Starting phenix.real_space_refine on Fri Feb 14 03:56:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sch_25035/02_2025/7sch_25035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sch_25035/02_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_25035/02_2025/7sch_25035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sch_25035/02_2025/7sch_25035.map" model { file = "/net/cci-nas-00/data/ceres_data/7sch_25035/02_2025/7sch_25035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sch_25035/02_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-5592/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: 5.92, 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 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: 1.09 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: 3.11 Time building geometry restraints manager: 2.99 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.590 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.750 ------------------------------------------------------------------------------- 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 9972 Z= 0.208 Angle : 0.621 9.790 13546 Z= 0.340 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 *********************** 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 : 1.103 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: 0.2588 time to fit residues: 109.7573 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 : 1.020 ------------------------------------------------------------------------------- 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: 4.9990 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 = 13704.759| |-----------------------------------------------------------------------------| 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 9972 Z= 0.160 Angle : 0.578 11.224 13546 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 *********************** 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 : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.7754 (tp40) cc_final: 0.7506 (tp40) REVERT: A 147 ASP cc_start: 0.7904 (t0) cc_final: 0.7508 (t0) REVERT: A 359 MET cc_start: 0.8212 (mpp) cc_final: 0.7724 (mpp) REVERT: A 453 PHE cc_start: 0.8164 (m-80) cc_final: 0.7942 (m-80) REVERT: A 599 TRP cc_start: 0.7719 (t-100) cc_final: 0.7491 (t-100) REVERT: A 605 ARG cc_start: 0.6700 (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: 0.8230 (OUTLIER) cc_final: 0.7602 (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: 0.7912 (t0) cc_final: 0.7674 (t0) REVERT: B 275 LYS cc_start: 0.8407 (tmtt) cc_final: 0.8164 (tmtt) REVERT: B 426 TYR cc_start: 0.4774 (OUTLIER) cc_final: 0.4080 (p90) REVERT: B 470 PHE cc_start: 0.7827 (m-80) cc_final: 0.7494 (m-80) REVERT: B 516 GLU cc_start: 0.7573 (mp0) cc_final: 0.7342 (mp0) REVERT: B 523 PHE cc_start: 0.7867 (m-80) cc_final: 0.7583 (m-80) REVERT: B 579 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7593 (mtmt) REVERT: B 607 LEU cc_start: 0.8436 (mt) cc_final: 0.8225 (mt) REVERT: B 612 MET cc_start: 0.7821 (tpp) cc_final: 0.7413 (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: 0.2566 time to fit residues: 102.9774 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 : 1.096 ------------------------------------------------------------------------------- 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: 5.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 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: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.140142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118957 restraints weight = 13838.763| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.18 r_work: 0.3358 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9972 Z= 0.238 Angle : 0.571 11.713 13546 Z= 0.287 Chirality : 0.044 0.141 1476 Planarity : 0.004 0.042 1725 Dihedral : 5.838 52.201 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: -0.08 (0.43), residues: 147 loop : -0.36 (0.25), residues: 651 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 *********************** 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 300 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 286 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7935 (t0) cc_final: 0.7517 (t0) REVERT: A 359 MET cc_start: 0.8281 (mpp) cc_final: 0.7807 (mpp) REVERT: A 599 TRP cc_start: 0.7722 (t-100) cc_final: 0.7373 (t-100) REVERT: A 605 ARG cc_start: 0.6728 (mtp-110) cc_final: 0.6380 (mtp-110) REVERT: A 609 THR cc_start: 0.8207 (m) cc_final: 0.7713 (p) REVERT: A 700 GLN cc_start: 0.7716 (mt0) cc_final: 0.7300 (mt0) REVERT: A 706 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7838 (m-40) REVERT: B 106 VAL cc_start: 0.8611 (m) cc_final: 0.8396 (t) REVERT: B 176 GLN cc_start: 0.7574 (tm-30) cc_final: 0.6935 (tm-30) REVERT: B 181 ASP cc_start: 0.7802 (t0) cc_final: 0.7505 (t0) REVERT: B 254 LEU cc_start: 0.8433 (tp) cc_final: 0.8233 (tt) REVERT: B 275 LYS cc_start: 0.8409 (tmtt) cc_final: 0.8073 (tmtt) REVERT: B 516 GLU cc_start: 0.7595 (mp0) cc_final: 0.7349 (mp0) REVERT: B 583 GLU cc_start: 0.7716 (tm-30) cc_final: 0.6983 (tm-30) REVERT: B 607 LEU cc_start: 0.8472 (mt) cc_final: 0.8226 (mt) REVERT: B 612 MET cc_start: 0.7863 (tpp) cc_final: 0.7531 (tpp) REVERT: B 620 VAL cc_start: 0.7735 (p) cc_final: 0.7521 (t) REVERT: B 627 GLU cc_start: 0.6998 (mp0) cc_final: 0.6350 (mp0) outliers start: 14 outliers final: 11 residues processed: 290 average time/residue: 0.2596 time to fit residues: 100.0138 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 : 1.146 ------------------------------------------------------------------------------- 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: 0.0020 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 overall best weight: 0.5948 ------------------------------------------------------------------------------- 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 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 = 0.3796 r_free = 0.3796 target = 0.140799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119766 restraints weight = 13622.853| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.16 r_work: 0.3369 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9972 Z= 0.183 Angle : 0.551 10.453 13546 Z= 0.276 Chirality : 0.043 0.140 1476 Planarity : 0.004 0.045 1725 Dihedral : 5.333 45.489 1372 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.97 % Allowed : 12.88 % Favored : 85.15 % 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: 0.36 (0.25), residues: 1174 helix: 1.35 (0.28), residues: 378 sheet: 0.09 (0.44), residues: 145 loop : -0.34 (0.25), residues: 651 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 0.016 0.001 TYR A 608 ARG 0.005 0.000 ARG B 182 *********************** 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 312 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 291 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7950 (t0) cc_final: 0.7522 (t0) REVERT: A 359 MET cc_start: 0.8271 (mpp) cc_final: 0.7778 (mpp) REVERT: A 599 TRP cc_start: 0.7703 (t-100) cc_final: 0.7348 (t-100) REVERT: A 605 ARG cc_start: 0.6713 (mtp-110) cc_final: 0.6350 (mtp-110) REVERT: A 609 THR cc_start: 0.8170 (m) cc_final: 0.7655 (p) REVERT: A 644 ASN cc_start: 0.7890 (m-40) cc_final: 0.7625 (m-40) REVERT: A 700 GLN cc_start: 0.7696 (mt0) cc_final: 0.7251 (mt0) REVERT: A 706 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7771 (m-40) REVERT: B 176 GLN cc_start: 0.7530 (tm-30) cc_final: 0.6856 (tm-30) REVERT: B 181 ASP cc_start: 0.7825 (t0) cc_final: 0.7475 (t0) REVERT: B 254 LEU cc_start: 0.8426 (tp) cc_final: 0.8222 (tt) REVERT: B 275 LYS cc_start: 0.8405 (tmtt) cc_final: 0.8086 (tmtt) REVERT: B 516 GLU cc_start: 0.7613 (mp0) cc_final: 0.7377 (mp0) REVERT: B 583 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7015 (tm-30) REVERT: B 607 LEU cc_start: 0.8456 (mt) cc_final: 0.8226 (mt) REVERT: B 612 MET cc_start: 0.7873 (tpp) cc_final: 0.7526 (tpp) REVERT: B 615 ASP cc_start: 0.7119 (m-30) cc_final: 0.6876 (t0) REVERT: B 627 GLU cc_start: 0.6961 (mp0) cc_final: 0.6631 (mp0) outliers start: 21 outliers final: 13 residues processed: 298 average time/residue: 0.2612 time to fit residues: 103.7909 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 : 1.014 ------------------------------------------------------------------------------- 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 103 LYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 644 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 631 HIS A 706 ASN B 415 ASN B 430 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.136146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115002 restraints weight = 13606.018| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.13 r_work: 0.3299 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 9972 Z= 0.488 Angle : 0.655 9.153 13546 Z= 0.336 Chirality : 0.049 0.166 1476 Planarity : 0.005 0.048 1725 Dihedral : 5.995 47.194 1372 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.26 % Allowed : 14.00 % Favored : 83.74 % 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: 0.77 (0.27), residues: 389 sheet: -0.26 (0.44), residues: 132 loop : -0.37 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 374 HIS 0.010 0.001 HIS A 285 PHE 0.019 0.002 PHE A 333 TYR 0.021 0.002 TYR B 582 ARG 0.005 0.001 ARG B 383 *********************** 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 314 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 290 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7977 (t0) cc_final: 0.7499 (t0) REVERT: A 159 ASP cc_start: 0.8442 (t0) cc_final: 0.8229 (t70) REVERT: A 359 MET cc_start: 0.8329 (mpp) cc_final: 0.7941 (mpp) REVERT: A 508 GLN cc_start: 0.8101 (pm20) cc_final: 0.7896 (pm20) REVERT: A 599 TRP cc_start: 0.7790 (t-100) cc_final: 0.7372 (t-100) REVERT: A 605 ARG cc_start: 0.6841 (mtp-110) cc_final: 0.6312 (mtp-110) REVERT: A 609 THR cc_start: 0.8258 (m) cc_final: 0.7774 (p) REVERT: A 706 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7376 (m-40) REVERT: B 105 LYS cc_start: 0.8077 (mttp) cc_final: 0.7797 (mtmm) REVERT: B 128 ARG cc_start: 0.7734 (ptt90) cc_final: 0.7531 (ptt90) REVERT: B 176 GLN cc_start: 0.7731 (tm-30) cc_final: 0.6997 (tm-30) REVERT: B 181 ASP cc_start: 0.7854 (t0) cc_final: 0.7538 (t0) REVERT: B 227 ASP cc_start: 0.7707 (m-30) cc_final: 0.7448 (m-30) REVERT: B 275 LYS cc_start: 0.8421 (tmtt) cc_final: 0.8049 (tmtt) REVERT: B 516 GLU cc_start: 0.7654 (mp0) cc_final: 0.7356 (mp0) REVERT: B 528 GLU cc_start: 0.6990 (mp0) cc_final: 0.6770 (mp0) REVERT: B 548 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7362 (mm-30) REVERT: B 607 LEU cc_start: 0.8518 (mt) cc_final: 0.8270 (mt) outliers start: 24 outliers final: 16 residues processed: 297 average time/residue: 0.2642 time to fit residues: 104.6517 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 : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS 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 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: 0.7980 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 30 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.118335 restraints weight = 13717.809| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.16 r_work: 0.3352 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9972 Z= 0.199 Angle : 0.567 10.282 13546 Z= 0.288 Chirality : 0.043 0.146 1476 Planarity : 0.004 0.047 1725 Dihedral : 5.285 36.921 1372 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.88 % Allowed : 15.41 % Favored : 82.71 % 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: 0.20 (0.25), residues: 1174 helix: 1.08 (0.27), residues: 384 sheet: 0.00 (0.46), residues: 125 loop : -0.36 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 396 HIS 0.007 0.001 HIS A 285 PHE 0.016 0.001 PHE B 317 TYR 0.020 0.001 TYR B 582 ARG 0.004 0.000 ARG A 346 *********************** 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 302 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 282 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8006 (t0) cc_final: 0.7553 (t0) REVERT: A 359 MET cc_start: 0.8336 (mpp) cc_final: 0.7804 (mpp) REVERT: A 443 LEU cc_start: 0.8466 (tt) cc_final: 0.8255 (tp) REVERT: A 599 TRP cc_start: 0.7744 (t-100) cc_final: 0.7370 (t-100) REVERT: A 605 ARG cc_start: 0.6843 (mtp-110) cc_final: 0.6344 (mtp-110) REVERT: A 609 THR cc_start: 0.8173 (m) cc_final: 0.7667 (p) REVERT: A 644 ASN cc_start: 0.7929 (m-40) cc_final: 0.7628 (m-40) REVERT: A 702 GLN cc_start: 0.7480 (mp10) cc_final: 0.7215 (mp10) REVERT: A 706 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7247 (m-40) REVERT: B 128 ARG cc_start: 0.7727 (ptt90) cc_final: 0.7524 (ptt90) REVERT: B 176 GLN cc_start: 0.7613 (tm-30) cc_final: 0.6885 (tm-30) REVERT: B 181 ASP cc_start: 0.7850 (t0) cc_final: 0.7476 (t0) REVERT: B 227 ASP cc_start: 0.7685 (m-30) cc_final: 0.7424 (m-30) REVERT: B 275 LYS cc_start: 0.8429 (tmtt) cc_final: 0.8103 (tmtt) REVERT: B 516 GLU cc_start: 0.7620 (mp0) cc_final: 0.7342 (mp0) REVERT: B 528 GLU cc_start: 0.6924 (mp0) cc_final: 0.6702 (mp0) REVERT: B 539 ASP cc_start: 0.7274 (p0) cc_final: 0.7041 (p0) REVERT: B 548 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7235 (mm-30) REVERT: B 607 LEU cc_start: 0.8486 (mt) cc_final: 0.8222 (mt) REVERT: B 627 GLU cc_start: 0.7077 (mp0) cc_final: 0.6624 (mp0) outliers start: 20 outliers final: 14 residues processed: 291 average time/residue: 0.2628 time to fit residues: 102.4581 Evaluate side-chains 290 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 275 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 207 VAL 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 621 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS 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 594 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 112 optimal weight: 0.4980 chunk 62 optimal weight: 0.0060 chunk 16 optimal weight: 5.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 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 = 0.140349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.119118 restraints weight = 13796.986| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.17 r_work: 0.3345 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9972 Z= 0.175 Angle : 0.551 9.346 13546 Z= 0.279 Chirality : 0.043 0.142 1476 Planarity : 0.004 0.046 1725 Dihedral : 4.897 32.923 1372 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.97 % Allowed : 15.60 % Favored : 82.42 % 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: 0.26 (0.25), residues: 1174 helix: 1.18 (0.28), residues: 386 sheet: 0.18 (0.47), residues: 121 loop : -0.39 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 396 HIS 0.006 0.001 HIS A 285 PHE 0.013 0.001 PHE B 470 TYR 0.016 0.001 TYR A 608 ARG 0.004 0.000 ARG A 346 *********************** 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 297 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 276 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7979 (t0) cc_final: 0.7548 (t0) REVERT: A 359 MET cc_start: 0.8328 (mpp) cc_final: 0.7801 (mpp) REVERT: A 443 LEU cc_start: 0.8456 (tt) cc_final: 0.8237 (tp) REVERT: A 599 TRP cc_start: 0.7738 (t-100) cc_final: 0.7329 (t-100) REVERT: A 605 ARG cc_start: 0.6871 (mtp-110) cc_final: 0.6335 (mtp-110) REVERT: A 609 THR cc_start: 0.8121 (m) cc_final: 0.7602 (p) REVERT: A 644 ASN cc_start: 0.7894 (m-40) cc_final: 0.7616 (m-40) REVERT: A 700 GLN cc_start: 0.7681 (mt0) cc_final: 0.7219 (mt0) REVERT: A 706 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.7794 (m-40) REVERT: B 128 ARG cc_start: 0.7683 (ptt90) cc_final: 0.7477 (ptt90) REVERT: B 176 GLN cc_start: 0.7521 (tm-30) cc_final: 0.6799 (tm-30) REVERT: B 181 ASP cc_start: 0.7830 (t0) cc_final: 0.7457 (t0) REVERT: B 227 ASP cc_start: 0.7686 (m-30) cc_final: 0.7413 (m-30) REVERT: B 254 LEU cc_start: 0.8363 (tt) cc_final: 0.8163 (tp) REVERT: B 275 LYS cc_start: 0.8442 (tmtt) cc_final: 0.8139 (tmtt) REVERT: B 370 MET cc_start: 0.8021 (mtm) cc_final: 0.7798 (mtp) REVERT: B 516 GLU cc_start: 0.7582 (mp0) cc_final: 0.7323 (mp0) REVERT: B 528 GLU cc_start: 0.6973 (mp0) cc_final: 0.6745 (mp0) REVERT: B 539 ASP cc_start: 0.7284 (p0) cc_final: 0.7014 (p0) REVERT: B 548 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7216 (mm-30) REVERT: B 583 GLU cc_start: 0.7680 (tm-30) cc_final: 0.6937 (tm-30) REVERT: B 607 LEU cc_start: 0.8494 (mt) cc_final: 0.8256 (mt) REVERT: B 627 GLU cc_start: 0.7081 (mp0) cc_final: 0.6646 (mp0) outliers start: 21 outliers final: 16 residues processed: 282 average time/residue: 0.2521 time to fit residues: 95.2758 Evaluate side-chains 299 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 282 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 207 VAL 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 424 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 594 LEU 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: 0.9980 chunk 4 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.118415 restraints weight = 13829.884| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.19 r_work: 0.3346 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9972 Z= 0.218 Angle : 0.564 8.785 13546 Z= 0.286 Chirality : 0.044 0.145 1476 Planarity : 0.004 0.046 1725 Dihedral : 4.797 30.127 1372 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.07 % Allowed : 15.70 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.27 (0.25), residues: 1174 helix: 1.19 (0.27), residues: 386 sheet: 0.22 (0.48), residues: 121 loop : -0.39 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 396 HIS 0.007 0.001 HIS A 285 PHE 0.013 0.001 PHE B 470 TYR 0.017 0.001 TYR A 608 ARG 0.008 0.000 ARG B 182 *********************** 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 299 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 277 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7963 (t0) cc_final: 0.7537 (t0) REVERT: A 359 MET cc_start: 0.8334 (mpp) cc_final: 0.7820 (mpp) REVERT: A 384 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7451 (mtm-85) REVERT: A 443 LEU cc_start: 0.8453 (tt) cc_final: 0.8239 (tp) REVERT: A 599 TRP cc_start: 0.7741 (t-100) cc_final: 0.7320 (t-100) REVERT: A 605 ARG cc_start: 0.6883 (mtp-110) cc_final: 0.6346 (mtp-110) REVERT: A 609 THR cc_start: 0.8140 (m) cc_final: 0.7612 (p) REVERT: A 644 ASN cc_start: 0.7914 (m-40) cc_final: 0.7634 (m-40) REVERT: A 706 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7836 (m-40) REVERT: B 176 GLN cc_start: 0.7539 (tm-30) cc_final: 0.6846 (tm-30) REVERT: B 181 ASP cc_start: 0.7836 (t0) cc_final: 0.7457 (t0) REVERT: B 227 ASP cc_start: 0.7693 (m-30) cc_final: 0.7477 (m-30) REVERT: B 275 LYS cc_start: 0.8432 (tmtt) cc_final: 0.8108 (tmtt) REVERT: B 370 MET cc_start: 0.8044 (mtm) cc_final: 0.7812 (mtp) REVERT: B 516 GLU cc_start: 0.7626 (mp0) cc_final: 0.7360 (mp0) REVERT: B 528 GLU cc_start: 0.6963 (mp0) cc_final: 0.6736 (mp0) REVERT: B 539 ASP cc_start: 0.7316 (p0) cc_final: 0.7039 (p0) REVERT: B 548 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7213 (mm-30) REVERT: B 583 GLU cc_start: 0.7703 (tm-30) cc_final: 0.6958 (tm-30) REVERT: B 607 LEU cc_start: 0.8506 (mt) cc_final: 0.8261 (mt) REVERT: B 627 GLU cc_start: 0.7099 (mp0) cc_final: 0.6711 (mp0) outliers start: 22 outliers final: 18 residues processed: 282 average time/residue: 0.2524 time to fit residues: 95.6214 Evaluate side-chains 300 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 281 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 207 VAL 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 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 135 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 454 GLN 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 620 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 39 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.0060 chunk 97 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 194 ASN A 376 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.140236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119115 restraints weight = 13684.434| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.15 r_work: 0.3349 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9972 Z= 0.198 Angle : 0.561 8.592 13546 Z= 0.285 Chirality : 0.043 0.143 1476 Planarity : 0.004 0.062 1725 Dihedral : 4.589 23.538 1370 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.26 % Allowed : 16.26 % Favored : 81.48 % 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: 0.31 (0.25), residues: 1174 helix: 1.23 (0.28), residues: 386 sheet: 0.25 (0.48), residues: 121 loop : -0.38 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 396 HIS 0.006 0.001 HIS A 285 PHE 0.011 0.001 PHE B 470 TYR 0.016 0.001 TYR A 608 ARG 0.005 0.000 ARG B 383 *********************** 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: 24 poor density : 278 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7948 (t0) cc_final: 0.7561 (t0) REVERT: A 359 MET cc_start: 0.8336 (mpp) cc_final: 0.7853 (mpp) REVERT: A 384 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7450 (mtm-85) REVERT: A 443 LEU cc_start: 0.8466 (tt) cc_final: 0.8250 (tp) REVERT: A 599 TRP cc_start: 0.7760 (t-100) cc_final: 0.7357 (t-100) REVERT: A 605 ARG cc_start: 0.6901 (mtp-110) cc_final: 0.6399 (mtp-110) REVERT: A 609 THR cc_start: 0.8112 (m) cc_final: 0.7602 (p) REVERT: A 644 ASN cc_start: 0.7910 (m-40) cc_final: 0.7641 (m-40) REVERT: A 700 GLN cc_start: 0.7711 (mt0) cc_final: 0.7269 (mt0) REVERT: A 706 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7874 (m-40) REVERT: B 176 GLN cc_start: 0.7493 (tm-30) cc_final: 0.6787 (tm-30) REVERT: B 181 ASP cc_start: 0.7855 (t0) cc_final: 0.7484 (t0) REVERT: B 227 ASP cc_start: 0.7655 (m-30) cc_final: 0.7444 (m-30) REVERT: B 275 LYS cc_start: 0.8446 (tmtt) cc_final: 0.8160 (tmtt) REVERT: B 370 MET cc_start: 0.8060 (mtm) cc_final: 0.7846 (mtp) REVERT: B 516 GLU cc_start: 0.7566 (mp0) cc_final: 0.7318 (mp0) REVERT: B 528 GLU cc_start: 0.6943 (mp0) cc_final: 0.6717 (mp0) REVERT: B 539 ASP cc_start: 0.7288 (p0) cc_final: 0.7012 (p0) REVERT: B 548 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7145 (mm-30) REVERT: B 583 GLU cc_start: 0.7698 (tm-30) cc_final: 0.6990 (tm-30) REVERT: B 607 LEU cc_start: 0.8501 (mt) cc_final: 0.8244 (mt) REVERT: B 627 GLU cc_start: 0.7070 (mp0) cc_final: 0.6696 (mp0) outliers start: 24 outliers final: 21 residues processed: 284 average time/residue: 0.2466 time to fit residues: 94.4901 Evaluate side-chains 303 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 281 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 454 GLN 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 620 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 300 HIS A 376 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119211 restraints weight = 13757.262| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.15 r_work: 0.3359 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9972 Z= 0.205 Angle : 0.570 8.489 13546 Z= 0.289 Chirality : 0.043 0.143 1476 Planarity : 0.004 0.056 1725 Dihedral : 4.523 21.547 1370 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.16 % Allowed : 16.64 % Favored : 81.20 % 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: 0.31 (0.25), residues: 1174 helix: 1.23 (0.28), residues: 386 sheet: 0.25 (0.48), residues: 121 loop : -0.38 (0.25), residues: 667 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 0.011 0.001 PHE B 470 TYR 0.016 0.001 TYR A 608 ARG 0.007 0.000 ARG B 383 ********************** 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 297 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 274 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7973 (t0) cc_final: 0.7550 (t0) REVERT: A 359 MET cc_start: 0.8348 (mpp) cc_final: 0.7837 (mpp) REVERT: A 384 ARG cc_start: 0.7730 (mtm110) cc_final: 0.7428 (mtm-85) REVERT: A 443 LEU cc_start: 0.8448 (tt) cc_final: 0.8236 (tp) REVERT: A 599 TRP cc_start: 0.7753 (t-100) cc_final: 0.7338 (t-100) REVERT: A 605 ARG cc_start: 0.6902 (mtp-110) cc_final: 0.6387 (mtp-110) REVERT: A 609 THR cc_start: 0.8103 (m) cc_final: 0.7587 (p) REVERT: A 644 ASN cc_start: 0.7914 (m-40) cc_final: 0.7635 (m-40) REVERT: A 700 GLN cc_start: 0.7683 (mt0) cc_final: 0.7231 (mt0) REVERT: A 706 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.7842 (m-40) REVERT: B 176 GLN cc_start: 0.7484 (tm-30) cc_final: 0.6767 (tm-30) REVERT: B 181 ASP cc_start: 0.7861 (t0) cc_final: 0.7488 (t0) REVERT: B 227 ASP cc_start: 0.7689 (m-30) cc_final: 0.7466 (m-30) REVERT: B 275 LYS cc_start: 0.8427 (tmtt) cc_final: 0.8115 (tmtt) REVERT: B 370 MET cc_start: 0.8021 (mtm) cc_final: 0.7803 (mtp) REVERT: B 516 GLU cc_start: 0.7559 (mp0) cc_final: 0.7304 (mp0) REVERT: B 528 GLU cc_start: 0.6952 (mp0) cc_final: 0.6725 (mp0) REVERT: B 539 ASP cc_start: 0.7341 (p0) cc_final: 0.7067 (p0) REVERT: B 548 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7117 (mm-30) REVERT: B 583 GLU cc_start: 0.7677 (tm-30) cc_final: 0.6954 (tm-30) REVERT: B 607 LEU cc_start: 0.8497 (mt) cc_final: 0.8252 (mt) REVERT: B 624 MET cc_start: 0.8037 (mmp) cc_final: 0.7752 (mmp) REVERT: B 627 GLU cc_start: 0.7106 (mp0) cc_final: 0.6756 (mp0) outliers start: 23 outliers final: 21 residues processed: 279 average time/residue: 0.2638 time to fit residues: 98.8247 Evaluate side-chains 300 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 0.0970 chunk 113 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3795 r_free = 0.3795 target = 0.140891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119295 restraints weight = 13642.788| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.24 r_work: 0.3347 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9972 Z= 0.176 Angle : 0.561 8.458 13546 Z= 0.284 Chirality : 0.043 0.142 1476 Planarity : 0.004 0.052 1725 Dihedral : 4.392 20.603 1370 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.16 % Allowed : 17.01 % 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: 0.43 (0.25), residues: 1174 helix: 1.41 (0.28), residues: 380 sheet: 0.14 (0.48), residues: 124 loop : -0.30 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 396 HIS 0.006 0.001 HIS A 285 PHE 0.010 0.001 PHE B 470 TYR 0.016 0.001 TYR A 608 ARG 0.007 0.000 ARG B 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5369.42 seconds wall clock time: 96 minutes 0.69 seconds (5760.69 seconds total)