Starting phenix.real_space_refine on Sun Jul 27 21:46:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sch_25035/07_2025/7sch_25035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sch_25035/07_2025/7sch_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sch_25035/07_2025/7sch_25035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sch_25035/07_2025/7sch_25035.map" model { file = "/net/cci-nas-00/data/ceres_data/7sch_25035/07_2025/7sch_25035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sch_25035/07_2025/7sch_25035.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.95, per 1000 atoms: 0.61 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.07 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: 2.73 Time building geometry restraints manager: 3.07 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 - 21.80: 5665 21.80 - 43.60: 306 43.60 - 65.40: 22 65.40 - 87.20: 12 87.20 - 109.00: 5 Dihedral angle restraints: 6010 sinusoidal: 2495 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 6007 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: 0.790 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.000 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 : 12.800 108.998 3711 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (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 TRP 0.015 0.001 TRP B 429 HIS 0.005 0.001 HIS B 88 PHE 0.011 0.001 PHE B 470 TYR 0.023 0.001 TYR B 582 ARG 0.006 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00044 ( 1) link_NAG-ASN : angle 1.53575 ( 3) link_BETA1-4 : bond 0.00555 ( 2) link_BETA1-4 : angle 1.29318 ( 6) hydrogen bonds : bond 0.20190 ( 310) hydrogen bonds : angle 6.49744 ( 843) SS BOND : bond 0.00222 ( 9) SS BOND : angle 1.07130 ( 18) covalent geometry : bond 0.00323 ( 9972) covalent geometry : angle 0.62072 (13546) *********************** 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 : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.7225 (mpp) cc_final: 0.6882 (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: 0.2507 time to fit residues: 106.9797 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 : 1.302 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.0470 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.0020 chunk 60 optimal weight: 0.0170 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 362 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.142278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121434 restraints weight = 13704.760| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.17 r_work: 0.3401 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9984 Z= 0.112 Angle : 0.580 11.224 13573 Z= 0.290 Chirality : 0.043 0.136 1476 Planarity : 0.004 0.037 1725 Dihedral : 6.632 67.753 1372 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.60 % Allowed : 8.65 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1174 helix: 1.03 (0.27), residues: 388 sheet: -0.07 (0.44), residues: 148 loop : -0.40 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 556 HIS 0.007 0.001 HIS A 285 PHE 0.012 0.001 PHE A 598 TYR 0.013 0.001 TYR B 582 ARG 0.005 0.000 ARG B 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 1) link_NAG-ASN : angle 1.34666 ( 3) link_BETA1-4 : bond 0.00412 ( 2) link_BETA1-4 : angle 2.15408 ( 6) hydrogen bonds : bond 0.04105 ( 310) hydrogen bonds : angle 5.15183 ( 843) SS BOND : bond 0.00272 ( 9) SS BOND : angle 0.88995 ( 18) covalent geometry : bond 0.00249 ( 9972) covalent geometry : angle 0.57794 (13546) *********************** 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 311 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 294 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.7754 (tp40) cc_final: 0.7505 (tp40) REVERT: A 147 ASP cc_start: 0.7904 (t0) cc_final: 0.7508 (t0) REVERT: A 359 MET cc_start: 0.8211 (mpp) cc_final: 0.7722 (mpp) REVERT: A 453 PHE cc_start: 0.8164 (m-80) cc_final: 0.7941 (m-80) REVERT: A 599 TRP cc_start: 0.7719 (t-100) cc_final: 0.7490 (t-100) REVERT: A 605 ARG cc_start: 0.6701 (mtp-110) cc_final: 0.6473 (mtp-110) REVERT: A 700 GLN cc_start: 0.7668 (mt0) cc_final: 0.7302 (mt0) REVERT: A 706 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7601 (m-40) REVERT: B 176 GLN cc_start: 0.7440 (tm-30) cc_final: 0.6850 (tm-30) REVERT: B 182 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7790 (ttp-110) REVERT: B 268 ASP cc_start: 0.7911 (t0) cc_final: 0.7673 (t0) REVERT: B 275 LYS cc_start: 0.8408 (tmtt) cc_final: 0.8165 (tmtt) REVERT: B 426 TYR cc_start: 0.4778 (OUTLIER) cc_final: 0.4083 (p90) REVERT: B 470 PHE cc_start: 0.7826 (m-80) cc_final: 0.7494 (m-80) REVERT: B 516 GLU cc_start: 0.7573 (mp0) cc_final: 0.7341 (mp0) REVERT: B 523 PHE cc_start: 0.7867 (m-80) cc_final: 0.7583 (m-80) REVERT: B 579 LYS cc_start: 0.7826 (mtmt) cc_final: 0.7592 (mtmt) REVERT: B 607 LEU cc_start: 0.8436 (mt) cc_final: 0.8225 (mt) REVERT: B 612 MET cc_start: 0.7819 (tpp) cc_final: 0.7411 (tpp) REVERT: B 615 ASP cc_start: 0.7041 (m-30) cc_final: 0.6612 (m-30) outliers start: 17 outliers final: 7 residues processed: 300 average time/residue: 0.2488 time to fit residues: 99.9987 Evaluate side-chains 296 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 287 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 57 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.140244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118991 restraints weight = 13845.061| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.19 r_work: 0.3361 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9984 Z= 0.158 Angle : 0.573 11.871 13573 Z= 0.288 Chirality : 0.044 0.141 1476 Planarity : 0.004 0.042 1725 Dihedral : 5.840 52.186 1372 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.32 % Allowed : 11.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1174 helix: 1.31 (0.28), residues: 376 sheet: -0.03 (0.43), residues: 146 loop : -0.37 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 200 HIS 0.007 0.001 HIS A 285 PHE 0.011 0.001 PHE B 217 TYR 0.016 0.001 TYR A 608 ARG 0.005 0.000 ARG A 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 1) link_NAG-ASN : angle 1.62155 ( 3) link_BETA1-4 : bond 0.00396 ( 2) link_BETA1-4 : angle 2.18450 ( 6) hydrogen bonds : bond 0.04155 ( 310) hydrogen bonds : angle 4.90767 ( 843) SS BOND : bond 0.00277 ( 9) SS BOND : angle 0.91788 ( 18) covalent geometry : bond 0.00371 ( 9972) covalent geometry : angle 0.57059 (13546) *********************** 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 299 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 285 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7936 (t0) cc_final: 0.7515 (t0) REVERT: A 359 MET cc_start: 0.8283 (mpp) cc_final: 0.7812 (mpp) REVERT: A 599 TRP cc_start: 0.7719 (t-100) cc_final: 0.7373 (t-100) REVERT: A 605 ARG cc_start: 0.6731 (mtp-110) cc_final: 0.6389 (mtp-110) REVERT: A 609 THR cc_start: 0.8205 (m) cc_final: 0.7713 (p) REVERT: A 700 GLN cc_start: 0.7720 (mt0) cc_final: 0.7304 (mt0) REVERT: A 706 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7821 (m-40) REVERT: B 176 GLN cc_start: 0.7581 (tm-30) cc_final: 0.6944 (tm-30) REVERT: B 181 ASP cc_start: 0.7795 (t0) cc_final: 0.7494 (t0) REVERT: B 275 LYS cc_start: 0.8412 (tmtt) cc_final: 0.8080 (tmtt) REVERT: B 516 GLU cc_start: 0.7591 (mp0) cc_final: 0.7343 (mp0) REVERT: B 583 GLU cc_start: 0.7723 (tm-30) cc_final: 0.6993 (tm-30) REVERT: B 607 LEU cc_start: 0.8470 (mt) cc_final: 0.8223 (mt) REVERT: B 612 MET cc_start: 0.7865 (tpp) cc_final: 0.7533 (tpp) REVERT: B 620 VAL cc_start: 0.7734 (p) cc_final: 0.7518 (t) REVERT: B 627 GLU cc_start: 0.6998 (mp0) cc_final: 0.6346 (mp0) outliers start: 14 outliers final: 11 residues processed: 289 average time/residue: 0.2610 time to fit residues: 100.7531 Evaluate side-chains 291 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 279 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 706 ASN 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 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 60 optimal weight: 0.0170 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120425 restraints weight = 13631.462| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.16 r_work: 0.3380 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1576 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= 0.108 Angle : 0.547 10.417 13573 Z= 0.272 Chirality : 0.043 0.139 1476 Planarity : 0.004 0.044 1725 Dihedral : 5.206 46.108 1372 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.07 % Allowed : 12.88 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1174 helix: 1.39 (0.28), residues: 378 sheet: 0.07 (0.44), residues: 147 loop : -0.34 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 396 HIS 0.006 0.001 HIS A 285 PHE 0.016 0.001 PHE B 91 TYR 0.015 0.001 TYR A 608 ARG 0.005 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 1) link_NAG-ASN : angle 1.40283 ( 3) link_BETA1-4 : bond 0.00345 ( 2) link_BETA1-4 : angle 2.17246 ( 6) hydrogen bonds : bond 0.03505 ( 310) hydrogen bonds : angle 4.74442 ( 843) SS BOND : bond 0.00290 ( 9) SS BOND : angle 0.85641 ( 18) covalent geometry : bond 0.00249 ( 9972) covalent geometry : angle 0.54459 (13546) *********************** 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 314 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 292 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7944 (t0) cc_final: 0.7513 (t0) REVERT: A 359 MET cc_start: 0.8290 (mpp) cc_final: 0.7808 (mpp) REVERT: A 599 TRP cc_start: 0.7697 (t-100) cc_final: 0.7314 (t-100) REVERT: A 605 ARG cc_start: 0.6714 (mtp-110) cc_final: 0.6334 (mtp-110) REVERT: A 609 THR cc_start: 0.8149 (m) cc_final: 0.7629 (p) REVERT: A 644 ASN cc_start: 0.7886 (m-40) cc_final: 0.7640 (m-40) REVERT: A 700 GLN cc_start: 0.7682 (mt0) cc_final: 0.7247 (mt0) REVERT: A 706 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7739 (m-40) REVERT: B 176 GLN cc_start: 0.7506 (tm-30) cc_final: 0.6839 (tm-30) REVERT: B 181 ASP cc_start: 0.7818 (t0) cc_final: 0.7487 (t0) REVERT: B 254 LEU cc_start: 0.8367 (tt) cc_final: 0.8162 (tp) REVERT: B 275 LYS cc_start: 0.8400 (tmtt) cc_final: 0.8085 (tmtt) REVERT: B 516 GLU cc_start: 0.7605 (mp0) cc_final: 0.7370 (mp0) REVERT: B 583 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7004 (tm-30) REVERT: B 607 LEU cc_start: 0.8453 (mt) cc_final: 0.8225 (mt) REVERT: B 612 MET cc_start: 0.7855 (tpp) cc_final: 0.7497 (tpp) REVERT: B 615 ASP cc_start: 0.7284 (m-30) cc_final: 0.7012 (t0) REVERT: B 627 GLU cc_start: 0.6970 (mp0) cc_final: 0.6639 (mp0) outliers start: 22 outliers final: 11 residues processed: 298 average time/residue: 0.2550 time to fit residues: 102.2419 Evaluate side-chains 296 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU 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 706 ASN 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 644 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.139855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118790 restraints weight = 13574.658| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.16 r_work: 0.3351 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9984 Z= 0.164 Angle : 0.563 9.673 13573 Z= 0.284 Chirality : 0.044 0.143 1476 Planarity : 0.004 0.045 1725 Dihedral : 5.162 43.420 1372 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.16 % Allowed : 14.47 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1174 helix: 1.33 (0.28), residues: 378 sheet: 0.07 (0.45), residues: 135 loop : -0.23 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 374 HIS 0.007 0.001 HIS A 285 PHE 0.010 0.001 PHE B 217 TYR 0.017 0.001 TYR B 582 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 1) link_NAG-ASN : angle 1.58503 ( 3) link_BETA1-4 : bond 0.00393 ( 2) link_BETA1-4 : angle 2.26169 ( 6) hydrogen bonds : bond 0.03841 ( 310) hydrogen bonds : angle 4.76474 ( 843) SS BOND : bond 0.00217 ( 9) SS BOND : angle 0.77426 ( 18) covalent geometry : bond 0.00386 ( 9972) covalent geometry : angle 0.56042 (13546) *********************** 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 315 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 292 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7974 (t0) cc_final: 0.7516 (t0) REVERT: A 159 ASP cc_start: 0.8342 (t0) cc_final: 0.8096 (t70) REVERT: A 160 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8445 (m) REVERT: A 359 MET cc_start: 0.8323 (mpp) cc_final: 0.7841 (mpp) REVERT: A 383 GLU cc_start: 0.6858 (pt0) cc_final: 0.6644 (pt0) REVERT: A 599 TRP cc_start: 0.7725 (t-100) cc_final: 0.7348 (t-100) REVERT: A 605 ARG cc_start: 0.6767 (mtp-110) cc_final: 0.6353 (mtp-110) REVERT: A 609 THR cc_start: 0.8168 (m) cc_final: 0.7648 (p) REVERT: A 644 ASN cc_start: 0.7887 (m-40) cc_final: 0.7616 (m-40) REVERT: A 700 GLN cc_start: 0.7713 (mt0) cc_final: 0.7263 (mt0) REVERT: A 706 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: B 176 GLN cc_start: 0.7549 (tm-30) cc_final: 0.6849 (tm-30) REVERT: B 181 ASP cc_start: 0.7824 (t0) cc_final: 0.7450 (t0) REVERT: B 254 LEU cc_start: 0.8365 (tt) cc_final: 0.8164 (tp) REVERT: B 275 LYS cc_start: 0.8395 (tmtt) cc_final: 0.8053 (tmtt) REVERT: B 425 SER cc_start: 0.7987 (p) cc_final: 0.7787 (t) REVERT: B 516 GLU cc_start: 0.7608 (mp0) cc_final: 0.7359 (mp0) REVERT: B 548 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7007 (tm-30) REVERT: B 583 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 607 LEU cc_start: 0.8465 (mt) cc_final: 0.8215 (mt) REVERT: B 612 MET cc_start: 0.7926 (tpp) cc_final: 0.7591 (tpp) REVERT: B 615 ASP cc_start: 0.7248 (m-30) cc_final: 0.7022 (t0) outliers start: 23 outliers final: 17 residues processed: 301 average time/residue: 0.2519 time to fit residues: 101.4749 Evaluate side-chains 305 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 286 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 141 SER 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 621 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 594 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 36 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 69 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119736 restraints weight = 13778.813| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.17 r_work: 0.3371 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9984 Z= 0.114 Angle : 0.544 9.271 13573 Z= 0.273 Chirality : 0.043 0.140 1476 Planarity : 0.004 0.045 1725 Dihedral : 4.837 41.556 1372 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.26 % Allowed : 15.23 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1174 helix: 1.44 (0.28), residues: 378 sheet: 0.14 (0.46), residues: 135 loop : -0.20 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 396 HIS 0.006 0.001 HIS A 285 PHE 0.008 0.001 PHE A 598 TYR 0.019 0.001 TYR B 582 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 1) link_NAG-ASN : angle 1.40504 ( 3) link_BETA1-4 : bond 0.00457 ( 2) link_BETA1-4 : angle 2.19843 ( 6) hydrogen bonds : bond 0.03412 ( 310) hydrogen bonds : angle 4.70059 ( 843) SS BOND : bond 0.00233 ( 9) SS BOND : angle 0.80344 ( 18) covalent geometry : bond 0.00265 ( 9972) covalent geometry : angle 0.54187 (13546) *********************** 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 310 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 286 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7869 (t0) cc_final: 0.7476 (t0) REVERT: A 159 ASP cc_start: 0.8321 (t0) cc_final: 0.8081 (t70) REVERT: A 160 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8452 (m) REVERT: A 359 MET cc_start: 0.8340 (mpp) cc_final: 0.7872 (mpp) REVERT: A 383 GLU cc_start: 0.6830 (pt0) cc_final: 0.6563 (pt0) REVERT: A 599 TRP cc_start: 0.7703 (t-100) cc_final: 0.7319 (t-100) REVERT: A 609 THR cc_start: 0.8112 (m) cc_final: 0.7596 (p) REVERT: A 644 ASN cc_start: 0.7843 (m-40) cc_final: 0.7594 (m-40) REVERT: B 176 GLN cc_start: 0.7456 (tm-30) cc_final: 0.6754 (tm-30) REVERT: B 181 ASP cc_start: 0.7765 (t0) cc_final: 0.7408 (t0) REVERT: B 275 LYS cc_start: 0.8422 (tmtt) cc_final: 0.8121 (tmtt) REVERT: B 516 GLU cc_start: 0.7604 (mp0) cc_final: 0.7382 (mp0) REVERT: B 548 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7002 (tm-30) REVERT: B 583 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7054 (tm-30) REVERT: B 607 LEU cc_start: 0.8459 (mt) cc_final: 0.8211 (mt) REVERT: B 612 MET cc_start: 0.7830 (tpp) cc_final: 0.7491 (tpp) REVERT: B 615 ASP cc_start: 0.7207 (m-30) cc_final: 0.6986 (t0) REVERT: B 627 GLU cc_start: 0.7064 (mp0) cc_final: 0.6452 (mp0) outliers start: 24 outliers final: 15 residues processed: 296 average time/residue: 0.2944 time to fit residues: 117.6895 Evaluate side-chains 298 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 282 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 141 SER 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 424 LEU Chi-restraints excluded: chain A residue 621 THR 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 570 LEU Chi-restraints excluded: chain B residue 594 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 108 optimal weight: 0.5980 chunk 115 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3800 r_free = 0.3800 target = 0.141235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120104 restraints weight = 13796.481| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.16 r_work: 0.3373 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1874 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= 0.116 Angle : 0.540 8.657 13573 Z= 0.272 Chirality : 0.043 0.141 1476 Planarity : 0.004 0.044 1725 Dihedral : 4.615 38.223 1372 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.35 % Allowed : 16.26 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1174 helix: 1.45 (0.28), residues: 381 sheet: 0.14 (0.46), residues: 136 loop : -0.20 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 396 HIS 0.006 0.001 HIS A 285 PHE 0.008 0.001 PHE A 598 TYR 0.028 0.001 TYR A 319 ARG 0.005 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 1) link_NAG-ASN : angle 1.36176 ( 3) link_BETA1-4 : bond 0.00490 ( 2) link_BETA1-4 : angle 2.21762 ( 6) hydrogen bonds : bond 0.03346 ( 310) hydrogen bonds : angle 4.63400 ( 843) SS BOND : bond 0.00225 ( 9) SS BOND : angle 0.76310 ( 18) covalent geometry : bond 0.00272 ( 9972) covalent geometry : angle 0.53783 (13546) *********************** 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 309 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 284 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7874 (t0) cc_final: 0.7486 (t0) REVERT: A 159 ASP cc_start: 0.8347 (t0) cc_final: 0.8107 (t70) REVERT: A 160 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8473 (m) REVERT: A 227 ARG cc_start: 0.8282 (mpp80) cc_final: 0.8018 (mtt90) REVERT: A 299 LYS cc_start: 0.7527 (mttt) cc_final: 0.7209 (mmmt) REVERT: A 359 MET cc_start: 0.8343 (mpp) cc_final: 0.7889 (mpp) REVERT: A 432 ASP cc_start: 0.7537 (m-30) cc_final: 0.7294 (t0) REVERT: A 599 TRP cc_start: 0.7697 (t-100) cc_final: 0.7294 (t-100) REVERT: A 609 THR cc_start: 0.8102 (m) cc_final: 0.7592 (p) REVERT: A 644 ASN cc_start: 0.7849 (m-40) cc_final: 0.7614 (m-40) REVERT: B 176 GLN cc_start: 0.7384 (tm-30) cc_final: 0.6726 (tm-30) REVERT: B 181 ASP cc_start: 0.7792 (t0) cc_final: 0.7420 (t0) REVERT: B 275 LYS cc_start: 0.8418 (tmtt) cc_final: 0.8146 (tmtt) REVERT: B 516 GLU cc_start: 0.7613 (mp0) cc_final: 0.7394 (mp0) REVERT: B 607 LEU cc_start: 0.8452 (mt) cc_final: 0.8196 (mt) REVERT: B 612 MET cc_start: 0.7877 (tpp) cc_final: 0.7564 (tpp) REVERT: B 615 ASP cc_start: 0.7247 (m-30) cc_final: 0.6988 (t0) REVERT: B 627 GLU cc_start: 0.7132 (mp0) cc_final: 0.6615 (mp0) outliers start: 25 outliers final: 17 residues processed: 290 average time/residue: 0.2622 time to fit residues: 101.8225 Evaluate side-chains 298 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 280 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 141 SER 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 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 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 570 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 285 HIS ** 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 415 ASN B 430 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 = 0.140155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118692 restraints weight = 13817.539| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.19 r_work: 0.3355 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9984 Z= 0.150 Angle : 0.567 8.323 13573 Z= 0.285 Chirality : 0.044 0.145 1476 Planarity : 0.004 0.045 1725 Dihedral : 4.636 33.724 1372 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.26 % Allowed : 16.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1174 helix: 1.26 (0.28), residues: 387 sheet: 0.17 (0.46), residues: 134 loop : -0.26 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 374 HIS 0.006 0.001 HIS A 285 PHE 0.009 0.001 PHE B 217 TYR 0.024 0.001 TYR A 319 ARG 0.008 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 1) link_NAG-ASN : angle 1.53256 ( 3) link_BETA1-4 : bond 0.00485 ( 2) link_BETA1-4 : angle 2.24119 ( 6) hydrogen bonds : bond 0.03620 ( 310) hydrogen bonds : angle 4.67674 ( 843) SS BOND : bond 0.00253 ( 9) SS BOND : angle 0.80094 ( 18) covalent geometry : bond 0.00353 ( 9972) covalent geometry : angle 0.56420 (13546) *********************** 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 310 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 286 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7919 (t0) cc_final: 0.7555 (t0) REVERT: A 159 ASP cc_start: 0.8409 (t0) cc_final: 0.8172 (t70) REVERT: A 359 MET cc_start: 0.8355 (mpp) cc_final: 0.7879 (mpp) REVERT: A 384 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7491 (mtm-85) REVERT: A 432 ASP cc_start: 0.7572 (m-30) cc_final: 0.7322 (t0) REVERT: A 443 LEU cc_start: 0.8487 (tt) cc_final: 0.8264 (tp) REVERT: A 599 TRP cc_start: 0.7721 (t-100) cc_final: 0.7317 (t-100) REVERT: A 605 ARG cc_start: 0.6873 (mtp-110) cc_final: 0.6383 (mtp-110) REVERT: A 609 THR cc_start: 0.8148 (m) cc_final: 0.7632 (p) REVERT: A 644 ASN cc_start: 0.7893 (m-40) cc_final: 0.7650 (m-40) REVERT: A 706 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7660 (m-40) REVERT: A 715 MET cc_start: 0.7324 (tpp) cc_final: 0.7054 (tpp) REVERT: B 176 GLN cc_start: 0.7451 (tm-30) cc_final: 0.6758 (tm-30) REVERT: B 181 ASP cc_start: 0.7802 (t0) cc_final: 0.7437 (t0) REVERT: B 275 LYS cc_start: 0.8419 (tmtt) cc_final: 0.8125 (tmtt) REVERT: B 516 GLU cc_start: 0.7604 (mp0) cc_final: 0.7374 (mp0) REVERT: B 539 ASP cc_start: 0.7375 (p0) cc_final: 0.7148 (p0) REVERT: B 548 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6926 (tm-30) REVERT: B 583 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7047 (tm-30) REVERT: B 607 LEU cc_start: 0.8460 (mt) cc_final: 0.8222 (mt) REVERT: B 612 MET cc_start: 0.7896 (tpp) cc_final: 0.7591 (tpp) REVERT: B 615 ASP cc_start: 0.7268 (m-30) cc_final: 0.7015 (t0) REVERT: B 627 GLU cc_start: 0.7154 (mp0) cc_final: 0.6723 (mp0) outliers start: 24 outliers final: 19 residues processed: 294 average time/residue: 0.2365 time to fit residues: 93.5555 Evaluate side-chains 306 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 286 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 221 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 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 460 VAL 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 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 39 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 70 optimal weight: 0.0270 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 285 HIS ** 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 415 ASN B 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120262 restraints weight = 13718.938| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.15 r_work: 0.3374 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9984 Z= 0.112 Angle : 0.552 8.447 13573 Z= 0.278 Chirality : 0.043 0.142 1476 Planarity : 0.004 0.052 1725 Dihedral : 4.439 32.123 1372 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.79 % Allowed : 16.92 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1174 helix: 1.39 (0.28), residues: 381 sheet: 0.35 (0.49), residues: 122 loop : -0.23 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 396 HIS 0.006 0.001 HIS A 285 PHE 0.008 0.001 PHE A 345 TYR 0.024 0.001 TYR A 319 ARG 0.006 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 1.41336 ( 3) link_BETA1-4 : bond 0.00400 ( 2) link_BETA1-4 : angle 2.11228 ( 6) hydrogen bonds : bond 0.03236 ( 310) hydrogen bonds : angle 4.60759 ( 843) SS BOND : bond 0.00214 ( 9) SS BOND : angle 0.70838 ( 18) covalent geometry : bond 0.00264 ( 9972) covalent geometry : angle 0.55001 (13546) *********************** 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 302 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 283 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7902 (t0) cc_final: 0.7556 (t0) REVERT: A 359 MET cc_start: 0.8385 (mpp) cc_final: 0.7914 (mpp) REVERT: A 384 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7433 (mtm-85) REVERT: A 432 ASP cc_start: 0.7560 (m-30) cc_final: 0.7309 (t0) REVERT: A 605 ARG cc_start: 0.6872 (mtp-110) cc_final: 0.6549 (mtp-110) REVERT: A 609 THR cc_start: 0.8088 (m) cc_final: 0.7574 (p) REVERT: A 644 ASN cc_start: 0.7878 (m-40) cc_final: 0.7634 (m-40) REVERT: A 706 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7688 (m-40) REVERT: B 176 GLN cc_start: 0.7344 (tm-30) cc_final: 0.6667 (tm-30) REVERT: B 181 ASP cc_start: 0.7837 (t0) cc_final: 0.7475 (t0) REVERT: B 275 LYS cc_start: 0.8423 (tmtt) cc_final: 0.8131 (tmtt) REVERT: B 370 MET cc_start: 0.8024 (mtm) cc_final: 0.7801 (mtp) REVERT: B 516 GLU cc_start: 0.7583 (mp0) cc_final: 0.7361 (mp0) REVERT: B 539 ASP cc_start: 0.7320 (p0) cc_final: 0.7106 (p0) REVERT: B 583 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7034 (tm-30) REVERT: B 607 LEU cc_start: 0.8457 (mt) cc_final: 0.8209 (mt) REVERT: B 612 MET cc_start: 0.7873 (tpp) cc_final: 0.7534 (tpp) REVERT: B 615 ASP cc_start: 0.7246 (m-30) cc_final: 0.6991 (t0) REVERT: B 624 MET cc_start: 0.8097 (mmp) cc_final: 0.7796 (mmp) REVERT: B 627 GLU cc_start: 0.7118 (mp0) cc_final: 0.6687 (mp0) outliers start: 19 outliers final: 15 residues processed: 289 average time/residue: 0.2587 time to fit residues: 102.2184 Evaluate side-chains 295 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 141 SER 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 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 460 VAL Chi-restraints excluded: chain B residue 488 VAL 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 38 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3790 r_free = 0.3790 target = 0.140485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119214 restraints weight = 13772.912| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.16 r_work: 0.3360 rms_B_bonded: 2.77 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: 0.7755 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9984 Z= 0.138 Angle : 0.563 8.118 13573 Z= 0.284 Chirality : 0.043 0.143 1476 Planarity : 0.004 0.048 1725 Dihedral : 4.393 30.727 1370 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.79 % Allowed : 17.48 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1174 helix: 1.39 (0.28), residues: 381 sheet: 0.37 (0.49), residues: 122 loop : -0.22 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 396 HIS 0.007 0.001 HIS A 285 PHE 0.010 0.001 PHE A 659 TYR 0.023 0.001 TYR A 319 ARG 0.006 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 1) link_NAG-ASN : angle 1.45373 ( 3) link_BETA1-4 : bond 0.00432 ( 2) link_BETA1-4 : angle 2.14141 ( 6) hydrogen bonds : bond 0.03448 ( 310) hydrogen bonds : angle 4.63387 ( 843) SS BOND : bond 0.00237 ( 9) SS BOND : angle 0.98670 ( 18) covalent geometry : bond 0.00329 ( 9972) covalent geometry : angle 0.56000 (13546) ********************** 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 299 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 280 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7910 (t0) cc_final: 0.7559 (t0) REVERT: A 359 MET cc_start: 0.8383 (mpp) cc_final: 0.7915 (mpp) REVERT: A 383 GLU cc_start: 0.6808 (pt0) cc_final: 0.6539 (pt0) REVERT: A 384 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7403 (mtm-85) REVERT: A 432 ASP cc_start: 0.7580 (m-30) cc_final: 0.7331 (t0) REVERT: A 605 ARG cc_start: 0.6902 (mtp-110) cc_final: 0.6568 (mtp-110) REVERT: A 609 THR cc_start: 0.8124 (m) cc_final: 0.7608 (p) REVERT: A 644 ASN cc_start: 0.7882 (m-40) cc_final: 0.7642 (m-40) REVERT: A 706 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.7753 (m-40) REVERT: B 176 GLN cc_start: 0.7342 (tm-30) cc_final: 0.6676 (tm-30) REVERT: B 181 ASP cc_start: 0.7822 (t0) cc_final: 0.7464 (t0) REVERT: B 275 LYS cc_start: 0.8426 (tmtt) cc_final: 0.8140 (tmtt) REVERT: B 370 MET cc_start: 0.8043 (mtm) cc_final: 0.7832 (mtp) REVERT: B 516 GLU cc_start: 0.7568 (mp0) cc_final: 0.7344 (mp0) REVERT: B 607 LEU cc_start: 0.8462 (mt) cc_final: 0.8207 (mt) REVERT: B 612 MET cc_start: 0.7890 (tpp) cc_final: 0.7599 (tpp) REVERT: B 615 ASP cc_start: 0.7243 (m-30) cc_final: 0.6993 (t0) REVERT: B 624 MET cc_start: 0.8089 (mmp) cc_final: 0.7828 (mmp) REVERT: B 627 GLU cc_start: 0.7098 (mp0) cc_final: 0.6704 (mp0) outliers start: 19 outliers final: 16 residues processed: 285 average time/residue: 0.2443 time to fit residues: 93.8010 Evaluate side-chains 293 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 231 ASP 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 424 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 460 VAL 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 86 optimal weight: 0.2980 chunk 110 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** 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 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119278 restraints weight = 13667.433| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.16 r_work: 0.3362 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2075 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= 0.131 Angle : 0.566 8.167 13573 Z= 0.283 Chirality : 0.043 0.143 1476 Planarity : 0.004 0.045 1725 Dihedral : 4.301 18.567 1368 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.97 % Allowed : 17.20 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1174 helix: 1.29 (0.27), residues: 387 sheet: 0.39 (0.50), residues: 122 loop : -0.25 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 396 HIS 0.006 0.001 HIS A 285 PHE 0.010 0.001 PHE A 659 TYR 0.023 0.001 TYR A 319 ARG 0.006 0.000 ARG B 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 1) link_NAG-ASN : angle 1.47132 ( 3) link_BETA1-4 : bond 0.00442 ( 2) link_BETA1-4 : angle 2.10064 ( 6) hydrogen bonds : bond 0.03372 ( 310) hydrogen bonds : angle 4.63399 ( 843) SS BOND : bond 0.00225 ( 9) SS BOND : angle 0.92545 ( 18) covalent geometry : bond 0.00313 ( 9972) covalent geometry : angle 0.56357 (13546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6068.06 seconds wall clock time: 105 minutes 56.61 seconds (6356.61 seconds total)