Starting phenix.real_space_refine on Thu Jul 2 18:43:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sch_25035/07_2026/7sch_25035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sch_25035/07_2026/7sch_25035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sch_25035/07_2026/7sch_25035.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sch_25035/07_2026/7sch_25035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sch_25035/07_2026/7sch_25035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sch_25035/07_2026/7sch_25035.map" model { file = "/net/cci-nas-00/data/ceres_data/7sch_25035/07_2026/7sch_25035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sch_25035/07_2026/7sch_25035.cif" } resolution = 3.1 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= 0.002 sd= 0.035 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 47 5.16 5 C 6250 2.51 5 N 1645 2.21 5 O 1769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9711 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4913 Classifications: {'peptide': 603} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 574} Chain breaks: 3 Chain: "B" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4759 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 548} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.03, per 1000 atoms: 0.21 Number of scatterers: 9711 At special positions: 0 Unit cell: (102.672, 87.768, 112.608, 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 47 16.00 O 1769 8.00 N 1645 7.00 C 6250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 637 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 317.6 milliseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 39.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.689A pdb=" N LEU A 108 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 Processing helix chain 'A' and resid 173 through 180 removed outlier: 3.588A pdb=" N GLN A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.578A pdb=" N ALA A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.295A pdb=" N VAL A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.875A pdb=" N GLN A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.750A pdb=" N GLU A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.526A pdb=" N GLN A 376 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 397 through 416 Processing helix chain 'A' and resid 418 through 432 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.884A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 496 through 506 Processing helix chain 'A' and resid 545 through 551 removed outlier: 3.911A pdb=" N ARG A 549 " --> pdb=" O MET A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.607A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.647A pdb=" N TYR A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.668A pdb=" N LYS A 643 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.978A pdb=" N ARG A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.932A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 312' Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.714A pdb=" N ASP B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.616A pdb=" N ARG B 360 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.823A pdb=" N MET B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.529A pdb=" N SER B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 420 through 423 Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.749A pdb=" N GLU B 475 " --> pdb=" O ARG B 471 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.055A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.711A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 626 through 640 removed outlier: 3.513A pdb=" N ALA B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145 removed outlier: 5.898A pdb=" N VAL A 116 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR A 117 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE A 154 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE A 193 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS A 190 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA A 217 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 192 " --> pdb=" O ALA A 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 297 removed outlier: 8.240A pdb=" N VAL A 293 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 264 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU A 295 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE A 266 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR A 297 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY A 268 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N MET A 263 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 335 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 265 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A 332 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 358 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS A 334 " --> pdb=" O VAL A 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 540 removed outlier: 8.299A pdb=" N VAL A 537 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE A 513 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE A 539 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 515 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N PHE A 480 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ILE A 514 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA A 482 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU A 516 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 484 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 481 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 564 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 483 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 609 removed outlier: 3.587A pdb=" N ARG A 605 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 722 through 726 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.380A pdb=" N LEU B 212 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 283 removed outlier: 7.924A pdb=" N LEU B 281 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 254 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU B 283 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER B 256 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE B 253 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL B 319 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 255 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 509 through 513 removed outlier: 6.645A pdb=" N LEU B 485 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 512 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 487 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE B 456 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 535 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 461 " --> pdb=" O ILE B 537 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 570 through 574 removed outlier: 3.565A pdb=" N LYS B 579 " --> pdb=" O ASP B 574 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2883 1.34 - 1.46: 1881 1.46 - 1.58: 5134 1.58 - 1.70: 1 1.70 - 1.82: 73 Bond restraints: 9972 Sorted by residual: bond pdb=" N ASN B 430 " pdb=" CA ASN B 430 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.18e-02 7.18e+03 1.32e+01 bond pdb=" N PRO B 648 " pdb=" CA PRO B 648 " ideal model delta sigma weight residual 1.469 1.429 0.039 1.28e-02 6.10e+03 9.51e+00 bond pdb=" N SER B 425 " pdb=" CA SER B 425 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.27e-02 6.20e+03 7.74e+00 bond pdb=" N LYS B 645 " pdb=" CA LYS B 645 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.91e+00 bond pdb=" N ARG B 649 " pdb=" CA ARG B 649 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.70e+00 ... (remaining 9967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 13258 1.96 - 3.92: 241 3.92 - 5.87: 41 5.87 - 7.83: 5 7.83 - 9.79: 1 Bond angle restraints: 13546 Sorted by residual: angle pdb=" N LYS B 645 " pdb=" CA LYS B 645 " pdb=" C LYS B 645 " ideal model delta sigma weight residual 110.55 105.46 5.09 1.35e+00 5.49e-01 1.42e+01 angle pdb=" CA LYS B 645 " pdb=" C LYS B 645 " pdb=" O LYS B 645 " ideal model delta sigma weight residual 121.81 117.49 4.32 1.18e+00 7.18e-01 1.34e+01 angle pdb=" CA LYS B 645 " pdb=" C LYS B 645 " pdb=" N VAL B 646 " ideal model delta sigma weight residual 115.27 119.65 -4.38 1.30e+00 5.92e-01 1.14e+01 angle pdb=" C TRP B 429 " pdb=" N ASN B 430 " pdb=" CA ASN B 430 " ideal model delta sigma weight residual 122.73 117.40 5.33 1.61e+00 3.86e-01 1.10e+01 angle pdb=" N ASN B 430 " pdb=" CA ASN B 430 " pdb=" C ASN B 430 " ideal model delta sigma weight residual 112.72 116.33 -3.61 1.14e+00 7.69e-01 1.00e+01 ... (remaining 13541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5500 17.93 - 35.86: 379 35.86 - 53.78: 58 53.78 - 71.71: 8 71.71 - 89.64: 4 Dihedral angle restraints: 5949 sinusoidal: 2434 harmonic: 3515 Sorted by residual: dihedral pdb=" CB CYS B 85 " pdb=" SG CYS B 85 " pdb=" SG CYS B 90 " pdb=" CB CYS B 90 " ideal model delta sinusoidal sigma weight residual -86.00 -157.29 71.29 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 151 " pdb=" CB CYS B 151 " ideal model delta sinusoidal sigma weight residual -86.00 -19.43 -66.57 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 312 " pdb=" CB CYS A 312 " ideal model delta sinusoidal sigma weight residual 93.00 145.56 -52.56 1 1.00e+01 1.00e-02 3.76e+01 ... (remaining 5946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1205 0.055 - 0.110: 239 0.110 - 0.164: 29 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 1476 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU B 594 " pdb=" CB LEU B 594 " pdb=" CD1 LEU B 594 " pdb=" CD2 LEU B 594 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL B 646 " pdb=" CA VAL B 646 " pdb=" CG1 VAL B 646 " pdb=" CG2 VAL B 646 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 1473 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 643 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C VAL B 643 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL B 643 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE B 644 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 248 " -0.046 5.00e-02 4.00e+02 6.87e-02 7.54e+00 pdb=" N PRO B 249 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 249 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 249 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 559 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 560 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 560 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 560 " -0.025 5.00e-02 4.00e+02 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1264 2.75 - 3.29: 9392 3.29 - 3.83: 16123 3.83 - 4.36: 19715 4.36 - 4.90: 33561 Nonbonded interactions: 80055 Sorted by model distance: nonbonded pdb=" OG SER A 547 " pdb=" OD1 ASP A 647 " model vdw 2.218 3.040 nonbonded pdb=" ND2 ASN B 99 " pdb=" O LYS B 101 " model vdw 2.248 3.120 nonbonded pdb=" O TYR A 592 " pdb=" NZ LYS A 671 " model vdw 2.254 3.120 nonbonded pdb=" OG1 THR A 673 " pdb=" OD1 ASP A 725 " model vdw 2.257 3.040 nonbonded pdb=" OD2 ASP A 382 " pdb=" NH2 ARG A 384 " model vdw 2.271 3.120 ... (remaining 80050 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.070 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.020 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 : 0.003 0.088 9984 Z= 0.173 Angle : 0.622 9.790 13573 Z= 0.341 Chirality : 0.045 0.274 1476 Planarity : 0.004 0.069 1725 Dihedral : 11.950 89.640 3650 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.25), residues: 1174 helix: 0.94 (0.28), residues: 382 sheet: -0.48 (0.44), residues: 140 loop : -0.37 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 182 TYR 0.023 0.001 TYR B 582 PHE 0.011 0.001 PHE B 470 TRP 0.015 0.001 TRP B 429 HIS 0.005 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 ( 9972) covalent geometry : angle 0.62072 / 0.34 (13546) SS BOND : bond 0.00222 / 0.13 ( 9) SS BOND : angle 1.07130 / 0.67 ( 18) hydrogen bonds : bond 0.20190 / 13.59 ( 310) hydrogen bonds : angle 6.49744 / 4.47 ( 843) link_BETA1-4 : bond 0.00555 / 0.38 ( 2) link_BETA1-4 : angle 1.29318 / 0.85 ( 6) link_NAG-ASN : bond 0.00044 / 0.03 ( 1) link_NAG-ASN : angle 1.53575 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.7225 (mpp) cc_final: 0.6883 (mpp) REVERT: B 176 GLN cc_start: 0.6978 (tm-30) cc_final: 0.6539 (tm-30) REVERT: B 607 LEU cc_start: 0.7947 (mt) cc_final: 0.7684 (mt) outliers start: 2 outliers final: 2 residues processed: 318 average time/residue: 0.1122 time to fit residues: 48.3541 Evaluate side-chains 287 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 285 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 117 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 362 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS A 706 ASN B 415 ASN B 550 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118962 restraints weight = 13843.383| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.18 r_work: 0.3364 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9984 Z= 0.149 Angle : 0.590 10.635 13573 Z= 0.298 Chirality : 0.044 0.141 1476 Planarity : 0.004 0.041 1725 Dihedral : 4.548 48.217 1311 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.69 % Allowed : 8.74 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 1174 helix: 1.04 (0.27), residues: 382 sheet: -0.14 (0.43), residues: 148 loop : -0.42 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 383 TYR 0.015 0.001 TYR B 582 PHE 0.014 0.001 PHE A 598 TRP 0.013 0.001 TRP B 556 HIS 0.008 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9972) covalent geometry : angle 0.58784 / 0.30 (13546) SS BOND : bond 0.00405 / 0.28 ( 9) SS BOND : angle 0.97196 / 0.64 ( 18) hydrogen bonds : bond 0.04756 / 3.15 ( 310) hydrogen bonds : angle 5.18559 / 3.63 ( 843) link_BETA1-4 : bond 0.00508 / 0.36 ( 2) link_BETA1-4 : angle 1.50207 / 1.04 ( 6) link_NAG-ASN : bond 0.00309 / 0.21 ( 1) link_NAG-ASN : angle 1.72497 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 296 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8510 (t) cc_final: 0.8288 (p) REVERT: A 359 MET cc_start: 0.8241 (mpp) cc_final: 0.7770 (mpp) REVERT: A 605 ARG cc_start: 0.6742 (mtp-110) cc_final: 0.6505 (mtp-110) REVERT: A 609 THR cc_start: 0.8245 (m) cc_final: 0.7787 (p) REVERT: A 700 GLN cc_start: 0.7688 (mt0) cc_final: 0.7274 (mt0) REVERT: A 706 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7675 (m-40) REVERT: B 176 GLN cc_start: 0.7584 (tm-30) cc_final: 0.6970 (tm-30) REVERT: B 268 ASP cc_start: 0.7916 (t0) cc_final: 0.7683 (t0) REVERT: B 275 LYS cc_start: 0.8405 (tmtt) cc_final: 0.8131 (tmtt) REVERT: B 310 GLN cc_start: 0.7855 (mp10) cc_final: 0.7625 (mp10) REVERT: B 470 PHE cc_start: 0.7917 (m-80) cc_final: 0.7564 (m-80) REVERT: B 516 GLU cc_start: 0.7593 (mp0) cc_final: 0.7334 (mp0) REVERT: B 579 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7564 (mtmt) REVERT: B 607 LEU cc_start: 0.8457 (mt) cc_final: 0.8226 (mt) REVERT: B 612 MET cc_start: 0.7868 (tpp) cc_final: 0.7545 (tpp) outliers start: 18 outliers final: 9 residues processed: 302 average time/residue: 0.1078 time to fit residues: 44.1290 Evaluate side-chains 296 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 286 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 644 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.0010 chunk 100 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS A 706 ASN B 415 ASN B 550 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119686 restraints weight = 13755.601| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.18 r_work: 0.3377 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9984 Z= 0.114 Angle : 0.550 11.790 13573 Z= 0.278 Chirality : 0.043 0.140 1476 Planarity : 0.004 0.044 1725 Dihedral : 4.398 46.945 1311 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.79 % Allowed : 11.28 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1174 helix: 1.32 (0.28), residues: 376 sheet: -0.08 (0.43), residues: 150 loop : -0.37 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 182 TYR 0.016 0.001 TYR A 608 PHE 0.010 0.001 PHE A 598 TRP 0.021 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 9972) covalent geometry : angle 0.54857 / 0.28 (13546) SS BOND : bond 0.00245 / 0.17 ( 9) SS BOND : angle 0.87438 / 0.61 ( 18) hydrogen bonds : bond 0.03806 / 2.49 ( 310) hydrogen bonds : angle 4.88093 / 3.43 ( 843) link_BETA1-4 : bond 0.00383 / 0.27 ( 2) link_BETA1-4 : angle 1.44186 / 0.96 ( 6) link_NAG-ASN : bond 0.00183 / 0.12 ( 1) link_NAG-ASN : angle 1.49403 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 293 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8503 (t) cc_final: 0.8300 (p) REVERT: A 147 ASP cc_start: 0.8005 (t0) cc_final: 0.7571 (t0) REVERT: A 359 MET cc_start: 0.8282 (mpp) cc_final: 0.7735 (mpp) REVERT: A 605 ARG cc_start: 0.6657 (mtp-110) cc_final: 0.6374 (mtp-110) REVERT: A 609 THR cc_start: 0.8175 (m) cc_final: 0.7676 (p) REVERT: A 700 GLN cc_start: 0.7717 (mt0) cc_final: 0.7303 (mt0) REVERT: A 706 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7800 (m-40) REVERT: B 128 ARG cc_start: 0.7783 (ptt90) cc_final: 0.7580 (ptt90) REVERT: B 176 GLN cc_start: 0.7523 (tm-30) cc_final: 0.6880 (tm-30) REVERT: B 181 ASP cc_start: 0.7791 (t0) cc_final: 0.7510 (t0) REVERT: B 275 LYS cc_start: 0.8418 (tmtt) cc_final: 0.8128 (tmtt) REVERT: B 310 GLN cc_start: 0.7753 (mp10) cc_final: 0.7522 (mp10) REVERT: B 516 GLU cc_start: 0.7591 (mp0) cc_final: 0.7359 (mp0) REVERT: B 539 ASP cc_start: 0.7190 (p0) cc_final: 0.6951 (p0) REVERT: B 579 LYS cc_start: 0.7806 (mtmt) cc_final: 0.7555 (mtmt) REVERT: B 583 GLU cc_start: 0.7696 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 607 LEU cc_start: 0.8461 (mt) cc_final: 0.8225 (mt) REVERT: B 612 MET cc_start: 0.7855 (tpp) cc_final: 0.7521 (tpp) REVERT: B 627 GLU cc_start: 0.6939 (mp0) cc_final: 0.6452 (mp0) outliers start: 19 outliers final: 14 residues processed: 298 average time/residue: 0.0966 time to fit residues: 39.1333 Evaluate side-chains 303 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 288 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 644 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 388 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS A 706 ASN B 415 ASN B 550 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119477 restraints weight = 13801.870| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.18 r_work: 0.3364 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9984 Z= 0.129 Angle : 0.539 10.174 13573 Z= 0.272 Chirality : 0.043 0.141 1476 Planarity : 0.004 0.045 1725 Dihedral : 4.356 44.965 1311 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.97 % Allowed : 13.25 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.25), residues: 1174 helix: 1.35 (0.28), residues: 378 sheet: 0.04 (0.44), residues: 148 loop : -0.34 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.016 0.001 TYR A 608 PHE 0.010 0.001 PHE A 598 TRP 0.015 0.001 TRP A 599 HIS 0.007 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9972) covalent geometry : angle 0.53712 / 0.27 (13546) SS BOND : bond 0.00218 / 0.14 ( 9) SS BOND : angle 0.80139 / 0.55 ( 18) hydrogen bonds : bond 0.03671 / 2.40 ( 310) hydrogen bonds : angle 4.78736 / 3.38 ( 843) link_BETA1-4 : bond 0.00310 / 0.22 ( 2) link_BETA1-4 : angle 1.43509 / 0.96 ( 6) link_NAG-ASN : bond 0.00232 / 0.15 ( 1) link_NAG-ASN : angle 1.60531 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 295 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8532 (t) cc_final: 0.8312 (p) REVERT: A 147 ASP cc_start: 0.8022 (t0) cc_final: 0.7573 (t0) REVERT: A 359 MET cc_start: 0.8295 (mpp) cc_final: 0.7756 (mpp) REVERT: A 605 ARG cc_start: 0.6687 (mtp-110) cc_final: 0.6381 (mtp-110) REVERT: A 609 THR cc_start: 0.8161 (m) cc_final: 0.7636 (p) REVERT: A 644 ASN cc_start: 0.7848 (m-40) cc_final: 0.7588 (m-40) REVERT: A 700 GLN cc_start: 0.7710 (mt0) cc_final: 0.7285 (mt0) REVERT: A 706 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7647 (m-40) REVERT: B 128 ARG cc_start: 0.7771 (ptt90) cc_final: 0.7569 (ptt90) REVERT: B 176 GLN cc_start: 0.7527 (tm-30) cc_final: 0.6858 (tm-30) REVERT: B 181 ASP cc_start: 0.7796 (t0) cc_final: 0.7452 (t0) REVERT: B 275 LYS cc_start: 0.8417 (tmtt) cc_final: 0.8091 (tmtt) REVERT: B 310 GLN cc_start: 0.7806 (mp10) cc_final: 0.7471 (mp10) REVERT: B 516 GLU cc_start: 0.7624 (mp0) cc_final: 0.7375 (mp0) REVERT: B 528 GLU cc_start: 0.7041 (mp0) cc_final: 0.6800 (mp0) REVERT: B 539 ASP cc_start: 0.7197 (p0) cc_final: 0.6864 (p0) REVERT: B 583 GLU cc_start: 0.7735 (tm-30) cc_final: 0.6995 (tm-30) REVERT: B 607 LEU cc_start: 0.8471 (mt) cc_final: 0.8233 (mt) REVERT: B 612 MET cc_start: 0.7874 (tpp) cc_final: 0.7531 (tpp) REVERT: B 615 ASP cc_start: 0.7118 (m-30) cc_final: 0.6864 (t0) outliers start: 21 outliers final: 12 residues processed: 303 average time/residue: 0.1074 time to fit residues: 44.1977 Evaluate side-chains 303 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 290 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 644 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 113 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 60 optimal weight: 0.0020 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 388 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS A 706 ASN B 328 GLN B 415 ASN B 550 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.141007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119889 restraints weight = 13746.988| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.18 r_work: 0.3372 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9984 Z= 0.117 Angle : 0.524 9.357 13573 Z= 0.267 Chirality : 0.042 0.139 1476 Planarity : 0.004 0.044 1725 Dihedral : 4.279 41.993 1311 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.16 % Allowed : 14.85 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1174 helix: 1.42 (0.28), residues: 378 sheet: 0.16 (0.44), residues: 147 loop : -0.30 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.016 0.001 TYR A 608 PHE 0.009 0.001 PHE A 598 TRP 0.018 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9972) covalent geometry : angle 0.52247 / 0.27 (13546) SS BOND : bond 0.00192 / 0.13 ( 9) SS BOND : angle 0.78741 / 0.55 ( 18) hydrogen bonds : bond 0.03469 / 2.28 ( 310) hydrogen bonds : angle 4.75159 / 3.36 ( 843) link_BETA1-4 : bond 0.00389 / 0.28 ( 2) link_BETA1-4 : angle 1.41917 / 0.94 ( 6) link_NAG-ASN : bond 0.00161 / 0.11 ( 1) link_NAG-ASN : angle 1.56765 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8525 (t) cc_final: 0.8301 (p) REVERT: A 147 ASP cc_start: 0.8049 (t0) cc_final: 0.7597 (t0) REVERT: A 159 ASP cc_start: 0.8355 (t0) cc_final: 0.8098 (t70) REVERT: A 160 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8422 (m) REVERT: A 359 MET cc_start: 0.8305 (mpp) cc_final: 0.7780 (mpp) REVERT: A 605 ARG cc_start: 0.6700 (mtp-110) cc_final: 0.6365 (mtp-110) REVERT: A 609 THR cc_start: 0.8142 (m) cc_final: 0.7610 (p) REVERT: A 644 ASN cc_start: 0.7857 (m-40) cc_final: 0.7607 (m-40) REVERT: A 700 GLN cc_start: 0.7706 (mt0) cc_final: 0.7271 (mt0) REVERT: A 706 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.7665 (m-40) REVERT: B 128 ARG cc_start: 0.7790 (ptt90) cc_final: 0.7583 (ptt90) REVERT: B 176 GLN cc_start: 0.7508 (tm-30) cc_final: 0.6836 (tm-30) REVERT: B 181 ASP cc_start: 0.7804 (t0) cc_final: 0.7446 (t0) REVERT: B 275 LYS cc_start: 0.8408 (tmtt) cc_final: 0.8078 (tmtt) REVERT: B 310 GLN cc_start: 0.7773 (mp10) cc_final: 0.7408 (mp10) REVERT: B 516 GLU cc_start: 0.7617 (mp0) cc_final: 0.7381 (mp0) REVERT: B 528 GLU cc_start: 0.6977 (mp0) cc_final: 0.6763 (mp0) REVERT: B 539 ASP cc_start: 0.7150 (p0) cc_final: 0.6767 (p0) REVERT: B 607 LEU cc_start: 0.8467 (mt) cc_final: 0.8218 (mt) REVERT: B 612 MET cc_start: 0.7853 (tpp) cc_final: 0.7503 (tpp) REVERT: B 615 ASP cc_start: 0.7255 (m-30) cc_final: 0.6986 (t0) outliers start: 23 outliers final: 15 residues processed: 300 average time/residue: 0.1118 time to fit residues: 45.6540 Evaluate side-chains 309 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 292 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 644 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 19 optimal weight: 8.9990 chunk 115 optimal weight: 0.0270 chunk 8 optimal weight: 0.2980 chunk 117 optimal weight: 0.9980 chunk 39 optimal weight: 0.0470 chunk 82 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.0030 chunk 113 optimal weight: 0.8980 overall best weight: 0.2546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.120584 restraints weight = 13771.541| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.18 r_work: 0.3384 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9984 Z= 0.097 Angle : 0.519 8.987 13573 Z= 0.263 Chirality : 0.042 0.136 1476 Planarity : 0.004 0.047 1725 Dihedral : 4.134 40.307 1311 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.26 % Allowed : 14.85 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 1174 helix: 1.48 (0.28), residues: 380 sheet: 0.18 (0.44), residues: 149 loop : -0.29 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 182 TYR 0.019 0.001 TYR B 582 PHE 0.008 0.001 PHE A 598 TRP 0.018 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 9972) covalent geometry : angle 0.51724 / 0.26 (13546) SS BOND : bond 0.00187 / 0.12 ( 9) SS BOND : angle 0.73493 / 0.52 ( 18) hydrogen bonds : bond 0.03158 / 2.07 ( 310) hydrogen bonds : angle 4.65833 / 3.30 ( 843) link_BETA1-4 : bond 0.00360 / 0.26 ( 2) link_BETA1-4 : angle 1.34281 / 0.89 ( 6) link_NAG-ASN : bond 0.00043 / 0.03 ( 1) link_NAG-ASN : angle 1.40670 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 289 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8530 (t) cc_final: 0.8313 (p) REVERT: A 147 ASP cc_start: 0.8046 (t0) cc_final: 0.7602 (t0) REVERT: A 359 MET cc_start: 0.8334 (mpp) cc_final: 0.7818 (mpp) REVERT: A 605 ARG cc_start: 0.6704 (mtp-110) cc_final: 0.6365 (mtp-110) REVERT: A 609 THR cc_start: 0.8094 (m) cc_final: 0.7558 (p) REVERT: A 644 ASN cc_start: 0.7833 (m-40) cc_final: 0.7573 (m-40) REVERT: A 706 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7660 (m-40) REVERT: B 128 ARG cc_start: 0.7755 (ptt90) cc_final: 0.7540 (ptt90) REVERT: B 176 GLN cc_start: 0.7381 (tm-30) cc_final: 0.6730 (tm-30) REVERT: B 181 ASP cc_start: 0.7815 (t0) cc_final: 0.7445 (t0) REVERT: B 254 LEU cc_start: 0.8310 (tt) cc_final: 0.8104 (tp) REVERT: B 275 LYS cc_start: 0.8407 (tmtt) cc_final: 0.8088 (tmtt) REVERT: B 310 GLN cc_start: 0.7724 (mp10) cc_final: 0.7340 (mp10) REVERT: B 516 GLU cc_start: 0.7594 (mp0) cc_final: 0.7363 (mp0) REVERT: B 539 ASP cc_start: 0.7169 (p0) cc_final: 0.6772 (p0) REVERT: B 607 LEU cc_start: 0.8458 (mt) cc_final: 0.8225 (mt) REVERT: B 612 MET cc_start: 0.7827 (tpp) cc_final: 0.7483 (tpp) REVERT: B 615 ASP cc_start: 0.7243 (m-30) cc_final: 0.6964 (t0) REVERT: B 627 GLU cc_start: 0.7030 (mp0) cc_final: 0.6549 (mp0) outliers start: 24 outliers final: 15 residues processed: 296 average time/residue: 0.1088 time to fit residues: 43.9029 Evaluate side-chains 305 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 289 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 17 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.141160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120101 restraints weight = 13634.101| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.15 r_work: 0.3377 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9984 Z= 0.113 Angle : 0.529 8.464 13573 Z= 0.268 Chirality : 0.042 0.137 1476 Planarity : 0.004 0.059 1725 Dihedral : 4.139 38.846 1311 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.26 % Allowed : 15.51 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1174 helix: 1.46 (0.28), residues: 381 sheet: 0.21 (0.44), residues: 147 loop : -0.26 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 182 TYR 0.016 0.001 TYR A 608 PHE 0.009 0.001 PHE A 106 TRP 0.018 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 9972) covalent geometry : angle 0.52756 / 0.27 (13546) SS BOND : bond 0.00211 / 0.14 ( 9) SS BOND : angle 0.78674 / 0.53 ( 18) hydrogen bonds : bond 0.03253 / 2.14 ( 310) hydrogen bonds : angle 4.64264 / 3.29 ( 843) link_BETA1-4 : bond 0.00375 / 0.27 ( 2) link_BETA1-4 : angle 1.36338 / 0.90 ( 6) link_NAG-ASN : bond 0.00145 / 0.10 ( 1) link_NAG-ASN : angle 1.55514 / 0.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 288 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8008 (t0) cc_final: 0.7622 (t0) REVERT: A 159 ASP cc_start: 0.8270 (t0) cc_final: 0.8068 (t70) REVERT: A 174 LEU cc_start: 0.8255 (tp) cc_final: 0.8010 (tp) REVERT: A 299 LYS cc_start: 0.7521 (mttt) cc_final: 0.7180 (mmmt) REVERT: A 359 MET cc_start: 0.8335 (mpp) cc_final: 0.7854 (mpp) REVERT: A 605 ARG cc_start: 0.6772 (mtp-110) cc_final: 0.6455 (mtp-110) REVERT: A 644 ASN cc_start: 0.7821 (m-40) cc_final: 0.7574 (m-40) REVERT: A 706 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7661 (m-40) REVERT: B 128 ARG cc_start: 0.7765 (ptt90) cc_final: 0.7556 (ptt90) REVERT: B 176 GLN cc_start: 0.7393 (tm-30) cc_final: 0.6729 (tm-30) REVERT: B 181 ASP cc_start: 0.7827 (t0) cc_final: 0.7478 (t0) REVERT: B 254 LEU cc_start: 0.8289 (tt) cc_final: 0.8076 (tp) REVERT: B 275 LYS cc_start: 0.8421 (tmtt) cc_final: 0.8126 (tmtt) REVERT: B 310 GLN cc_start: 0.7765 (mp10) cc_final: 0.7446 (mp10) REVERT: B 516 GLU cc_start: 0.7565 (mp0) cc_final: 0.7347 (mp0) REVERT: B 539 ASP cc_start: 0.7107 (p0) cc_final: 0.6697 (p0) REVERT: B 583 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 607 LEU cc_start: 0.8461 (mt) cc_final: 0.8212 (mt) REVERT: B 612 MET cc_start: 0.7834 (tpp) cc_final: 0.7469 (tpp) REVERT: B 615 ASP cc_start: 0.7189 (m-30) cc_final: 0.6966 (t0) REVERT: B 627 GLU cc_start: 0.7089 (mp0) cc_final: 0.6634 (mp0) outliers start: 24 outliers final: 20 residues processed: 294 average time/residue: 0.1032 time to fit residues: 41.5389 Evaluate side-chains 311 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 290 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 693 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 0.1980 chunk 38 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 388 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN B 550 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120786 restraints weight = 13789.204| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.16 r_work: 0.3386 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9984 Z= 0.105 Angle : 0.533 8.246 13573 Z= 0.269 Chirality : 0.042 0.136 1476 Planarity : 0.004 0.070 1725 Dihedral : 4.123 37.905 1311 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.88 % Allowed : 16.35 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1174 helix: 1.54 (0.28), residues: 380 sheet: 0.17 (0.46), residues: 137 loop : -0.19 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 182 TYR 0.019 0.001 TYR B 582 PHE 0.007 0.001 PHE B 217 TRP 0.019 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 ( 9972) covalent geometry : angle 0.53139 / 0.27 (13546) SS BOND : bond 0.00254 / 0.17 ( 9) SS BOND : angle 0.67338 / 0.43 ( 18) hydrogen bonds : bond 0.03150 / 2.07 ( 310) hydrogen bonds : angle 4.60596 / 3.26 ( 843) link_BETA1-4 : bond 0.00368 / 0.26 ( 2) link_BETA1-4 : angle 1.33172 / 0.88 ( 6) link_NAG-ASN : bond 0.00073 / 0.05 ( 1) link_NAG-ASN : angle 1.49288 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 298 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.7782 (tp40) cc_final: 0.7436 (tp40) REVERT: A 147 ASP cc_start: 0.8027 (t0) cc_final: 0.7639 (t0) REVERT: A 299 LYS cc_start: 0.7523 (mttt) cc_final: 0.7183 (mmmt) REVERT: A 359 MET cc_start: 0.8330 (mpp) cc_final: 0.7838 (mpp) REVERT: A 605 ARG cc_start: 0.6779 (mtp-110) cc_final: 0.6441 (mtp-110) REVERT: A 609 THR cc_start: 0.8162 (m) cc_final: 0.7779 (p) REVERT: A 644 ASN cc_start: 0.7821 (m-40) cc_final: 0.7585 (m-40) REVERT: A 706 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.7706 (m-40) REVERT: B 176 GLN cc_start: 0.7359 (tm-30) cc_final: 0.6681 (tm-30) REVERT: B 181 ASP cc_start: 0.7839 (t0) cc_final: 0.7473 (t0) REVERT: B 254 LEU cc_start: 0.8242 (tt) cc_final: 0.8028 (tp) REVERT: B 275 LYS cc_start: 0.8436 (tmtt) cc_final: 0.8177 (tmtt) REVERT: B 310 GLN cc_start: 0.7790 (mp10) cc_final: 0.7379 (mp10) REVERT: B 370 MET cc_start: 0.8007 (mtm) cc_final: 0.7778 (mtp) REVERT: B 516 GLU cc_start: 0.7574 (mp0) cc_final: 0.7351 (mp0) REVERT: B 539 ASP cc_start: 0.7109 (p0) cc_final: 0.6695 (p0) REVERT: B 583 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7061 (tm-30) REVERT: B 607 LEU cc_start: 0.8459 (mt) cc_final: 0.8212 (mt) REVERT: B 612 MET cc_start: 0.7829 (tpp) cc_final: 0.7502 (tpp) REVERT: B 615 ASP cc_start: 0.7200 (m-30) cc_final: 0.6971 (t0) REVERT: B 627 GLU cc_start: 0.7034 (mp0) cc_final: 0.6603 (mp0) outliers start: 20 outliers final: 19 residues processed: 303 average time/residue: 0.1133 time to fit residues: 46.3382 Evaluate side-chains 319 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 299 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 693 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 113 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 194 ASN A 376 GLN A 388 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.140013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118616 restraints weight = 13672.100| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.18 r_work: 0.3358 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9984 Z= 0.152 Angle : 0.565 8.610 13573 Z= 0.285 Chirality : 0.043 0.140 1476 Planarity : 0.004 0.083 1725 Dihedral : 4.245 35.530 1311 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.16 % Allowed : 16.17 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1174 helix: 1.34 (0.28), residues: 387 sheet: 0.40 (0.49), residues: 123 loop : -0.24 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 182 TYR 0.025 0.001 TYR B 582 PHE 0.010 0.001 PHE A 659 TRP 0.019 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9972) covalent geometry : angle 0.56341 / 0.28 (13546) SS BOND : bond 0.00245 / 0.17 ( 9) SS BOND : angle 0.76715 / 0.48 ( 18) hydrogen bonds : bond 0.03488 / 2.31 ( 310) hydrogen bonds : angle 4.66867 / 3.31 ( 843) link_BETA1-4 : bond 0.00346 / 0.25 ( 2) link_BETA1-4 : angle 1.40381 / 0.93 ( 6) link_NAG-ASN : bond 0.00284 / 0.19 ( 1) link_NAG-ASN : angle 1.74601 / 0.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 301 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8049 (t0) cc_final: 0.7641 (t0) REVERT: A 359 MET cc_start: 0.8329 (mpp) cc_final: 0.7854 (mpp) REVERT: A 605 ARG cc_start: 0.6843 (mtp-110) cc_final: 0.6466 (mtp-110) REVERT: A 609 THR cc_start: 0.8193 (m) cc_final: 0.7816 (p) REVERT: A 644 ASN cc_start: 0.7874 (m-40) cc_final: 0.7631 (m-40) REVERT: A 700 GLN cc_start: 0.7733 (mt0) cc_final: 0.7312 (mt0) REVERT: A 706 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7702 (m-40) REVERT: B 176 GLN cc_start: 0.7413 (tm-30) cc_final: 0.6725 (tm-30) REVERT: B 181 ASP cc_start: 0.7876 (t0) cc_final: 0.7518 (t0) REVERT: B 254 LEU cc_start: 0.8284 (tt) cc_final: 0.8078 (tp) REVERT: B 275 LYS cc_start: 0.8421 (tmtt) cc_final: 0.8135 (tmtt) REVERT: B 310 GLN cc_start: 0.7861 (mp10) cc_final: 0.7446 (mp10) REVERT: B 370 MET cc_start: 0.8046 (mtm) cc_final: 0.7812 (mtp) REVERT: B 516 GLU cc_start: 0.7593 (mp0) cc_final: 0.7366 (mp0) REVERT: B 539 ASP cc_start: 0.7202 (p0) cc_final: 0.6789 (p0) REVERT: B 583 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7093 (tm-30) REVERT: B 607 LEU cc_start: 0.8467 (mt) cc_final: 0.8238 (mt) REVERT: B 612 MET cc_start: 0.7892 (tpp) cc_final: 0.7568 (tpp) REVERT: B 615 ASP cc_start: 0.7220 (m-30) cc_final: 0.6960 (t0) REVERT: B 627 GLU cc_start: 0.7110 (mp0) cc_final: 0.6763 (mp0) outliers start: 23 outliers final: 20 residues processed: 307 average time/residue: 0.1043 time to fit residues: 43.2216 Evaluate side-chains 317 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 296 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 693 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.0040 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 HIS ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN B 550 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.140474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119098 restraints weight = 13686.121| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.19 r_work: 0.3360 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9984 Z= 0.142 Angle : 0.574 7.822 13573 Z= 0.289 Chirality : 0.043 0.142 1476 Planarity : 0.004 0.083 1725 Dihedral : 4.245 33.070 1311 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.16 % Allowed : 16.73 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1174 helix: 1.26 (0.27), residues: 393 sheet: 0.33 (0.48), residues: 124 loop : -0.18 (0.26), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 128 TYR 0.025 0.001 TYR B 582 PHE 0.009 0.001 PHE B 445 TRP 0.020 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 9972) covalent geometry : angle 0.57301 / 0.29 (13546) SS BOND : bond 0.00226 / 0.16 ( 9) SS BOND : angle 0.77030 / 0.50 ( 18) hydrogen bonds : bond 0.03468 / 2.29 ( 310) hydrogen bonds : angle 4.66757 / 3.30 ( 843) link_BETA1-4 : bond 0.00276 / 0.20 ( 2) link_BETA1-4 : angle 1.37476 / 0.90 ( 6) link_NAG-ASN : bond 0.00252 / 0.17 ( 1) link_NAG-ASN : angle 1.70413 / 0.95 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 291 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.7820 (tp40) cc_final: 0.7457 (tp40) REVERT: A 147 ASP cc_start: 0.8081 (t0) cc_final: 0.7623 (t0) REVERT: A 359 MET cc_start: 0.8325 (mpp) cc_final: 0.7839 (mpp) REVERT: A 447 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8031 (mtmm) REVERT: A 605 ARG cc_start: 0.6834 (mtp-110) cc_final: 0.6443 (mtp-110) REVERT: A 609 THR cc_start: 0.8212 (m) cc_final: 0.7803 (p) REVERT: A 644 ASN cc_start: 0.7895 (m-40) cc_final: 0.7654 (m-40) REVERT: A 700 GLN cc_start: 0.7717 (mt0) cc_final: 0.7269 (mt0) REVERT: A 706 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7689 (m-40) REVERT: A 715 MET cc_start: 0.7442 (tpp) cc_final: 0.7190 (tpt) REVERT: B 176 GLN cc_start: 0.7386 (tm-30) cc_final: 0.6703 (tm-30) REVERT: B 181 ASP cc_start: 0.7861 (t0) cc_final: 0.7500 (t0) REVERT: B 227 ASP cc_start: 0.7712 (m-30) cc_final: 0.7467 (m-30) REVERT: B 254 LEU cc_start: 0.8265 (tt) cc_final: 0.8063 (tp) REVERT: B 275 LYS cc_start: 0.8394 (tmtt) cc_final: 0.8089 (tmtt) REVERT: B 310 GLN cc_start: 0.7844 (mp10) cc_final: 0.7415 (mp10) REVERT: B 370 MET cc_start: 0.8066 (mtm) cc_final: 0.7832 (mtp) REVERT: B 516 GLU cc_start: 0.7603 (mp0) cc_final: 0.7360 (mp0) REVERT: B 539 ASP cc_start: 0.7251 (p0) cc_final: 0.6840 (p0) REVERT: B 583 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7042 (tm-30) REVERT: B 607 LEU cc_start: 0.8462 (mt) cc_final: 0.8218 (mt) REVERT: B 612 MET cc_start: 0.7907 (tpp) cc_final: 0.7619 (tpp) REVERT: B 615 ASP cc_start: 0.7246 (m-30) cc_final: 0.6946 (t0) REVERT: B 627 GLU cc_start: 0.7130 (mp0) cc_final: 0.6785 (mp0) outliers start: 23 outliers final: 17 residues processed: 299 average time/residue: 0.1106 time to fit residues: 44.4847 Evaluate side-chains 308 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 289 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 693 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 376 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119224 restraints weight = 13581.122| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.16 r_work: 0.3355 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9984 Z= 0.150 Angle : 0.582 8.084 13573 Z= 0.293 Chirality : 0.044 0.144 1476 Planarity : 0.005 0.081 1725 Dihedral : 4.287 30.980 1311 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.88 % Allowed : 17.86 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1174 helix: 1.25 (0.27), residues: 393 sheet: 0.34 (0.49), residues: 124 loop : -0.21 (0.26), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.025 0.001 TYR B 582 PHE 0.010 0.001 PHE B 217 TRP 0.020 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 9972) covalent geometry : angle 0.57982 / 0.29 (13546) SS BOND : bond 0.00186 / 0.13 ( 9) SS BOND : angle 1.05995 / 0.71 ( 18) hydrogen bonds : bond 0.03535 / 2.33 ( 310) hydrogen bonds : angle 4.69016 / 3.31 ( 843) link_BETA1-4 : bond 0.00331 / 0.24 ( 2) link_BETA1-4 : angle 1.39309 / 0.91 ( 6) link_NAG-ASN : bond 0.00216 / 0.14 ( 1) link_NAG-ASN : angle 1.76860 / 0.99 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2648.96 seconds wall clock time: 46 minutes 4.11 seconds (2764.11 seconds total)