Starting phenix.real_space_refine on Thu Sep 18 10:01:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7l_61206/09_2025/9j7l_61206.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7l_61206/09_2025/9j7l_61206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j7l_61206/09_2025/9j7l_61206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7l_61206/09_2025/9j7l_61206.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7l_61206/09_2025/9j7l_61206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7l_61206/09_2025/9j7l_61206.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 9970 2.51 5 N 2710 2.21 5 O 2984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15720 Number of models: 1 Model: "" Number of chains: 7 Chain: "5" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 681 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain breaks: 3 Chain: "6" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3336 Classifications: {'peptide': 410} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 380} Chain breaks: 10 Chain: "7" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2769 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 320} Chain breaks: 10 Chain: "A" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2735 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 18, 'TRANS': 326} Chain breaks: 7 Chain: "c" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain breaks: 3 Chain: "o" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3861 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 449} Chain breaks: 5 Chain: "p" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1352 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 157} Chain breaks: 12 Time building chain proxies: 3.37, per 1000 atoms: 0.21 Number of scatterers: 15720 At special positions: 0 Unit cell: (112.35, 127.33, 109.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 2984 8.00 N 2710 7.00 C 9970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 621.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3628 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 43 sheets defined 13.0% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain '6' and resid 270 through 274 removed outlier: 3.609A pdb=" N ASN 6 273 " --> pdb=" O THR 6 270 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR 6 274 " --> pdb=" O ASN 6 271 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 270 through 274' Processing helix chain '6' and resid 289 through 293 Processing helix chain '6' and resid 295 through 304 Processing helix chain '6' and resid 397 through 401 removed outlier: 3.617A pdb=" N PHE 6 401 " --> pdb=" O LEU 6 398 " (cutoff:3.500A) Processing helix chain '6' and resid 469 through 476 removed outlier: 4.077A pdb=" N MET 6 473 " --> pdb=" O PRO 6 470 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA 6 474 " --> pdb=" O ASN 6 471 " (cutoff:3.500A) Processing helix chain '6' and resid 494 through 498 Processing helix chain '6' and resid 502 through 507 removed outlier: 4.679A pdb=" N THR 6 506 " --> pdb=" O ASN 6 502 " (cutoff:3.500A) Processing helix chain '6' and resid 556 through 558 No H-bonds generated for 'chain '6' and resid 556 through 558' Processing helix chain '6' and resid 565 through 571 removed outlier: 4.303A pdb=" N THR 6 570 " --> pdb=" O GLU 6 567 " (cutoff:3.500A) Processing helix chain '7' and resid 270 through 274 Processing helix chain '7' and resid 397 through 401 removed outlier: 3.529A pdb=" N PHE 7 401 " --> pdb=" O LEU 7 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 75 Processing helix chain 'A' and resid 143 through 162 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 215 through 219 removed outlier: 3.928A pdb=" N SER A 219 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 284 through 299 removed outlier: 3.981A pdb=" N ASN A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 299 " --> pdb=" O TYR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.733A pdb=" N TYR A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 379 removed outlier: 4.345A pdb=" N ARG A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLN A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLU A 371 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'c' and resid 432 through 436 removed outlier: 4.080A pdb=" N LEU c 436 " --> pdb=" O LEU c 433 " (cutoff:3.500A) Processing helix chain 'c' and resid 472 through 476 Processing helix chain 'c' and resid 565 through 569 removed outlier: 3.709A pdb=" N LYS c 569 " --> pdb=" O GLU c 566 " (cutoff:3.500A) Processing helix chain 'o' and resid 270 through 274 removed outlier: 3.557A pdb=" N THR o 274 " --> pdb=" O ASN o 271 " (cutoff:3.500A) Processing helix chain 'o' and resid 289 through 293 Processing helix chain 'o' and resid 295 through 305 removed outlier: 3.670A pdb=" N ASN o 305 " --> pdb=" O ARG o 301 " (cutoff:3.500A) Processing helix chain 'o' and resid 397 through 401 removed outlier: 3.512A pdb=" N PHE o 401 " --> pdb=" O LEU o 398 " (cutoff:3.500A) Processing helix chain 'o' and resid 472 through 476 removed outlier: 3.553A pdb=" N GLN o 476 " --> pdb=" O MET o 473 " (cutoff:3.500A) Processing helix chain 'o' and resid 494 through 498 Processing helix chain 'o' and resid 556 through 558 No H-bonds generated for 'chain 'o' and resid 556 through 558' Processing helix chain 'o' and resid 565 through 569 Processing helix chain 'p' and resid 270 through 274 Processing helix chain 'p' and resid 397 through 401 Processing sheet with id=AA1, first strand: chain '5' and resid 446 through 452 removed outlier: 6.800A pdb=" N GLY 5 464 " --> pdb=" O SER 5 449 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR 5 451 " --> pdb=" O THR 5 462 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '5' and resid 481 through 482 removed outlier: 6.353A pdb=" N LEU 5 481 " --> pdb=" O VAL 5 608 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET 5 607 " --> pdb=" O PHE 6 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '5' and resid 580 through 583 removed outlier: 3.728A pdb=" N GLY 5 580 " --> pdb=" O VAL 5 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '5' and resid 629 through 630 Processing sheet with id=AA5, first strand: chain '6' and resid 233 through 236 Processing sheet with id=AA6, first strand: chain '6' and resid 259 through 263 removed outlier: 3.786A pdb=" N TYR 6 275 " --> pdb=" O ASN 6 263 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR 6 280 " --> pdb=" O TYR 6 380 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N TYR 6 380 " --> pdb=" O THR 6 280 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TRP 6 282 " --> pdb=" O TYR 6 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '6' and resid 427 through 429 Processing sheet with id=AA8, first strand: chain '6' and resid 446 through 452 removed outlier: 5.367A pdb=" N LEU 6 448 " --> pdb=" O SER 6 466 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER 6 466 " --> pdb=" O LEU 6 448 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN 6 452 " --> pdb=" O THR 6 462 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N THR 6 462 " --> pdb=" O GLN 6 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '6' and resid 481 through 482 removed outlier: 6.346A pdb=" N LEU 6 481 " --> pdb=" O VAL 6 608 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET 6 607 " --> pdb=" O PHE 7 631 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '6' and resid 485 through 486 Processing sheet with id=AB2, first strand: chain '6' and resid 490 through 492 Processing sheet with id=AB3, first strand: chain '6' and resid 510 through 511 Processing sheet with id=AB4, first strand: chain '6' and resid 544 through 546 Processing sheet with id=AB5, first strand: chain '6' and resid 595 through 598 removed outlier: 3.666A pdb=" N GLY 6 580 " --> pdb=" O VAL 6 598 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '6' and resid 621 through 623 removed outlier: 6.111A pdb=" N ALA 6 622 " --> pdb=" O LEU 6 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '7' and resid 245 through 250 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 245 through 250 current: chain '7' and resid 334 through 337 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '7' and resid 259 through 263 Processing sheet with id=AB9, first strand: chain '7' and resid 384 through 385 Processing sheet with id=AC1, first strand: chain '7' and resid 485 through 486 Processing sheet with id=AC2, first strand: chain '7' and resid 490 through 492 Processing sheet with id=AC3, first strand: chain '7' and resid 544 through 546 Processing sheet with id=AC4, first strand: chain '7' and resid 621 through 623 removed outlier: 6.127A pdb=" N ALA 7 622 " --> pdb=" O LEU 7 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 80 through 87 removed outlier: 6.730A pdb=" N LEU A 94 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 132 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU A 179 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 134 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN A 131 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLY A 254 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS A 133 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 256 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A 135 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N GLY A 258 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER A 253 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU A 349 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN A 255 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 351 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N HIS A 257 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA A 263 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=AC7, first strand: chain 'A' and resid 411 through 412 Processing sheet with id=AC8, first strand: chain 'A' and resid 426 through 428 Processing sheet with id=AC9, first strand: chain 'c' and resid 446 through 452 removed outlier: 6.840A pdb=" N GLY c 464 " --> pdb=" O SER c 449 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR c 451 " --> pdb=" O THR c 462 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 595 through 598 removed outlier: 3.737A pdb=" N GLY c 580 " --> pdb=" O VAL c 598 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU o 513 " --> pdb=" O ARG o 516 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 607 through 609 removed outlier: 3.880A pdb=" N MET c 607 " --> pdb=" O PHE o 631 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'o' and resid 232 through 236 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 239 through 250 current: chain 'o' and resid 334 through 337 Processing sheet with id=AD4, first strand: chain 'o' and resid 259 through 263 Processing sheet with id=AD5, first strand: chain 'o' and resid 384 through 385 Processing sheet with id=AD6, first strand: chain 'o' and resid 427 through 429 Processing sheet with id=AD7, first strand: chain 'o' and resid 446 through 447 Processing sheet with id=AD8, first strand: chain 'o' and resid 485 through 486 Processing sheet with id=AD9, first strand: chain 'o' and resid 490 through 492 Processing sheet with id=AE1, first strand: chain 'o' and resid 544 through 546 Processing sheet with id=AE2, first strand: chain 'o' and resid 596 through 598 removed outlier: 3.678A pdb=" N GLY o 580 " --> pdb=" O VAL o 598 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'o' and resid 607 through 609 removed outlier: 3.861A pdb=" N MET o 607 " --> pdb=" O PHE p 631 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'o' and resid 621 through 623 removed outlier: 6.112A pdb=" N ALA o 622 " --> pdb=" O LEU o 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'p' and resid 259 through 263 removed outlier: 4.656A pdb=" N PHE p 276 " --> pdb=" O THR p 382 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'p' and resid 485 through 486 Processing sheet with id=AE7, first strand: chain 'p' and resid 621 through 623 removed outlier: 6.009A pdb=" N ALA p 622 " --> pdb=" O LEU p 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 266 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5112 1.34 - 1.45: 3031 1.45 - 1.57: 7909 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 16142 Sorted by residual: bond pdb=" CB ILE c 581 " pdb=" CG2 ILE c 581 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CA ASN o 693 " pdb=" CB ASN o 693 " ideal model delta sigma weight residual 1.531 1.572 -0.041 3.12e-02 1.03e+03 1.75e+00 bond pdb=" C SER 7 279 " pdb=" N THR 7 280 " ideal model delta sigma weight residual 1.327 1.291 0.036 2.86e-02 1.22e+03 1.60e+00 bond pdb=" C SER p 279 " pdb=" N THR p 280 " ideal model delta sigma weight residual 1.329 1.294 0.034 3.03e-02 1.09e+03 1.27e+00 bond pdb=" C TYR A 265 " pdb=" N PRO A 266 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.20e+00 ... (remaining 16137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 21154 1.21 - 2.42: 610 2.42 - 3.62: 141 3.62 - 4.83: 15 4.83 - 6.04: 10 Bond angle restraints: 21930 Sorted by residual: angle pdb=" C LEU A 232 " pdb=" N ASP A 233 " pdb=" CA ASP A 233 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.75e+00 angle pdb=" CA TYR A 265 " pdb=" CB TYR A 265 " pdb=" CG TYR A 265 " ideal model delta sigma weight residual 113.90 118.18 -4.28 1.80e+00 3.09e-01 5.66e+00 angle pdb=" N PRO A 266 " pdb=" CA PRO A 266 " pdb=" C PRO A 266 " ideal model delta sigma weight residual 112.47 117.36 -4.89 2.06e+00 2.36e-01 5.64e+00 angle pdb=" OG1 THR 7 382 " pdb=" CB THR 7 382 " pdb=" CG2 THR 7 382 " ideal model delta sigma weight residual 109.30 104.84 4.46 2.00e+00 2.50e-01 4.96e+00 angle pdb=" C PHE A 55 " pdb=" N ASP A 56 " pdb=" CA ASP A 56 " ideal model delta sigma weight residual 122.46 125.20 -2.74 1.41e+00 5.03e-01 3.77e+00 ... (remaining 21925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8537 18.00 - 36.00: 708 36.00 - 53.99: 113 53.99 - 71.99: 21 71.99 - 89.99: 18 Dihedral angle restraints: 9397 sinusoidal: 3750 harmonic: 5647 Sorted by residual: dihedral pdb=" CB CYS A 309 " pdb=" SG CYS A 309 " pdb=" SG CYS A 353 " pdb=" CB CYS A 353 " ideal model delta sinusoidal sigma weight residual -86.00 -39.18 -46.82 1 1.00e+01 1.00e-02 3.03e+01 dihedral pdb=" CA TYR 7 486 " pdb=" C TYR 7 486 " pdb=" N ARG 7 487 " pdb=" CA ARG 7 487 " ideal model delta harmonic sigma weight residual 180.00 -159.86 -20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TYR p 486 " pdb=" C TYR p 486 " pdb=" N ARG p 487 " pdb=" CA ARG p 487 " ideal model delta harmonic sigma weight residual -180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 9394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1768 0.043 - 0.086: 396 0.086 - 0.129: 121 0.129 - 0.171: 11 0.171 - 0.214: 1 Chirality restraints: 2297 Sorted by residual: chirality pdb=" CB ILE c 595 " pdb=" CA ILE c 595 " pdb=" CG1 ILE c 595 " pdb=" CG2 ILE c 595 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PRO A 266 " pdb=" N PRO A 266 " pdb=" C PRO A 266 " pdb=" CB PRO A 266 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA ILE 6 241 " pdb=" N ILE 6 241 " pdb=" C ILE 6 241 " pdb=" CB ILE 6 241 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 2294 not shown) Planarity restraints: 2875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 265 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 266 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 266 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 266 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 424 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO A 425 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 233 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C ASP A 233 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 233 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 234 " 0.010 2.00e-02 2.50e+03 ... (remaining 2872 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 589 2.70 - 3.25: 15628 3.25 - 3.80: 27982 3.80 - 4.35: 36524 4.35 - 4.90: 60416 Nonbonded interactions: 141139 Sorted by model distance: nonbonded pdb=" OE1 GLN c 601 " pdb=" OG SER o 600 " model vdw 2.152 3.040 nonbonded pdb=" NH1 ARG A 92 " pdb=" OD1 ASP A 185 " model vdw 2.156 3.120 nonbonded pdb=" OH TYR 7 416 " pdb=" O HIS 7 644 " model vdw 2.161 3.040 nonbonded pdb=" OE1 GLN 5 601 " pdb=" OG SER 6 600 " model vdw 2.167 3.040 nonbonded pdb=" OE1 GLN o 601 " pdb=" OG SER p 600 " model vdw 2.181 3.040 ... (remaining 141134 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 '6' and (resid 229 through 449 or resid 465 through 584 or resid 595 thro \ ugh 738)) selection = (chain 'o' and (resid 229 through 249 or resid 253 through 254 or resid 258 thro \ ugh 263 or resid 270 through 318 or resid 345 through 382 or resid 394 through 4 \ 03 or resid 412 through 512 or resid 517 through 650 or resid 679 through 738)) } 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.290 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 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 : 0.004 0.047 16144 Z= 0.172 Angle : 0.525 6.041 21934 Z= 0.275 Chirality : 0.041 0.214 2297 Planarity : 0.004 0.052 2875 Dihedral : 13.829 89.989 5763 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.06 % Allowed : 0.18 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.19), residues: 1854 helix: 0.06 (0.43), residues: 158 sheet: 0.09 (0.26), residues: 390 loop : -0.19 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 727 TYR 0.020 0.001 TYR A 265 PHE 0.013 0.001 PHE 6 316 TRP 0.009 0.001 TRP 5 480 HIS 0.006 0.001 HIS o 291 Details of bonding type rmsd covalent geometry : bond 0.00392 (16142) covalent geometry : angle 0.52455 (21930) SS BOND : bond 0.00336 ( 2) SS BOND : angle 1.28953 ( 4) hydrogen bonds : bond 0.17651 ( 266) hydrogen bonds : angle 7.10961 ( 591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.503 Fit side-chains REVERT: 6 684 GLU cc_start: 0.8613 (pt0) cc_final: 0.8368 (pt0) REVERT: A 141 ASP cc_start: 0.8111 (p0) cc_final: 0.7735 (t0) REVERT: A 222 ASP cc_start: 0.6347 (p0) cc_final: 0.4838 (p0) REVERT: o 236 LEU cc_start: 0.8733 (mm) cc_final: 0.8489 (mp) REVERT: o 437 MET cc_start: 0.9176 (pmm) cc_final: 0.8771 (pmm) REVERT: p 597 THR cc_start: 0.8289 (t) cc_final: 0.7931 (m) REVERT: p 637 MET cc_start: 0.9300 (mtm) cc_final: 0.9096 (mtm) outliers start: 1 outliers final: 1 residues processed: 275 average time/residue: 0.6600 time to fit residues: 198.7504 Evaluate side-chains 134 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 590 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 377 GLN 6 521 ASN ** 6 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 702 GLN 7 632 HIS A 131 GLN A 137 ASN A 255 ASN A 299 HIS c 424 HIS ** c 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 587 GLN o 254 ASN o 540 ASN ** o 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 706 ASN p 256 HIS p 271 ASN p 362 GLN p 626 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.084520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.066823 restraints weight = 34248.010| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.89 r_work: 0.2807 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 16144 Z= 0.383 Angle : 0.668 8.225 21934 Z= 0.346 Chirality : 0.047 0.183 2297 Planarity : 0.005 0.071 2875 Dihedral : 5.185 75.776 2112 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.40 % Allowed : 10.02 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.19), residues: 1854 helix: 0.46 (0.43), residues: 153 sheet: 0.02 (0.27), residues: 365 loop : -0.21 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 612 TYR 0.019 0.002 TYR o 703 PHE 0.017 0.002 PHE A 345 TRP 0.014 0.002 TRP 6 687 HIS 0.017 0.002 HIS 6 291 Details of bonding type rmsd covalent geometry : bond 0.00894 (16142) covalent geometry : angle 0.66799 (21930) SS BOND : bond 0.01794 ( 2) SS BOND : angle 1.04965 ( 4) hydrogen bonds : bond 0.03750 ( 266) hydrogen bonds : angle 5.96002 ( 591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7927 (p0) cc_final: 0.6550 (t0) REVERT: c 533 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: c 566 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8370 (pp20) REVERT: c 567 GLU cc_start: 0.8688 (mp0) cc_final: 0.8444 (mp0) REVERT: c 584 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: o 236 LEU cc_start: 0.8973 (mm) cc_final: 0.8510 (mt) REVERT: o 325 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: o 437 MET cc_start: 0.9398 (pmm) cc_final: 0.9013 (ptp) REVERT: p 510 LYS cc_start: 0.9003 (mtmt) cc_final: 0.8770 (mtmt) outliers start: 41 outliers final: 17 residues processed: 164 average time/residue: 0.6288 time to fit residues: 113.3205 Evaluate side-chains 141 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 430 SER Chi-restraints excluded: chain 6 residue 382 THR Chi-restraints excluded: chain 6 residue 598 VAL Chi-restraints excluded: chain 6 residue 682 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain c residue 417 THR Chi-restraints excluded: chain c residue 430 SER Chi-restraints excluded: chain c residue 432 SER Chi-restraints excluded: chain c residue 533 GLU Chi-restraints excluded: chain c residue 584 ASP Chi-restraints excluded: chain c residue 586 LEU Chi-restraints excluded: chain o residue 315 SER Chi-restraints excluded: chain o residue 325 GLU Chi-restraints excluded: chain o residue 577 GLU Chi-restraints excluded: chain p residue 270 THR Chi-restraints excluded: chain p residue 349 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 187 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 702 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN c 431 GLN o 260 GLN o 702 GLN p 611 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.086205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.068916 restraints weight = 34286.145| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.84 r_work: 0.2875 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16144 Z= 0.140 Angle : 0.501 4.886 21934 Z= 0.260 Chirality : 0.040 0.155 2297 Planarity : 0.004 0.058 2875 Dihedral : 4.692 74.170 2110 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.34 % Allowed : 11.43 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.19), residues: 1854 helix: 0.78 (0.43), residues: 147 sheet: 0.11 (0.27), residues: 347 loop : -0.08 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 612 TYR 0.015 0.001 TYR A 356 PHE 0.015 0.001 PHE 7 423 TRP 0.036 0.001 TRP A 341 HIS 0.006 0.001 HIS 6 291 Details of bonding type rmsd covalent geometry : bond 0.00320 (16142) covalent geometry : angle 0.50091 (21930) SS BOND : bond 0.00581 ( 2) SS BOND : angle 1.06097 ( 4) hydrogen bonds : bond 0.03082 ( 266) hydrogen bonds : angle 5.55768 ( 591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.630 Fit side-chains REVERT: A 141 ASP cc_start: 0.7851 (p0) cc_final: 0.6511 (t0) REVERT: A 341 TRP cc_start: 0.8251 (m-90) cc_final: 0.7539 (m-90) REVERT: c 566 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8324 (pp20) REVERT: c 577 GLU cc_start: 0.8678 (pt0) cc_final: 0.8427 (pt0) REVERT: c 613 ASP cc_start: 0.6770 (OUTLIER) cc_final: 0.6410 (t70) REVERT: o 236 LEU cc_start: 0.8920 (mm) cc_final: 0.8568 (mt) REVERT: o 325 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: o 437 MET cc_start: 0.9415 (pmm) cc_final: 0.9190 (pmm) REVERT: o 691 LYS cc_start: 0.8213 (tppt) cc_final: 0.7966 (mmmt) outliers start: 40 outliers final: 15 residues processed: 157 average time/residue: 0.6535 time to fit residues: 113.1303 Evaluate side-chains 131 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 454 THR Chi-restraints excluded: chain 6 residue 413 GLN Chi-restraints excluded: chain 6 residue 472 THR Chi-restraints excluded: chain 6 residue 682 SER Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain c residue 430 SER Chi-restraints excluded: chain c residue 432 SER Chi-restraints excluded: chain c residue 566 GLU Chi-restraints excluded: chain c residue 613 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 315 SER Chi-restraints excluded: chain o residue 325 GLU Chi-restraints excluded: chain o residue 326 VAL Chi-restraints excluded: chain o residue 577 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 26 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.070954 restraints weight = 35111.874| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.80 r_work: 0.2866 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16144 Z= 0.162 Angle : 0.494 5.185 21934 Z= 0.255 Chirality : 0.040 0.151 2297 Planarity : 0.004 0.058 2875 Dihedral : 4.576 72.662 2110 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.52 % Allowed : 12.25 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.19), residues: 1854 helix: 0.99 (0.44), residues: 147 sheet: 0.13 (0.27), residues: 352 loop : -0.07 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 5 450 TYR 0.015 0.001 TYR o 707 PHE 0.018 0.001 PHE 7 423 TRP 0.019 0.001 TRP A 341 HIS 0.007 0.001 HIS 6 291 Details of bonding type rmsd covalent geometry : bond 0.00375 (16142) covalent geometry : angle 0.49439 (21930) SS BOND : bond 0.00472 ( 2) SS BOND : angle 0.89645 ( 4) hydrogen bonds : bond 0.02925 ( 266) hydrogen bonds : angle 5.37151 ( 591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.640 Fit side-chains REVERT: 7 322 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: A 141 ASP cc_start: 0.7827 (p0) cc_final: 0.6571 (t0) REVERT: A 341 TRP cc_start: 0.8372 (m-90) cc_final: 0.7587 (m-90) REVERT: A 350 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: c 442 ASP cc_start: 0.8715 (m-30) cc_final: 0.7448 (m-30) REVERT: c 566 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8388 (pp20) REVERT: c 586 LEU cc_start: 0.8927 (mt) cc_final: 0.8647 (tp) REVERT: c 613 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6582 (t70) REVERT: o 236 LEU cc_start: 0.8948 (mm) cc_final: 0.8579 (mt) REVERT: o 325 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: o 437 MET cc_start: 0.9433 (pmm) cc_final: 0.9196 (pmm) REVERT: o 552 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7229 (tpt-90) REVERT: p 510 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8791 (mtmt) outliers start: 43 outliers final: 18 residues processed: 151 average time/residue: 0.6368 time to fit residues: 106.2918 Evaluate side-chains 138 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 430 SER Chi-restraints excluded: chain 6 residue 240 VAL Chi-restraints excluded: chain 6 residue 413 GLN Chi-restraints excluded: chain 6 residue 682 SER Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 322 GLN Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain c residue 426 SER Chi-restraints excluded: chain c residue 430 SER Chi-restraints excluded: chain c residue 432 SER Chi-restraints excluded: chain c residue 566 GLU Chi-restraints excluded: chain c residue 613 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 315 SER Chi-restraints excluded: chain o residue 325 GLU Chi-restraints excluded: chain o residue 326 VAL Chi-restraints excluded: chain o residue 552 ARG Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 577 GLU Chi-restraints excluded: chain p residue 349 SER Chi-restraints excluded: chain p residue 510 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 611 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN ** c 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 611 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.070882 restraints weight = 35308.120| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.91 r_work: 0.2876 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16144 Z= 0.128 Angle : 0.472 5.766 21934 Z= 0.243 Chirality : 0.040 0.145 2297 Planarity : 0.004 0.054 2875 Dihedral : 4.415 70.554 2110 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.64 % Allowed : 13.19 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.20), residues: 1854 helix: 1.18 (0.44), residues: 147 sheet: 0.10 (0.27), residues: 357 loop : -0.03 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 450 TYR 0.017 0.001 TYR 6 707 PHE 0.013 0.001 PHE 7 423 TRP 0.015 0.001 TRP A 341 HIS 0.005 0.001 HIS 6 291 Details of bonding type rmsd covalent geometry : bond 0.00295 (16142) covalent geometry : angle 0.47194 (21930) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.88704 ( 4) hydrogen bonds : bond 0.02755 ( 266) hydrogen bonds : angle 5.20761 ( 591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 0.643 Fit side-chains REVERT: 7 322 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: A 62 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: A 141 ASP cc_start: 0.7894 (p0) cc_final: 0.6696 (t0) REVERT: A 247 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.8040 (ptp-110) REVERT: A 341 TRP cc_start: 0.8365 (m-90) cc_final: 0.7568 (m-90) REVERT: A 350 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: c 613 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6611 (t70) REVERT: o 236 LEU cc_start: 0.8935 (mm) cc_final: 0.8592 (mt) REVERT: o 325 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8222 (pm20) REVERT: o 437 MET cc_start: 0.9394 (pmm) cc_final: 0.9096 (pmm) REVERT: p 510 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8805 (mtmt) outliers start: 45 outliers final: 22 residues processed: 154 average time/residue: 0.6854 time to fit residues: 115.9868 Evaluate side-chains 141 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 430 SER Chi-restraints excluded: chain 5 residue 454 THR Chi-restraints excluded: chain 6 residue 240 VAL Chi-restraints excluded: chain 6 residue 413 GLN Chi-restraints excluded: chain 6 residue 472 THR Chi-restraints excluded: chain 6 residue 600 SER Chi-restraints excluded: chain 6 residue 682 SER Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 322 GLN Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain c residue 417 THR Chi-restraints excluded: chain c residue 430 SER Chi-restraints excluded: chain c residue 432 SER Chi-restraints excluded: chain c residue 613 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 315 SER Chi-restraints excluded: chain o residue 325 GLU Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 577 GLU Chi-restraints excluded: chain o residue 597 THR Chi-restraints excluded: chain p residue 349 SER Chi-restraints excluded: chain p residue 510 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 146 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 499 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS A 343 ASN ** c 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 611 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.083457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.066733 restraints weight = 35683.992| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.79 r_work: 0.2782 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 16144 Z= 0.401 Angle : 0.640 6.121 21934 Z= 0.329 Chirality : 0.047 0.200 2297 Planarity : 0.005 0.064 2875 Dihedral : 5.040 73.546 2110 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.22 % Allowed : 13.42 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.19), residues: 1854 helix: 1.02 (0.44), residues: 147 sheet: 0.03 (0.27), residues: 349 loop : -0.23 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 727 TYR 0.018 0.002 TYR o 703 PHE 0.021 0.002 PHE 7 423 TRP 0.011 0.002 TRP 6 687 HIS 0.012 0.002 HIS 6 291 Details of bonding type rmsd covalent geometry : bond 0.00929 (16142) covalent geometry : angle 0.63944 (21930) SS BOND : bond 0.00296 ( 2) SS BOND : angle 1.21651 ( 4) hydrogen bonds : bond 0.03462 ( 266) hydrogen bonds : angle 5.56972 ( 591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 123 time to evaluate : 0.675 Fit side-chains REVERT: 6 241 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9106 (mm) REVERT: 7 322 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8495 (pm20) REVERT: A 62 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: A 141 ASP cc_start: 0.7888 (p0) cc_final: 0.6734 (t0) REVERT: A 341 TRP cc_start: 0.8421 (m-90) cc_final: 0.7626 (m-90) REVERT: A 350 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: c 566 GLU cc_start: 0.8872 (pp20) cc_final: 0.8570 (pp20) REVERT: c 567 GLU cc_start: 0.8659 (mp0) cc_final: 0.8380 (mp0) REVERT: c 586 LEU cc_start: 0.9178 (mt) cc_final: 0.8927 (tp) REVERT: c 613 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6400 (t70) REVERT: o 325 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8148 (pm20) REVERT: o 437 MET cc_start: 0.9436 (pmm) cc_final: 0.9033 (ptp) REVERT: o 552 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7382 (tpt-90) outliers start: 55 outliers final: 23 residues processed: 159 average time/residue: 0.6628 time to fit residues: 116.1525 Evaluate side-chains 148 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 430 SER Chi-restraints excluded: chain 5 residue 595 ILE Chi-restraints excluded: chain 6 residue 240 VAL Chi-restraints excluded: chain 6 residue 241 ILE Chi-restraints excluded: chain 6 residue 382 THR Chi-restraints excluded: chain 6 residue 598 VAL Chi-restraints excluded: chain 6 residue 682 SER Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 322 GLN Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain c residue 417 THR Chi-restraints excluded: chain c residue 426 SER Chi-restraints excluded: chain c residue 430 SER Chi-restraints excluded: chain c residue 432 SER Chi-restraints excluded: chain c residue 613 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 236 LEU Chi-restraints excluded: chain o residue 315 SER Chi-restraints excluded: chain o residue 325 GLU Chi-restraints excluded: chain o residue 326 VAL Chi-restraints excluded: chain o residue 552 ARG Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 577 GLU Chi-restraints excluded: chain o residue 597 THR Chi-restraints excluded: chain p residue 349 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 488 GLN 7 549 ASN A 255 ASN A 343 ASN ** c 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 666 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.086338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.069785 restraints weight = 34754.405| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.79 r_work: 0.2850 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16144 Z= 0.148 Angle : 0.502 5.675 21934 Z= 0.260 Chirality : 0.040 0.151 2297 Planarity : 0.004 0.055 2875 Dihedral : 4.661 72.585 2110 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.05 % Allowed : 14.95 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.19), residues: 1854 helix: 1.28 (0.44), residues: 142 sheet: 0.09 (0.28), residues: 334 loop : -0.10 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG o 727 TYR 0.018 0.001 TYR 6 707 PHE 0.014 0.001 PHE 7 423 TRP 0.015 0.001 TRP A 341 HIS 0.004 0.001 HIS 6 291 Details of bonding type rmsd covalent geometry : bond 0.00342 (16142) covalent geometry : angle 0.50175 (21930) SS BOND : bond 0.00374 ( 2) SS BOND : angle 1.13817 ( 4) hydrogen bonds : bond 0.02833 ( 266) hydrogen bonds : angle 5.26285 ( 591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.710 Fit side-chains REVERT: 6 241 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9084 (mm) REVERT: 6 643 LYS cc_start: 0.9406 (mtpp) cc_final: 0.9034 (mtpm) REVERT: 7 322 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8437 (pm20) REVERT: 7 534 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7033 (mt-10) REVERT: A 62 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: A 141 ASP cc_start: 0.7883 (p0) cc_final: 0.6741 (t0) REVERT: A 247 ARG cc_start: 0.8289 (ttp-110) cc_final: 0.8065 (ptp-110) REVERT: A 341 TRP cc_start: 0.8434 (m-90) cc_final: 0.7838 (m-90) REVERT: A 350 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: c 566 GLU cc_start: 0.8865 (pp20) cc_final: 0.8607 (pp20) REVERT: c 613 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6588 (t70) REVERT: o 325 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: o 437 MET cc_start: 0.9449 (pmm) cc_final: 0.9099 (pmm) REVERT: o 707 TYR cc_start: 0.7755 (t80) cc_final: 0.7423 (t80) outliers start: 35 outliers final: 21 residues processed: 149 average time/residue: 0.6685 time to fit residues: 109.9575 Evaluate side-chains 138 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 430 SER Chi-restraints excluded: chain 6 residue 240 VAL Chi-restraints excluded: chain 6 residue 241 ILE Chi-restraints excluded: chain 6 residue 413 GLN Chi-restraints excluded: chain 6 residue 682 SER Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 322 GLN Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain 7 residue 534 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain c residue 430 SER Chi-restraints excluded: chain c residue 432 SER Chi-restraints excluded: chain c residue 613 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 315 SER Chi-restraints excluded: chain o residue 325 GLU Chi-restraints excluded: chain o residue 326 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 577 GLU Chi-restraints excluded: chain o residue 597 THR Chi-restraints excluded: chain p residue 349 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 134 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 549 ASN ** c 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 666 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.084809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.068281 restraints weight = 35418.486| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.78 r_work: 0.2817 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 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 : 0.006 0.049 16144 Z= 0.255 Angle : 0.547 7.310 21934 Z= 0.282 Chirality : 0.042 0.177 2297 Planarity : 0.004 0.055 2875 Dihedral : 4.750 73.431 2110 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.52 % Allowed : 14.54 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.19), residues: 1854 helix: 1.15 (0.43), residues: 142 sheet: 0.06 (0.27), residues: 341 loop : -0.14 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG o 727 TYR 0.015 0.002 TYR o 703 PHE 0.016 0.001 PHE 7 423 TRP 0.009 0.001 TRP A 341 HIS 0.009 0.001 HIS 6 291 Details of bonding type rmsd covalent geometry : bond 0.00590 (16142) covalent geometry : angle 0.54715 (21930) SS BOND : bond 0.00289 ( 2) SS BOND : angle 1.15381 ( 4) hydrogen bonds : bond 0.03024 ( 266) hydrogen bonds : angle 5.35933 ( 591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.562 Fit side-chains REVERT: 6 643 LYS cc_start: 0.9394 (mtpp) cc_final: 0.9037 (mtpm) REVERT: 7 322 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8464 (pm20) REVERT: 7 534 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7085 (mt-10) REVERT: A 141 ASP cc_start: 0.7856 (p0) cc_final: 0.6793 (t0) REVERT: A 247 ARG cc_start: 0.8301 (ttp-110) cc_final: 0.8070 (ptp-110) REVERT: A 341 TRP cc_start: 0.8463 (m-90) cc_final: 0.7903 (m-90) REVERT: A 350 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: c 566 GLU cc_start: 0.8835 (pp20) cc_final: 0.8537 (pp20) REVERT: c 586 LEU cc_start: 0.9085 (mt) cc_final: 0.8821 (tp) REVERT: c 613 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6610 (t70) REVERT: o 325 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: o 437 MET cc_start: 0.9457 (pmm) cc_final: 0.9144 (pmm) REVERT: o 707 TYR cc_start: 0.7781 (t80) cc_final: 0.7441 (t80) outliers start: 43 outliers final: 26 residues processed: 142 average time/residue: 0.6378 time to fit residues: 100.3035 Evaluate side-chains 143 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 430 SER Chi-restraints excluded: chain 6 residue 240 VAL Chi-restraints excluded: chain 6 residue 382 THR Chi-restraints excluded: chain 6 residue 682 SER Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 322 GLN Chi-restraints excluded: chain 7 residue 323 VAL Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain 7 residue 534 GLU Chi-restraints excluded: chain 7 residue 549 ASN Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain c residue 417 THR Chi-restraints excluded: chain c residue 426 SER Chi-restraints excluded: chain c residue 430 SER Chi-restraints excluded: chain c residue 432 SER Chi-restraints excluded: chain c residue 531 ASP Chi-restraints excluded: chain c residue 613 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 236 LEU Chi-restraints excluded: chain o residue 315 SER Chi-restraints excluded: chain o residue 325 GLU Chi-restraints excluded: chain o residue 326 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 577 GLU Chi-restraints excluded: chain o residue 597 THR Chi-restraints excluded: chain p residue 349 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 153 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 100 optimal weight: 0.0980 chunk 184 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 109 optimal weight: 0.0040 chunk 7 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 488 GLN 7 549 ASN ** c 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 385 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.086925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.070095 restraints weight = 33781.293| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.83 r_work: 0.2891 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16144 Z= 0.100 Angle : 0.494 8.415 21934 Z= 0.254 Chirality : 0.040 0.145 2297 Planarity : 0.004 0.055 2875 Dihedral : 4.473 70.844 2110 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.52 % Allowed : 15.47 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.19), residues: 1854 helix: 1.29 (0.44), residues: 142 sheet: 0.22 (0.29), residues: 319 loop : -0.10 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG o 727 TYR 0.022 0.001 TYR 6 707 PHE 0.012 0.001 PHE 7 423 TRP 0.014 0.001 TRP A 341 HIS 0.003 0.001 HIS o 424 Details of bonding type rmsd covalent geometry : bond 0.00225 (16142) covalent geometry : angle 0.49342 (21930) SS BOND : bond 0.00249 ( 2) SS BOND : angle 1.01230 ( 4) hydrogen bonds : bond 0.02695 ( 266) hydrogen bonds : angle 5.12543 ( 591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.511 Fit side-chains REVERT: 6 241 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9109 (mm) REVERT: 6 643 LYS cc_start: 0.9386 (mtpp) cc_final: 0.9034 (mtpm) REVERT: 7 322 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: 7 510 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8762 (mttt) REVERT: 7 534 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: A 141 ASP cc_start: 0.7884 (p0) cc_final: 0.6805 (t0) REVERT: A 341 TRP cc_start: 0.8382 (m-90) cc_final: 0.7859 (m-90) REVERT: A 350 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: c 566 GLU cc_start: 0.8802 (pp20) cc_final: 0.8575 (pp20) REVERT: c 586 LEU cc_start: 0.8964 (mt) cc_final: 0.8667 (tp) REVERT: c 613 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6632 (t70) REVERT: o 325 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: o 437 MET cc_start: 0.9369 (pmm) cc_final: 0.9087 (pmm) REVERT: o 577 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: o 707 TYR cc_start: 0.7802 (t80) cc_final: 0.7430 (t80) REVERT: p 510 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8770 (mtmt) outliers start: 26 outliers final: 14 residues processed: 146 average time/residue: 0.6679 time to fit residues: 107.5557 Evaluate side-chains 136 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 241 ILE Chi-restraints excluded: chain 7 residue 322 GLN Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain 7 residue 510 LYS Chi-restraints excluded: chain 7 residue 534 GLU Chi-restraints excluded: chain 7 residue 549 ASN Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain c residue 432 SER Chi-restraints excluded: chain c residue 531 ASP Chi-restraints excluded: chain c residue 581 ILE Chi-restraints excluded: chain c residue 613 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 325 GLU Chi-restraints excluded: chain o residue 326 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 577 GLU Chi-restraints excluded: chain o residue 597 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 19 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 180 optimal weight: 0.0020 chunk 80 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 549 ASN ** c 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 589 GLN p 666 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.086613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.069744 restraints weight = 33608.326| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.82 r_work: 0.2891 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16144 Z= 0.127 Angle : 0.500 13.140 21934 Z= 0.254 Chirality : 0.040 0.331 2297 Planarity : 0.004 0.055 2875 Dihedral : 4.404 69.373 2110 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.52 % Allowed : 15.59 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.19), residues: 1854 helix: 1.25 (0.44), residues: 142 sheet: 0.23 (0.28), residues: 330 loop : -0.11 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG o 727 TYR 0.012 0.001 TYR A 265 PHE 0.012 0.001 PHE 7 423 TRP 0.017 0.001 TRP A 327 HIS 0.004 0.001 HIS 6 291 Details of bonding type rmsd covalent geometry : bond 0.00292 (16142) covalent geometry : angle 0.50033 (21930) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.98247 ( 4) hydrogen bonds : bond 0.02745 ( 266) hydrogen bonds : angle 5.09734 ( 591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.675 Fit side-chains REVERT: 6 241 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9111 (mm) REVERT: 6 643 LYS cc_start: 0.9386 (mtpp) cc_final: 0.9040 (mtpm) REVERT: 7 322 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8467 (pm20) REVERT: A 141 ASP cc_start: 0.7881 (p0) cc_final: 0.6814 (t0) REVERT: A 341 TRP cc_start: 0.8430 (m-90) cc_final: 0.7840 (m-90) REVERT: A 350 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: c 566 GLU cc_start: 0.8749 (pp20) cc_final: 0.8505 (pp20) REVERT: c 586 LEU cc_start: 0.8971 (mt) cc_final: 0.8670 (tp) REVERT: c 613 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6603 (t70) REVERT: o 325 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: o 437 MET cc_start: 0.9386 (pmm) cc_final: 0.9117 (pmm) REVERT: o 577 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: o 707 TYR cc_start: 0.7784 (t80) cc_final: 0.7420 (t80) REVERT: p 510 LYS cc_start: 0.9033 (mtmt) cc_final: 0.8792 (mtmt) outliers start: 26 outliers final: 14 residues processed: 138 average time/residue: 0.6967 time to fit residues: 105.8587 Evaluate side-chains 133 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 241 ILE Chi-restraints excluded: chain 7 residue 314 LEU Chi-restraints excluded: chain 7 residue 322 GLN Chi-restraints excluded: chain 7 residue 382 THR Chi-restraints excluded: chain 7 residue 549 ASN Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain c residue 432 SER Chi-restraints excluded: chain c residue 531 ASP Chi-restraints excluded: chain c residue 613 ASP Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 234 THR Chi-restraints excluded: chain o residue 236 LEU Chi-restraints excluded: chain o residue 325 GLU Chi-restraints excluded: chain o residue 326 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 577 GLU Chi-restraints excluded: chain o residue 597 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 192 optimal weight: 0.3980 chunk 31 optimal weight: 0.0870 chunk 137 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 693 ASN 7 549 ASN A 147 GLN ** c 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.070604 restraints weight = 33339.157| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.80 r_work: 0.2906 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16144 Z= 0.108 Angle : 0.493 12.298 21934 Z= 0.250 Chirality : 0.040 0.332 2297 Planarity : 0.004 0.055 2875 Dihedral : 4.298 66.972 2110 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.64 % Allowed : 15.77 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 1854 helix: 1.28 (0.44), residues: 142 sheet: 0.27 (0.29), residues: 319 loop : -0.08 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 6 727 TYR 0.024 0.001 TYR 6 707 PHE 0.011 0.001 PHE 7 423 TRP 0.021 0.001 TRP A 327 HIS 0.003 0.001 HIS 6 291 Details of bonding type rmsd covalent geometry : bond 0.00250 (16142) covalent geometry : angle 0.49301 (21930) SS BOND : bond 0.00227 ( 2) SS BOND : angle 0.90768 ( 4) hydrogen bonds : bond 0.02654 ( 266) hydrogen bonds : angle 4.99231 ( 591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4622.79 seconds wall clock time: 79 minutes 58.20 seconds (4798.20 seconds total)