Starting phenix.real_space_refine on Wed Mar 4 15:20:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rh9_24458/03_2026/7rh9_24458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rh9_24458/03_2026/7rh9_24458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rh9_24458/03_2026/7rh9_24458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rh9_24458/03_2026/7rh9_24458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rh9_24458/03_2026/7rh9_24458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rh9_24458/03_2026/7rh9_24458.map" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 82 5.16 5 C 9594 2.51 5 N 2387 2.21 5 O 2617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14680 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "B" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3542 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 1 Chain: "A" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3732 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 14, 'TRANS': 441} Chain: "D" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Time building chain proxies: 3.27, per 1000 atoms: 0.22 Number of scatterers: 14680 At special positions: 0 Unit cell: (97.672, 100.198, 121.248, 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 82 16.00 O 2617 8.00 N 2387 7.00 C 9594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 542.5 milliseconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 12 sheets defined 69.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.506A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.027A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.645A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 221 Processing helix chain 'C' and resid 232 through 243 removed outlier: 3.602A pdb=" N ASN C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 253 removed outlier: 4.107A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 258 through 264 removed outlier: 3.700A pdb=" N LYS C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.883A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.722A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 360 Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 404 through 424 Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 458 through 476 removed outlier: 5.983A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 588 through 605 Processing helix chain 'B' and resid 653 through 680 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 687 through 708 removed outlier: 3.807A pdb=" N TRP B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 713 Processing helix chain 'B' and resid 724 through 735 Processing helix chain 'B' and resid 735 through 746 removed outlier: 3.723A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 Proline residue: B 764 - end of helix removed outlier: 3.621A pdb=" N LYS B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 783 Processing helix chain 'B' and resid 786 through 817 Processing helix chain 'B' and resid 832 through 844 Processing helix chain 'B' and resid 854 through 887 Processing helix chain 'B' and resid 887 through 907 Processing helix chain 'B' and resid 910 through 929 Processing helix chain 'B' and resid 932 through 940 removed outlier: 4.163A pdb=" N LEU B 936 " --> pdb=" O ASP B 932 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 939 " --> pdb=" O GLU B 935 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 940 " --> pdb=" O LEU B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 960 removed outlier: 6.264A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 964 removed outlier: 3.548A pdb=" N GLN B 964 " --> pdb=" O ALA B 961 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 961 through 964' Processing helix chain 'B' and resid 967 through 978 Processing helix chain 'B' and resid 1029 through 1034 Processing helix chain 'B' and resid 1059 through 1067 Processing helix chain 'B' and resid 1069 through 1084 removed outlier: 3.736A pdb=" N LEU B1084 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.554A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 4.883A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.767A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 Processing helix chain 'A' and resid 232 through 243 Processing helix chain 'A' and resid 243 through 253 removed outlier: 4.034A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 4.906A pdb=" N ASP A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 258 " --> pdb=" O PRO A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 258' Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.199A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.833A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 424 removed outlier: 4.684A pdb=" N ALA A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ARG A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 458 through 476 removed outlier: 6.243A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 545 through 551 removed outlier: 3.582A pdb=" N ILE A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 551' Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 588 through 607 Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.564A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.076A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.786A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 221 Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.510A pdb=" N ASN D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 253 removed outlier: 4.061A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 removed outlier: 3.648A pdb=" N LEU D 258 " --> pdb=" O PRO D 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 258' Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.977A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.516A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 404 Processing helix chain 'D' and resid 404 through 425 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.679A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 476 removed outlier: 6.195A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 482 removed outlier: 4.632A pdb=" N ASP D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 495 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 588 through 606 Processing sheet with id=AA1, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'C' and resid 496 through 500 Processing sheet with id=AA3, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.225A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS C 507 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 524 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL C 537 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 526 " --> pdb=" O PHE C 535 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.532A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.437A pdb=" N ASN B1053 " --> pdb=" O GLN B1003 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 988 through 990 removed outlier: 6.418A pdb=" N TYR B 988 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA B1048 " --> pdb=" O TYR B 988 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY B1011 " --> pdb=" O VAL B1018 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL B1018 " --> pdb=" O GLY B1011 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.689A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.191A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER A 567 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 524 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 537 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 526 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.496A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU D 576 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR D 517 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.138A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS D 507 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU D 524 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL D 537 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 526 " --> pdb=" O PHE D 535 " (cutoff:3.500A) 961 hydrogen bonds defined for protein. 2769 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: 2.49 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4527 1.34 - 1.46: 2690 1.46 - 1.57: 7671 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 15026 Sorted by residual: bond pdb=" CB VAL A 492 " pdb=" CG1 VAL A 492 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.65e+00 bond pdb=" CA SER D 279 " pdb=" C SER D 279 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.30e-02 5.92e+03 3.40e+00 bond pdb=" C SER D 279 " pdb=" N ARG D 280 " ideal model delta sigma weight residual 1.335 1.318 0.017 1.31e-02 5.83e+03 1.63e+00 bond pdb=" CB VAL A 350 " pdb=" CG1 VAL A 350 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CB VAL D 492 " pdb=" CG1 VAL D 492 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 15021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 19972 1.76 - 3.51: 337 3.51 - 5.27: 34 5.27 - 7.02: 13 7.02 - 8.78: 2 Bond angle restraints: 20358 Sorted by residual: angle pdb=" N PHE D 278 " pdb=" CA PHE D 278 " pdb=" C PHE D 278 " ideal model delta sigma weight residual 111.75 116.36 -4.61 1.28e+00 6.10e-01 1.30e+01 angle pdb=" C GLY D 558 " pdb=" N ASN D 559 " pdb=" CA ASN D 559 " ideal model delta sigma weight residual 122.46 127.21 -4.75 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C ASN B 830 " pdb=" N SER B 831 " pdb=" CA SER B 831 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C GLY C 558 " pdb=" N ASN C 559 " pdb=" CA ASN C 559 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.70e+00 angle pdb=" C GLY A 558 " pdb=" N ASN A 559 " pdb=" CA ASN A 559 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.47e+00 ... (remaining 20353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 8046 16.77 - 33.54: 730 33.54 - 50.31: 107 50.31 - 67.07: 24 67.07 - 83.84: 17 Dihedral angle restraints: 8924 sinusoidal: 3634 harmonic: 5290 Sorted by residual: dihedral pdb=" CA VAL C 469 " pdb=" C VAL C 469 " pdb=" N HIS C 470 " pdb=" CA HIS C 470 " ideal model delta harmonic sigma weight residual -180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA VAL A 469 " pdb=" C VAL A 469 " pdb=" N HIS A 470 " pdb=" CA HIS A 470 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL D 469 " pdb=" C VAL D 469 " pdb=" N HIS D 470 " pdb=" CA HIS D 470 " ideal model delta harmonic sigma weight residual 180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 8921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1467 0.032 - 0.065: 529 0.065 - 0.097: 206 0.097 - 0.130: 67 0.130 - 0.162: 7 Chirality restraints: 2276 Sorted by residual: chirality pdb=" CA ASN D 559 " pdb=" N ASN D 559 " pdb=" C ASN D 559 " pdb=" CB ASN D 559 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CA ASN A 559 " pdb=" N ASN A 559 " pdb=" C ASN A 559 " pdb=" CB ASN A 559 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA THR B1043 " pdb=" N THR B1043 " pdb=" C THR B1043 " pdb=" CB THR B1043 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2273 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO B 764 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 284 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C PHE A 284 " 0.038 2.00e-02 2.50e+03 pdb=" O PHE A 284 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 285 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 806 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C SER B 806 " 0.034 2.00e-02 2.50e+03 pdb=" O SER B 806 " -0.013 2.00e-02 2.50e+03 pdb=" N CYS B 807 " -0.011 2.00e-02 2.50e+03 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1503 2.75 - 3.29: 15268 3.29 - 3.83: 27125 3.83 - 4.36: 31001 4.36 - 4.90: 52355 Nonbonded interactions: 127252 Sorted by model distance: nonbonded pdb=" OE2 GLU D 515 " pdb=" OH TYR D 517 " model vdw 2.214 3.040 nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.220 3.040 nonbonded pdb=" O LEU C 169 " pdb=" OG1 THR C 173 " model vdw 2.250 3.040 nonbonded pdb=" N GLU C 365 " pdb=" OE2 GLU D 365 " model vdw 2.269 3.120 nonbonded pdb=" OG1 THR B 684 " pdb=" OD1 ASN B 687 " model vdw 2.275 3.040 ... (remaining 127247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 156 through 605) selection = chain 'C' selection = (chain 'D' and resid 156 through 605) } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 0.063 15026 Z= 0.151 Angle : 0.571 8.779 20358 Z= 0.314 Chirality : 0.041 0.162 2276 Planarity : 0.005 0.075 2523 Dihedral : 13.273 83.843 5534 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.19), residues: 1782 helix: 1.18 (0.14), residues: 1157 sheet: 1.52 (0.66), residues: 44 loop : 0.36 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 280 TYR 0.018 0.002 TYR D 306 PHE 0.032 0.002 PHE D 382 TRP 0.021 0.002 TRP D 168 HIS 0.009 0.002 HIS D 422 Details of bonding type rmsd covalent geometry : bond 0.00325 (15026) covalent geometry : angle 0.57051 (20358) hydrogen bonds : bond 0.11472 ( 961) hydrogen bonds : angle 5.41155 ( 2769) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.525 Fit side-chains REVERT: C 234 LEU cc_start: 0.7461 (tp) cc_final: 0.7148 (tp) REVERT: C 484 GLU cc_start: 0.6315 (tt0) cc_final: 0.5898 (tt0) REVERT: B 690 HIS cc_start: 0.6111 (m-70) cc_final: 0.5575 (m-70) REVERT: A 422 HIS cc_start: 0.6844 (t-90) cc_final: 0.6303 (t-90) REVERT: A 490 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6802 (mm-30) REVERT: A 521 GLU cc_start: 0.7227 (tt0) cc_final: 0.7004 (tt0) REVERT: A 594 MET cc_start: 0.6264 (tmm) cc_final: 0.5832 (tpp) REVERT: D 262 LYS cc_start: 0.6262 (mptt) cc_final: 0.5758 (mmtm) REVERT: D 399 MET cc_start: 0.8018 (ttm) cc_final: 0.7731 (ttm) REVERT: D 553 LYS cc_start: 0.4058 (tmtt) cc_final: 0.3745 (tptp) REVERT: D 602 ILE cc_start: 0.7654 (mt) cc_final: 0.7352 (mt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.6651 time to fit residues: 164.4408 Evaluate side-chains 196 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 710 GLN B 805 ASN B 864 ASN B 969 GLN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.098903 restraints weight = 16705.435| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.22 r_work: 0.2949 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15026 Z= 0.113 Angle : 0.451 6.892 20358 Z= 0.246 Chirality : 0.038 0.137 2276 Planarity : 0.004 0.062 2523 Dihedral : 3.740 16.990 1991 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.68 % Allowed : 7.26 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.19), residues: 1782 helix: 1.97 (0.15), residues: 1146 sheet: 1.60 (0.66), residues: 44 loop : 0.57 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 287 TYR 0.013 0.001 TYR A 349 PHE 0.017 0.001 PHE C 298 TRP 0.015 0.001 TRP C 168 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00237 (15026) covalent geometry : angle 0.45092 (20358) hydrogen bonds : bond 0.03959 ( 961) hydrogen bonds : angle 4.21575 ( 2769) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 0.577 Fit side-chains REVERT: C 234 LEU cc_start: 0.7616 (tp) cc_final: 0.7244 (tt) REVERT: B 690 HIS cc_start: 0.6591 (m-70) cc_final: 0.6085 (m-70) REVERT: A 413 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7980 (mtt-85) REVERT: A 422 HIS cc_start: 0.7205 (t-90) cc_final: 0.6526 (t-90) REVERT: A 490 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7294 (mm-30) REVERT: A 521 GLU cc_start: 0.8147 (tt0) cc_final: 0.7569 (mt-10) REVERT: A 594 MET cc_start: 0.7104 (tmm) cc_final: 0.6602 (tpp) REVERT: D 262 LYS cc_start: 0.6120 (mptt) cc_final: 0.5511 (mmtm) REVERT: D 516 MET cc_start: 0.8742 (ttp) cc_final: 0.8482 (ttp) REVERT: D 553 LYS cc_start: 0.4091 (tmtt) cc_final: 0.3742 (tmtt) outliers start: 11 outliers final: 3 residues processed: 213 average time/residue: 0.6150 time to fit residues: 143.3169 Evaluate side-chains 194 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain A residue 451 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 85 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 140 optimal weight: 0.0050 chunk 149 optimal weight: 6.9990 chunk 133 optimal weight: 0.0470 chunk 48 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 0.0040 chunk 43 optimal weight: 9.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 816 GLN B 969 GLN A 411 GLN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.100502 restraints weight = 16875.215| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.25 r_work: 0.2974 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15026 Z= 0.095 Angle : 0.412 5.139 20358 Z= 0.224 Chirality : 0.037 0.139 2276 Planarity : 0.003 0.056 2523 Dihedral : 3.545 16.672 1991 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.18 % Allowed : 8.50 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.20), residues: 1782 helix: 2.19 (0.15), residues: 1155 sheet: 1.68 (0.66), residues: 43 loop : 0.50 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 712 TYR 0.011 0.001 TYR C 354 PHE 0.016 0.001 PHE D 298 TRP 0.015 0.001 TRP C 168 HIS 0.002 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00194 (15026) covalent geometry : angle 0.41234 (20358) hydrogen bonds : bond 0.03549 ( 961) hydrogen bonds : angle 3.94653 ( 2769) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.598 Fit side-chains REVERT: C 234 LEU cc_start: 0.7583 (tp) cc_final: 0.7258 (tp) REVERT: C 305 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7990 (tmm) REVERT: C 471 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7572 (tt) REVERT: B 690 HIS cc_start: 0.6579 (m-70) cc_final: 0.6029 (m-70) REVERT: B 897 MET cc_start: 0.8622 (ttt) cc_final: 0.8368 (tpp) REVERT: A 413 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7956 (mtt-85) REVERT: A 422 HIS cc_start: 0.7208 (t-90) cc_final: 0.6531 (t-90) REVERT: A 490 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7275 (mm-30) REVERT: A 521 GLU cc_start: 0.8079 (tt0) cc_final: 0.7565 (mt-10) REVERT: A 594 MET cc_start: 0.7185 (tmm) cc_final: 0.6657 (tpp) REVERT: D 262 LYS cc_start: 0.6146 (mptt) cc_final: 0.5623 (mmtm) REVERT: D 305 MET cc_start: 0.8615 (ttm) cc_final: 0.8390 (ttp) REVERT: D 516 MET cc_start: 0.8777 (ttp) cc_final: 0.8575 (ttp) REVERT: D 553 LYS cc_start: 0.4206 (tmtt) cc_final: 0.3789 (tmtt) REVERT: D 572 ASP cc_start: 0.7840 (t70) cc_final: 0.7461 (m-30) outliers start: 19 outliers final: 4 residues processed: 210 average time/residue: 0.6032 time to fit residues: 138.8267 Evaluate side-chains 197 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN B 915 ASN B 969 GLN B1006 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN D 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.098281 restraints weight = 16870.018| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.36 r_work: 0.2912 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15026 Z= 0.114 Angle : 0.431 6.170 20358 Z= 0.234 Chirality : 0.038 0.142 2276 Planarity : 0.003 0.052 2523 Dihedral : 3.568 16.832 1991 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.12 % Allowed : 9.93 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.20), residues: 1782 helix: 2.34 (0.15), residues: 1145 sheet: 1.61 (0.64), residues: 44 loop : 0.62 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 560 TYR 0.016 0.001 TYR A 349 PHE 0.018 0.001 PHE D 298 TRP 0.015 0.001 TRP C 168 HIS 0.003 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00246 (15026) covalent geometry : angle 0.43113 (20358) hydrogen bonds : bond 0.03669 ( 961) hydrogen bonds : angle 3.92428 ( 2769) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.581 Fit side-chains REVERT: C 234 LEU cc_start: 0.7626 (tp) cc_final: 0.7291 (tp) REVERT: C 471 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7667 (tt) REVERT: C 604 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6615 (mpt) REVERT: B 690 HIS cc_start: 0.6564 (m-70) cc_final: 0.6057 (m-70) REVERT: B 721 ILE cc_start: 0.7764 (mm) cc_final: 0.7489 (pp) REVERT: A 413 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7964 (mtt-85) REVERT: A 422 HIS cc_start: 0.7267 (t-90) cc_final: 0.6583 (t-90) REVERT: A 490 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 521 GLU cc_start: 0.8224 (tt0) cc_final: 0.7552 (mt-10) REVERT: A 594 MET cc_start: 0.7265 (tmm) cc_final: 0.6735 (tpp) REVERT: D 262 LYS cc_start: 0.6081 (mptt) cc_final: 0.5583 (mmtm) REVERT: D 305 MET cc_start: 0.8644 (ttm) cc_final: 0.8394 (ttp) REVERT: D 572 ASP cc_start: 0.7992 (t70) cc_final: 0.7623 (m-30) outliers start: 18 outliers final: 6 residues processed: 203 average time/residue: 0.5971 time to fit residues: 133.5051 Evaluate side-chains 197 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 189 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 GLN B1006 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.097858 restraints weight = 16881.927| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.05 r_work: 0.2900 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15026 Z= 0.154 Angle : 0.474 5.056 20358 Z= 0.258 Chirality : 0.039 0.148 2276 Planarity : 0.004 0.048 2523 Dihedral : 3.769 17.328 1991 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.30 % Allowed : 10.73 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.19), residues: 1782 helix: 2.21 (0.15), residues: 1144 sheet: 1.50 (0.64), residues: 44 loop : 0.60 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 424 TYR 0.019 0.002 TYR A 349 PHE 0.020 0.002 PHE C 298 TRP 0.017 0.002 TRP C 168 HIS 0.005 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00342 (15026) covalent geometry : angle 0.47425 (20358) hydrogen bonds : bond 0.04076 ( 961) hydrogen bonds : angle 4.05516 ( 2769) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.549 Fit side-chains REVERT: C 234 LEU cc_start: 0.7553 (tp) cc_final: 0.7245 (tp) REVERT: C 445 LYS cc_start: 0.6971 (mmtm) cc_final: 0.6749 (mmtm) REVERT: C 471 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7716 (tt) REVERT: B 690 HIS cc_start: 0.6624 (m-70) cc_final: 0.6102 (m-70) REVERT: B 897 MET cc_start: 0.8648 (ttt) cc_final: 0.8381 (mtp) REVERT: A 337 ILE cc_start: 0.8245 (pt) cc_final: 0.7995 (pt) REVERT: A 413 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7835 (mtt-85) REVERT: A 422 HIS cc_start: 0.7224 (t-90) cc_final: 0.6539 (t-90) REVERT: A 490 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7214 (mm-30) REVERT: A 521 GLU cc_start: 0.8194 (tt0) cc_final: 0.7903 (tt0) REVERT: A 594 MET cc_start: 0.7113 (tmm) cc_final: 0.6609 (tpp) REVERT: D 262 LYS cc_start: 0.6236 (mptt) cc_final: 0.5676 (mmtm) REVERT: D 305 MET cc_start: 0.8512 (ttm) cc_final: 0.8267 (ttp) REVERT: D 572 ASP cc_start: 0.7932 (t70) cc_final: 0.7646 (m-30) outliers start: 21 outliers final: 10 residues processed: 205 average time/residue: 0.6162 time to fit residues: 138.3796 Evaluate side-chains 201 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 451 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 ASN B 969 GLN B1006 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.094646 restraints weight = 16727.766| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.04 r_work: 0.2830 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 15026 Z= 0.255 Angle : 0.587 6.350 20358 Z= 0.317 Chirality : 0.043 0.178 2276 Planarity : 0.005 0.046 2523 Dihedral : 4.206 18.417 1991 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.80 % Allowed : 10.79 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.19), residues: 1782 helix: 1.81 (0.14), residues: 1143 sheet: 1.52 (0.61), residues: 49 loop : 0.45 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 424 TYR 0.026 0.003 TYR C 349 PHE 0.027 0.003 PHE C 298 TRP 0.020 0.003 TRP A 168 HIS 0.008 0.002 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00584 (15026) covalent geometry : angle 0.58729 (20358) hydrogen bonds : bond 0.04813 ( 961) hydrogen bonds : angle 4.38439 ( 2769) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.579 Fit side-chains REVERT: C 234 LEU cc_start: 0.7538 (tp) cc_final: 0.7253 (tp) REVERT: C 445 LYS cc_start: 0.6930 (mmtm) cc_final: 0.6722 (mmtm) REVERT: C 471 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7723 (tt) REVERT: C 484 GLU cc_start: 0.6693 (tt0) cc_final: 0.6035 (tt0) REVERT: B 991 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7793 (mttp) REVERT: A 445 LYS cc_start: 0.7163 (mppt) cc_final: 0.6948 (mppt) REVERT: A 490 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 521 GLU cc_start: 0.8240 (tt0) cc_final: 0.7963 (tt0) REVERT: A 594 MET cc_start: 0.7070 (tmm) cc_final: 0.6585 (tpp) REVERT: D 262 LYS cc_start: 0.6348 (mptt) cc_final: 0.5724 (mmtm) REVERT: D 305 MET cc_start: 0.8488 (ttm) cc_final: 0.8238 (ttp) outliers start: 29 outliers final: 20 residues processed: 208 average time/residue: 0.6219 time to fit residues: 142.1443 Evaluate side-chains 202 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 608 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 ASN B 816 GLN B 969 GLN B1006 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098327 restraints weight = 16799.208| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.05 r_work: 0.2905 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15026 Z= 0.123 Angle : 0.459 5.392 20358 Z= 0.249 Chirality : 0.038 0.136 2276 Planarity : 0.003 0.045 2523 Dihedral : 3.884 18.883 1991 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.12 % Allowed : 11.85 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.19), residues: 1782 helix: 2.09 (0.15), residues: 1144 sheet: 1.56 (0.63), residues: 49 loop : 0.57 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.013 0.001 TYR A 349 PHE 0.016 0.001 PHE D 298 TRP 0.020 0.002 TRP C 168 HIS 0.005 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00270 (15026) covalent geometry : angle 0.45946 (20358) hydrogen bonds : bond 0.03898 ( 961) hydrogen bonds : angle 4.10156 ( 2769) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.707 Fit side-chains REVERT: C 234 LEU cc_start: 0.7483 (tp) cc_final: 0.7224 (tp) REVERT: C 305 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8078 (tmm) REVERT: C 471 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7679 (tt) REVERT: C 484 GLU cc_start: 0.6635 (tt0) cc_final: 0.5988 (tt0) REVERT: C 509 LYS cc_start: 0.7883 (mtpp) cc_final: 0.7589 (mtpp) REVERT: C 597 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6681 (tm-30) REVERT: B 991 LYS cc_start: 0.8343 (mtmm) cc_final: 0.7766 (mttp) REVERT: A 422 HIS cc_start: 0.7167 (t-90) cc_final: 0.6487 (t-90) REVERT: A 445 LYS cc_start: 0.7093 (mppt) cc_final: 0.6872 (mptt) REVERT: A 490 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7188 (mm-30) REVERT: A 521 GLU cc_start: 0.8191 (tt0) cc_final: 0.7937 (tt0) REVERT: A 594 MET cc_start: 0.7088 (tmm) cc_final: 0.6607 (tpp) REVERT: A 604 MET cc_start: 0.7275 (mtm) cc_final: 0.7014 (mtt) REVERT: D 262 LYS cc_start: 0.6364 (mptt) cc_final: 0.5731 (mmtm) REVERT: D 305 MET cc_start: 0.8533 (ttm) cc_final: 0.8298 (ttp) outliers start: 18 outliers final: 6 residues processed: 205 average time/residue: 0.6199 time to fit residues: 139.7259 Evaluate side-chains 195 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 608 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 21 optimal weight: 0.0020 chunk 159 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 HIS C 496 GLN ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 ASN B 969 GLN B1006 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN D 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.097488 restraints weight = 16817.123| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.03 r_work: 0.2892 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15026 Z= 0.146 Angle : 0.480 5.485 20358 Z= 0.260 Chirality : 0.039 0.146 2276 Planarity : 0.003 0.045 2523 Dihedral : 3.867 18.865 1991 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.30 % Allowed : 12.16 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.19), residues: 1782 helix: 2.11 (0.15), residues: 1144 sheet: 1.58 (0.62), residues: 49 loop : 0.54 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.018 0.002 TYR A 349 PHE 0.018 0.002 PHE C 298 TRP 0.018 0.002 TRP C 168 HIS 0.005 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00326 (15026) covalent geometry : angle 0.48032 (20358) hydrogen bonds : bond 0.04039 ( 961) hydrogen bonds : angle 4.10271 ( 2769) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.554 Fit side-chains REVERT: C 234 LEU cc_start: 0.7487 (tp) cc_final: 0.7227 (tp) REVERT: C 471 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7731 (tt) REVERT: C 484 GLU cc_start: 0.6672 (tt0) cc_final: 0.6003 (tt0) REVERT: C 509 LYS cc_start: 0.7876 (mtpp) cc_final: 0.7567 (mtpp) REVERT: C 597 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6681 (tm-30) REVERT: A 413 ARG cc_start: 0.8275 (mtt180) cc_final: 0.8025 (mtt-85) REVERT: A 422 HIS cc_start: 0.7196 (t-90) cc_final: 0.6529 (t-90) REVERT: A 445 LYS cc_start: 0.7092 (mppt) cc_final: 0.6868 (mptt) REVERT: A 490 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7164 (mm-30) REVERT: A 516 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8467 (ttt) REVERT: A 521 GLU cc_start: 0.8225 (tt0) cc_final: 0.7965 (tt0) REVERT: A 594 MET cc_start: 0.7090 (tmm) cc_final: 0.6607 (tpp) REVERT: D 262 LYS cc_start: 0.6340 (mptt) cc_final: 0.5710 (mmtm) REVERT: D 305 MET cc_start: 0.8505 (ttm) cc_final: 0.8260 (ttp) REVERT: D 572 ASP cc_start: 0.7906 (m-30) cc_final: 0.7678 (m-30) outliers start: 21 outliers final: 11 residues processed: 202 average time/residue: 0.6165 time to fit residues: 136.4507 Evaluate side-chains 195 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 536 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 2 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 146 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 683 GLN B 730 ASN B 969 GLN B1006 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.099160 restraints weight = 16858.717| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.04 r_work: 0.2932 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15026 Z= 0.109 Angle : 0.440 5.701 20358 Z= 0.239 Chirality : 0.038 0.137 2276 Planarity : 0.003 0.045 2523 Dihedral : 3.716 18.764 1991 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.18 % Allowed : 12.59 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.20), residues: 1782 helix: 2.27 (0.15), residues: 1142 sheet: 1.54 (0.63), residues: 49 loop : 0.58 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.014 0.001 TYR B 787 PHE 0.015 0.001 PHE C 298 TRP 0.020 0.001 TRP C 168 HIS 0.004 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00236 (15026) covalent geometry : angle 0.43983 (20358) hydrogen bonds : bond 0.03663 ( 961) hydrogen bonds : angle 3.98391 ( 2769) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.627 Fit side-chains REVERT: C 234 LEU cc_start: 0.7479 (tp) cc_final: 0.7217 (tp) REVERT: C 471 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7743 (tt) REVERT: C 509 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7568 (mtpp) REVERT: C 597 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6664 (tm-30) REVERT: B 1071 GLU cc_start: 0.7552 (mp0) cc_final: 0.7315 (tp30) REVERT: A 337 ILE cc_start: 0.8336 (pt) cc_final: 0.8033 (pt) REVERT: A 413 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7958 (mtt-85) REVERT: A 422 HIS cc_start: 0.7183 (t-90) cc_final: 0.6514 (t-90) REVERT: A 445 LYS cc_start: 0.7081 (mppt) cc_final: 0.6858 (mptt) REVERT: A 490 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7188 (mm-30) REVERT: A 521 GLU cc_start: 0.8185 (tt0) cc_final: 0.7921 (tt0) REVERT: A 594 MET cc_start: 0.7071 (tmm) cc_final: 0.6594 (tpp) REVERT: A 604 MET cc_start: 0.7272 (mtm) cc_final: 0.7016 (mtt) REVERT: D 233 GLU cc_start: 0.6420 (mm-30) cc_final: 0.6168 (mm-30) REVERT: D 262 LYS cc_start: 0.6356 (mptt) cc_final: 0.5723 (mmtm) REVERT: D 305 MET cc_start: 0.8499 (ttm) cc_final: 0.8279 (ttp) REVERT: D 572 ASP cc_start: 0.7775 (m-30) cc_final: 0.7565 (m-30) outliers start: 19 outliers final: 9 residues processed: 202 average time/residue: 0.6229 time to fit residues: 138.2959 Evaluate side-chains 196 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 536 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 64 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 GLN B1006 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.096718 restraints weight = 17054.830| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.08 r_work: 0.2911 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15026 Z= 0.118 Angle : 0.456 6.459 20358 Z= 0.246 Chirality : 0.038 0.140 2276 Planarity : 0.003 0.045 2523 Dihedral : 3.708 18.684 1991 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.05 % Allowed : 12.90 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.20), residues: 1782 helix: 2.26 (0.15), residues: 1146 sheet: 1.62 (0.64), residues: 49 loop : 0.59 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.015 0.001 TYR A 349 PHE 0.017 0.001 PHE A 285 TRP 0.018 0.002 TRP C 168 HIS 0.004 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00256 (15026) covalent geometry : angle 0.45619 (20358) hydrogen bonds : bond 0.03735 ( 961) hydrogen bonds : angle 3.97363 ( 2769) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.617 Fit side-chains REVERT: C 234 LEU cc_start: 0.7487 (tp) cc_final: 0.7223 (tp) REVERT: C 471 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7723 (tt) REVERT: C 509 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7600 (mtpp) REVERT: C 594 MET cc_start: 0.7080 (tmm) cc_final: 0.6713 (tmt) REVERT: C 597 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6675 (tm-30) REVERT: B 690 HIS cc_start: 0.6603 (m90) cc_final: 0.6232 (m-70) REVERT: A 337 ILE cc_start: 0.8344 (pt) cc_final: 0.8032 (pt) REVERT: A 413 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7968 (mtt-85) REVERT: A 422 HIS cc_start: 0.7237 (t-90) cc_final: 0.6559 (t-90) REVERT: A 445 LYS cc_start: 0.7100 (mppt) cc_final: 0.6844 (mptt) REVERT: A 490 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7144 (mm-30) REVERT: A 515 GLU cc_start: 0.7555 (pm20) cc_final: 0.7338 (mp0) REVERT: A 521 GLU cc_start: 0.8193 (tt0) cc_final: 0.7943 (tt0) REVERT: A 594 MET cc_start: 0.7132 (tmm) cc_final: 0.6641 (tpp) REVERT: A 604 MET cc_start: 0.7222 (mtm) cc_final: 0.6947 (mtt) REVERT: D 233 GLU cc_start: 0.6348 (mm-30) cc_final: 0.6086 (mm-30) REVERT: D 262 LYS cc_start: 0.6284 (mptt) cc_final: 0.5631 (mmtm) REVERT: D 305 MET cc_start: 0.8528 (ttm) cc_final: 0.8293 (ttp) REVERT: D 553 LYS cc_start: 0.4286 (tmtt) cc_final: 0.3858 (tmtt) outliers start: 17 outliers final: 12 residues processed: 197 average time/residue: 0.6347 time to fit residues: 137.2442 Evaluate side-chains 197 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 536 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN B 969 GLN B1006 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN D 496 GLN D 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.094131 restraints weight = 16711.269| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.09 r_work: 0.2851 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15026 Z= 0.198 Angle : 0.533 6.117 20358 Z= 0.289 Chirality : 0.041 0.153 2276 Planarity : 0.004 0.045 2523 Dihedral : 3.999 19.011 1991 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.12 % Allowed : 12.90 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.19), residues: 1782 helix: 2.03 (0.15), residues: 1143 sheet: 1.60 (0.61), residues: 49 loop : 0.52 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 424 TYR 0.023 0.002 TYR C 349 PHE 0.022 0.002 PHE C 298 TRP 0.017 0.002 TRP C 265 HIS 0.006 0.002 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00452 (15026) covalent geometry : angle 0.53332 (20358) hydrogen bonds : bond 0.04386 ( 961) hydrogen bonds : angle 4.21551 ( 2769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4764.51 seconds wall clock time: 81 minutes 58.45 seconds (4918.45 seconds total)