.311 26773 Z= 0.300 Chirality : 0.043 0.152 2775 Planarity : 0.004 0.059 3558 Dihedral : 4.752 20.873 2616 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.24 % Allowed : 15.74 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2390 helix: -2.92 (0.46), residues: 92 sheet: 0.04 (0.20), residues: 592 loop : -0.40 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 509 HIS 0.006 0.001 HIS C 290 PHE 0.019 0.002 PHE A 662 TYR 0.033 0.002 TYR B 484 ARG 0.015 0.001 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 239) hydrogen bonds : angle 5.68753 ( 453) SS BOND : bond 0.00485 ( 2) SS BOND : angle 1.21335 ( 4) covalent geometry : bond 0.00424 (19654) covalent geometry : angle 0.57761 (26769) ********************** 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 257 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 2.231 Fit side-chains REVERT: A 367 PHE cc_start: 0.7358 (t80) cc_final: 0.5668 (m-10) REVERT: A 533 ARG cc_start: 0.7052 (ptt-90) cc_final: 0.6764 (ptt-90) REVERT: A 585 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6875 (pm20) REVERT: B 425 SER cc_start: 0.7745 (p) cc_final: 0.7386 (t) REVERT: B 514 ARG cc_start: 0.7849 (mtm180) cc_final: 0.6076 (mmt180) REVERT: B 519 ASN cc_start: 0.7771 (t0) cc_final: 0.7109 (p0) REVERT: C 238 ARG cc_start: 0.8604 (ptp90) cc_final: 0.8127 (ptt180) REVERT: C 259 GLN cc_start: 0.7754 (tt0) cc_final: 0.5764 (pm20) REVERT: C 412 GLN cc_start: 0.7888 (pp30) cc_final: 0.7396 (pp30) REVERT: D 550 ARG cc_start: 0.7127 (ttp80) cc_final: 0.6667 (ttt-90) REVERT: E 514 ARG cc_start: 0.7397 (mtm180) cc_final: 0.4752 (tpt170) REVERT: E 518 MET cc_start: 0.7282 (ttm) cc_final: 0.6828 (ttp) REVERT: E 564 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6364 (pp20) REVERT: F 316 LYS cc_start: 0.8394 (mttt) cc_final: 0.8182 (mmtt) REVERT: F 691 ASN cc_start: 0.8063 (t0) cc_final: 0.7686 (t0) REVERT: H 138 GLN cc_start: 0.8868 (mp-120) cc_final: 0.8636 (mp10) outliers start: 47 outliers final: 37 residues processed: 238 average time/residue: 1.2369 time to fit residues: 335.0004 Evaluate side-chains 239 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 512 ASN Chi-restraints excluded: chain E residue 564 GLU Chi-restraints excluded: chain E residue 569 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 425 SER Chi-restraints excluded: chain F residue 640 MET Chi-restraints excluded: chain F residue 676 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 736 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 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 101 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 39 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 234 optimal weight: 0.2980 chunk 110 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 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** L 21 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.121605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098015 restraints weight = 32393.674| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.18 r_work: 0.3203 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3556 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= 0.119 Angle : 0.549 8.108 26773 Z= 0.281 Chirality : 0.042 0.147 2775 Planarity : 0.004 0.060 3558 Dihedral : 4.531 19.927 2616 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.86 % Allowed : 16.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2390 helix: -2.68 (0.49), residues: 92 sheet: 0.11 (0.21), residues: 591 loop : -0.32 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 228 HIS 0.004 0.001 HIS C 290 PHE 0.017 0.001 PHE A 662 TYR 0.028 0.001 TYR B 484 ARG 0.014 0.001 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 239) hydrogen bonds : angle 5.51431 ( 453) SS BOND : bond 0.00350 ( 2) SS BOND : angle 1.17244 ( 4) covalent geometry : bond 0.00278 (19654) covalent geometry : angle 0.54844 (26769) =============================================================================== Job complete usr+sys time: 14903.66 seconds wall clock time: 258 minutes 36.13 seconds (15516.13 seconds total)