Starting phenix.real_space_refine on Mon Aug 25 19:50:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qgy_18396/08_2025/8qgy_18396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qgy_18396/08_2025/8qgy_18396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qgy_18396/08_2025/8qgy_18396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qgy_18396/08_2025/8qgy_18396.map" model { file = "/net/cci-nas-00/data/ceres_data/8qgy_18396/08_2025/8qgy_18396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qgy_18396/08_2025/8qgy_18396.cif" } resolution = 3.71 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6009 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 62 5.16 5 C 8184 2.51 5 N 2119 2.21 5 O 2379 1.98 5 H 12699 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.12s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25443 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 12499 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 26, 'TRANS': 753} Chain breaks: 4 Chain: "B" Number of atoms: 12944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 12944 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 29, 'TRANS': 779} Chain breaks: 2 Time building chain proxies: 4.20, per 1000 atoms: 0.17 Number of scatterers: 25443 At special positions: 0 Unit cell: (100.866, 115.87, 153.382, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 O 2379 8.00 N 2119 7.00 C 8184 6.00 H 12699 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 250 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 725.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3006 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 52.5% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.840A pdb=" N VAL A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 4.183A pdb=" N LEU A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.851A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N HIS A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 249 through 269 removed outlier: 4.181A pdb=" N SER A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 284 Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.512A pdb=" N ASN A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 removed outlier: 3.593A pdb=" N VAL A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.689A pdb=" N LYS A 352 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 353 " --> pdb=" O HIS A 349 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.775A pdb=" N LYS A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 386 through 404 removed outlier: 3.679A pdb=" N TYR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 426 Processing helix chain 'A' and resid 429 through 442 removed outlier: 4.073A pdb=" N ILE A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 467 removed outlier: 3.691A pdb=" N LYS A 458 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 489 removed outlier: 3.960A pdb=" N PHE A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 504 removed outlier: 3.563A pdb=" N GLN A 496 " --> pdb=" O MET A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 523 removed outlier: 3.709A pdb=" N LEU A 511 " --> pdb=" O PRO A 507 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 550 removed outlier: 3.707A pdb=" N THR A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 654 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 776 through 797 removed outlier: 4.505A pdb=" N ILE A 780 " --> pdb=" O ASN A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 854 Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 859 through 877 Processing helix chain 'A' and resid 908 through 919 Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 939 Processing helix chain 'B' and resid 103 through 109 removed outlier: 4.039A pdb=" N VAL B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 109' Processing helix chain 'B' and resid 109 through 123 removed outlier: 4.041A pdb=" N LEU B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.841A pdb=" N TYR B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 194 through 203 removed outlier: 3.553A pdb=" N ILE B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 269 Processing helix chain 'B' and resid 269 through 287 removed outlier: 4.483A pdb=" N SER B 275 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 304 Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.858A pdb=" N ASN B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 349 through 363 removed outlier: 3.561A pdb=" N HIS B 354 " --> pdb=" O HIS B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 381 Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 386 through 404 removed outlier: 3.947A pdb=" N TYR B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 404 " --> pdb=" O MET B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 426 removed outlier: 3.520A pdb=" N HIS B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 443 removed outlier: 4.005A pdb=" N ILE B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B 434 " --> pdb=" O GLN B 430 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 467 removed outlier: 4.168A pdb=" N VAL B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 488 Processing helix chain 'B' and resid 493 through 505 removed outlier: 3.540A pdb=" N ALA B 497 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 525 removed outlier: 3.516A pdb=" N ILE B 520 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 521 " --> pdb=" O THR B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 549 removed outlier: 3.575A pdb=" N ALA B 549 " --> pdb=" O PHE B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 653 Processing helix chain 'B' and resid 719 through 731 removed outlier: 4.333A pdb=" N HIS B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 769 Processing helix chain 'B' and resid 777 through 797 Processing helix chain 'B' and resid 822 through 826 removed outlier: 4.149A pdb=" N THR B 825 " --> pdb=" O ASP B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 852 Processing helix chain 'B' and resid 859 through 877 removed outlier: 3.874A pdb=" N ASP B 863 " --> pdb=" O GLY B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 898 Processing helix chain 'B' and resid 908 through 919 Processing helix chain 'B' and resid 928 through 934 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 155 removed outlier: 6.588A pdb=" N VAL A 154 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N CYS A 185 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE A 182 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR A 215 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TYR A 184 " --> pdb=" O TYR A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 565 removed outlier: 3.637A pdb=" N ILE A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 612 through 614 Processing sheet with id=AA5, first strand: chain 'A' and resid 673 through 675 removed outlier: 7.219A pdb=" N VAL A 694 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 673 through 675 removed outlier: 3.522A pdb=" N ILE A 693 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY A 742 " --> pdb=" O PHE A 753 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 760 through 761 removed outlier: 3.971A pdb=" N VAL A 817 " --> pdb=" O ASN A 812 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 799 through 800 Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.987A pdb=" N MET B 156 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 605 removed outlier: 4.088A pdb=" N GLU B 580 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B 585 " --> pdb=" O ASN B 578 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 609 through 614 removed outlier: 6.669A pdb=" N TYR B 625 " --> pdb=" O ARG B 610 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 612 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE B 623 " --> pdb=" O VAL B 612 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 673 through 674 removed outlier: 4.533A pdb=" N GLY B 742 " --> pdb=" O PHE B 753 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU B 755 " --> pdb=" O TYR B 740 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N TYR B 740 " --> pdb=" O GLU B 755 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 760 through 761 removed outlier: 4.102A pdb=" N GLY B 760 " --> pdb=" O ILE B 811 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 811 " --> pdb=" O GLY B 760 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1761 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: 4.74 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12669 1.03 - 1.23: 57 1.23 - 1.43: 5456 1.43 - 1.62: 7443 1.62 - 1.82: 94 Bond restraints: 25719 Sorted by residual: bond pdb=" N TYR B 95 " pdb=" CA TYR B 95 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N TYR B 95 " pdb=" H TYR B 95 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C PHE A 559 " pdb=" N PRO A 560 " ideal model delta sigma weight residual 1.335 1.347 -0.012 8.70e-03 1.32e+04 1.96e+00 bond pdb=" CA PHE B 272 " pdb=" CB PHE B 272 " ideal model delta sigma weight residual 1.535 1.555 -0.020 1.69e-02 3.50e+03 1.39e+00 bond pdb=" C LEU B 251 " pdb=" N PRO B 252 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.32e+00 ... (remaining 25714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.77: 46470 10.77 - 21.54: 2 21.54 - 32.32: 6 32.32 - 43.09: 24 43.09 - 53.86: 2 Bond angle restraints: 46504 Sorted by residual: angle pdb=" C LEU B 794 " pdb=" N HIS B 795 " pdb=" H HIS B 795 " ideal model delta sigma weight residual 125.00 71.15 53.86 3.00e+00 1.11e-01 3.22e+02 angle pdb=" CA HIS B 795 " pdb=" N HIS B 795 " pdb=" H HIS B 795 " ideal model delta sigma weight residual 114.70 61.11 53.59 3.00e+00 1.11e-01 3.19e+02 angle pdb=" C PRO B 855 " pdb=" CA PRO B 855 " pdb=" HA PRO B 855 " ideal model delta sigma weight residual 109.00 70.84 38.16 3.00e+00 1.11e-01 1.62e+02 angle pdb=" C PRO B 923 " pdb=" CA PRO B 923 " pdb=" HA PRO B 923 " ideal model delta sigma weight residual 109.00 71.54 37.46 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C PHE B 839 " pdb=" CA PHE B 839 " pdb=" HA PHE B 839 " ideal model delta sigma weight residual 109.00 72.58 36.42 3.00e+00 1.11e-01 1.47e+02 ... (remaining 46499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 11052 17.70 - 35.40: 718 35.40 - 53.11: 238 53.11 - 70.81: 72 70.81 - 88.51: 7 Dihedral angle restraints: 12087 sinusoidal: 6507 harmonic: 5580 Sorted by residual: dihedral pdb=" CA TYR A 521 " pdb=" C TYR A 521 " pdb=" N LYS A 522 " pdb=" CA LYS A 522 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C LEU A 402 " pdb=" N LEU A 402 " pdb=" CA LEU A 402 " pdb=" CB LEU A 402 " ideal model delta harmonic sigma weight residual -122.60 -132.87 10.27 0 2.50e+00 1.60e-01 1.69e+01 dihedral pdb=" C LEU A 519 " pdb=" N LEU A 519 " pdb=" CA LEU A 519 " pdb=" CB LEU A 519 " ideal model delta harmonic sigma weight residual -122.60 -132.35 9.75 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 12084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 1954 0.290 - 0.579: 9 0.579 - 0.869: 0 0.869 - 1.159: 0 1.159 - 1.448: 1 Chirality restraints: 1964 Sorted by residual: chirality pdb=" CB THR B 836 " pdb=" CA THR B 836 " pdb=" OG1 THR B 836 " pdb=" CG2 THR B 836 " both_signs ideal model delta sigma weight residual False 2.55 1.10 1.45 2.00e-01 2.50e+01 5.24e+01 chirality pdb=" CA PRO B 923 " pdb=" N PRO B 923 " pdb=" C PRO B 923 " pdb=" CB PRO B 923 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA GLU B 837 " pdb=" N GLU B 837 " pdb=" C GLU B 837 " pdb=" CB GLU B 837 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 1961 not shown) Planarity restraints: 3769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 162 " 0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO B 163 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 163 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 163 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 162 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 163 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 571 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO B 572 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 572 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 572 " 0.020 5.00e-02 4.00e+02 ... (remaining 3766 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1057 2.19 - 2.79: 51948 2.79 - 3.40: 70613 3.40 - 4.00: 88251 4.00 - 4.60: 137085 Nonbonded interactions: 348954 Sorted by model distance: nonbonded pdb=" H HIS B 795 " pdb=" HA HIS B 795 " model vdw 1.591 1.816 nonbonded pdb=" H GLU B 837 " pdb=" HA GLU B 837 " model vdw 1.610 1.816 nonbonded pdb=" H THR B 836 " pdb=" HA THR B 836 " model vdw 1.613 1.816 nonbonded pdb=" H PHE B 839 " pdb=" HA PHE B 839 " model vdw 1.656 1.816 nonbonded pdb=" HA LEU A 519 " pdb=" HB2 LEU A 519 " model vdw 1.691 1.952 ... (remaining 348949 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 95 through 225 or resid 247 through 653 or resid 670 throu \ gh 940)) selection = (chain 'B' and (resid 95 through 830 or resid 844 through 879 or resid 900 throu \ gh 940)) } 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 group one per residue 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.120 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.420 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 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 0.035 13021 Z= 0.144 Angle : 0.616 11.966 17606 Z= 0.334 Chirality : 0.058 1.448 1964 Planarity : 0.004 0.051 2243 Dihedral : 11.945 77.328 4810 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.17 % Favored : 93.77 % Rotamer: Outliers : 3.91 % Allowed : 5.41 % Favored : 90.68 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: 0.12 (0.22), residues: 1573 helix: 1.81 (0.19), residues: 729 sheet: -1.22 (0.39), residues: 170 loop : -1.57 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 161 TYR 0.014 0.001 TYR B 167 PHE 0.016 0.001 PHE B 212 TRP 0.006 0.001 TRP B 476 HIS 0.005 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00320 (13020) covalent geometry : angle 0.61562 (17604) SS BOND : bond 0.00388 ( 1) SS BOND : angle 0.98460 ( 2) hydrogen bonds : bond 0.17832 ( 600) hydrogen bonds : angle 6.48134 ( 1761) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.7314 (tttt) cc_final: 0.7088 (tttm) REVERT: A 493 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7225 (mmt-90) REVERT: A 605 SER cc_start: 0.7893 (m) cc_final: 0.7509 (t) REVERT: A 614 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7947 (mt) REVERT: A 858 TYR cc_start: 0.6884 (m-80) cc_final: 0.6626 (m-80) REVERT: B 102 GLN cc_start: 0.5440 (OUTLIER) cc_final: 0.5203 (pm20) REVERT: B 201 GLN cc_start: 0.7619 (mm110) cc_final: 0.7284 (mm110) REVERT: B 287 TYR cc_start: 0.7521 (m-80) cc_final: 0.7310 (m-10) REVERT: B 290 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7211 (pmmt) REVERT: B 649 MET cc_start: 0.7340 (mtm) cc_final: 0.6973 (mtt) REVERT: B 694 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8176 (p) REVERT: B 698 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6366 (ptp-110) outliers start: 55 outliers final: 24 residues processed: 266 average time/residue: 0.2745 time to fit residues: 101.0408 Evaluate side-chains 183 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 698 ARG Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN A 360 ASN A 808 ASN B 325 GLN B 360 ASN B 430 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.139455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.113983 restraints weight = 95630.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.115952 restraints weight = 48287.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.117083 restraints weight = 37987.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.117790 restraints weight = 31690.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.117873 restraints weight = 30509.657| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13021 Z= 0.142 Angle : 0.556 12.555 17606 Z= 0.305 Chirality : 0.060 1.655 1964 Planarity : 0.004 0.045 2243 Dihedral : 6.648 59.313 1780 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.20 % Allowed : 10.39 % Favored : 86.41 % 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 aren not related in a simple way. whole: 0.22 (0.22), residues: 1573 helix: 1.82 (0.19), residues: 756 sheet: -1.25 (0.38), residues: 167 loop : -1.55 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 802 TYR 0.016 0.001 TYR B 167 PHE 0.016 0.001 PHE B 914 TRP 0.008 0.001 TRP A 589 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00311 (13020) covalent geometry : angle 0.55598 (17604) SS BOND : bond 0.00702 ( 1) SS BOND : angle 0.67399 ( 2) hydrogen bonds : bond 0.04636 ( 600) hydrogen bonds : angle 5.42338 ( 1761) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7416 (mmtt) REVERT: A 420 LYS cc_start: 0.7859 (tttt) cc_final: 0.7578 (tttm) REVERT: A 493 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7548 (mmt180) REVERT: A 605 SER cc_start: 0.8292 (m) cc_final: 0.7771 (t) REVERT: A 858 TYR cc_start: 0.6992 (m-80) cc_final: 0.6741 (m-80) REVERT: B 201 GLN cc_start: 0.7622 (mm110) cc_final: 0.7278 (mm110) REVERT: B 216 MET cc_start: 0.2563 (mpp) cc_final: 0.2342 (mpp) REVERT: B 434 ASN cc_start: 0.7037 (OUTLIER) cc_final: 0.6530 (m-40) REVERT: B 694 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8081 (p) REVERT: B 883 GLU cc_start: 0.7670 (pm20) cc_final: 0.7296 (pm20) outliers start: 45 outliers final: 27 residues processed: 198 average time/residue: 0.2597 time to fit residues: 71.3440 Evaluate side-chains 167 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 141 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN B 360 ASN B 430 GLN B 523 HIS B 579 ASN B 776 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.136496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.109968 restraints weight = 95778.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.112535 restraints weight = 49706.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.113399 restraints weight = 37453.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.113864 restraints weight = 33365.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.113987 restraints weight = 31125.852| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13021 Z= 0.179 Angle : 0.571 12.084 17606 Z= 0.315 Chirality : 0.059 1.542 1964 Planarity : 0.004 0.042 2243 Dihedral : 6.298 57.466 1759 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.99 % Allowed : 11.96 % Favored : 85.05 % 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 aren not related in a simple way. whole: -0.18 (0.21), residues: 1573 helix: 1.53 (0.19), residues: 759 sheet: -1.47 (0.38), residues: 163 loop : -1.82 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 395 TYR 0.028 0.001 TYR B 147 PHE 0.018 0.002 PHE B 541 TRP 0.008 0.001 TRP A 509 HIS 0.005 0.001 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00392 (13020) covalent geometry : angle 0.57058 (17604) SS BOND : bond 0.01439 ( 1) SS BOND : angle 1.62543 ( 2) hydrogen bonds : bond 0.04236 ( 600) hydrogen bonds : angle 5.30091 ( 1761) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7404 (mmtt) REVERT: A 420 LYS cc_start: 0.7957 (tttt) cc_final: 0.7604 (tttm) REVERT: A 471 LYS cc_start: 0.8299 (ttpp) cc_final: 0.8085 (tmtt) REVERT: A 493 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7969 (mpt-90) REVERT: A 605 SER cc_start: 0.8216 (m) cc_final: 0.7663 (t) REVERT: A 858 TYR cc_start: 0.7045 (m-80) cc_final: 0.6764 (m-80) REVERT: B 201 GLN cc_start: 0.7745 (mm110) cc_final: 0.7543 (mp10) REVERT: B 314 VAL cc_start: 0.6695 (OUTLIER) cc_final: 0.6490 (p) REVERT: B 434 ASN cc_start: 0.7155 (OUTLIER) cc_final: 0.6899 (m-40) REVERT: B 694 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8204 (p) outliers start: 42 outliers final: 29 residues processed: 183 average time/residue: 0.2922 time to fit residues: 74.6580 Evaluate side-chains 169 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 148 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 131 HIS A 808 ASN B 360 ASN B 430 GLN B 776 ASN B 795 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.137003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.109578 restraints weight = 95352.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.113355 restraints weight = 49523.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.115850 restraints weight = 33600.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.117371 restraints weight = 26481.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.118322 restraints weight = 22886.111| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13021 Z= 0.136 Angle : 0.542 11.897 17606 Z= 0.296 Chirality : 0.058 1.493 1964 Planarity : 0.004 0.040 2243 Dihedral : 6.172 57.179 1756 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.06 % Favored : 92.88 % Rotamer: Outliers : 2.78 % Allowed : 12.95 % Favored : 84.27 % 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 aren not related in a simple way. whole: -0.09 (0.22), residues: 1573 helix: 1.69 (0.19), residues: 755 sheet: -1.49 (0.38), residues: 163 loop : -1.84 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 717 TYR 0.017 0.001 TYR B 167 PHE 0.014 0.001 PHE B 541 TRP 0.007 0.001 TRP A 509 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00300 (13020) covalent geometry : angle 0.54056 (17604) SS BOND : bond 0.01448 ( 1) SS BOND : angle 3.46969 ( 2) hydrogen bonds : bond 0.03807 ( 600) hydrogen bonds : angle 5.10696 ( 1761) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 SER cc_start: 0.3064 (OUTLIER) cc_final: 0.2810 (p) REVERT: A 420 LYS cc_start: 0.7878 (tttt) cc_final: 0.7528 (tttm) REVERT: A 471 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8082 (tmtt) REVERT: A 493 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7931 (mpt-90) REVERT: A 605 SER cc_start: 0.8175 (m) cc_final: 0.7731 (t) REVERT: A 858 TYR cc_start: 0.6886 (m-80) cc_final: 0.6678 (m-80) REVERT: B 197 GLU cc_start: 0.7415 (tp30) cc_final: 0.6817 (tp30) REVERT: B 314 VAL cc_start: 0.6793 (OUTLIER) cc_final: 0.6591 (p) REVERT: B 477 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7918 (mm-30) REVERT: B 694 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8186 (p) outliers start: 39 outliers final: 32 residues processed: 180 average time/residue: 0.2672 time to fit residues: 68.4333 Evaluate side-chains 169 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 64 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 0.0770 chunk 68 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 808 ASN B 162 GLN B 360 ASN B 430 GLN B 776 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.136288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.110469 restraints weight = 95812.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.112250 restraints weight = 53346.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.114257 restraints weight = 39791.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.114688 restraints weight = 36063.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.114606 restraints weight = 31862.832| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13021 Z= 0.156 Angle : 0.553 11.905 17606 Z= 0.303 Chirality : 0.058 1.486 1964 Planarity : 0.004 0.042 2243 Dihedral : 6.190 59.215 1756 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.06 % Favored : 92.88 % Rotamer: Outliers : 3.35 % Allowed : 13.17 % Favored : 83.49 % 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 aren not related in a simple way. whole: -0.16 (0.22), residues: 1573 helix: 1.66 (0.19), residues: 756 sheet: -1.55 (0.38), residues: 164 loop : -1.91 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 395 TYR 0.019 0.001 TYR B 167 PHE 0.016 0.002 PHE B 541 TRP 0.008 0.001 TRP A 509 HIS 0.005 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00344 (13020) covalent geometry : angle 0.55272 (17604) SS BOND : bond 0.00712 ( 1) SS BOND : angle 1.57254 ( 2) hydrogen bonds : bond 0.03767 ( 600) hydrogen bonds : angle 5.09109 ( 1761) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.7946 (tttt) cc_final: 0.7587 (tttm) REVERT: A 471 LYS cc_start: 0.8315 (ttpp) cc_final: 0.8102 (tmtt) REVERT: A 493 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7948 (mpt-90) REVERT: A 605 SER cc_start: 0.8199 (m) cc_final: 0.7699 (t) REVERT: A 858 TYR cc_start: 0.7055 (m-80) cc_final: 0.6804 (m-80) REVERT: A 864 ILE cc_start: 0.7447 (mm) cc_final: 0.7167 (mm) REVERT: B 168 HIS cc_start: 0.5577 (OUTLIER) cc_final: 0.5322 (p-80) REVERT: B 364 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5897 (mm) REVERT: B 434 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6853 (m-40) REVERT: B 511 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5820 (tt) REVERT: B 694 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8174 (p) REVERT: B 883 GLU cc_start: 0.7739 (pm20) cc_final: 0.7500 (pm20) outliers start: 47 outliers final: 34 residues processed: 183 average time/residue: 0.2627 time to fit residues: 68.5487 Evaluate side-chains 175 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 92 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 808 ASN B 360 ASN B 430 GLN B 776 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.136210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.109847 restraints weight = 94289.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.113348 restraints weight = 50507.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.115632 restraints weight = 34786.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.116953 restraints weight = 27686.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.117859 restraints weight = 24179.324| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13021 Z= 0.140 Angle : 0.543 11.947 17606 Z= 0.296 Chirality : 0.058 1.497 1964 Planarity : 0.003 0.034 2243 Dihedral : 6.013 58.939 1754 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.63 % Favored : 92.31 % Rotamer: Outliers : 3.20 % Allowed : 13.52 % Favored : 83.27 % 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 aren not related in a simple way. whole: -0.10 (0.22), residues: 1573 helix: 1.72 (0.19), residues: 755 sheet: -1.50 (0.38), residues: 163 loop : -1.90 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 300 TYR 0.018 0.001 TYR B 167 PHE 0.022 0.002 PHE A 480 TRP 0.008 0.001 TRP A 509 HIS 0.005 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00311 (13020) covalent geometry : angle 0.54283 (17604) SS BOND : bond 0.00567 ( 1) SS BOND : angle 1.03214 ( 2) hydrogen bonds : bond 0.03634 ( 600) hydrogen bonds : angle 4.98076 ( 1761) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LEU cc_start: 0.8915 (tp) cc_final: 0.8640 (tt) REVERT: A 420 LYS cc_start: 0.7860 (tttt) cc_final: 0.7524 (tttm) REVERT: A 471 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8101 (tmtt) REVERT: A 493 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8022 (mpt-90) REVERT: A 605 SER cc_start: 0.8179 (m) cc_final: 0.7762 (t) REVERT: B 168 HIS cc_start: 0.5618 (OUTLIER) cc_final: 0.5349 (p-80) REVERT: B 434 ASN cc_start: 0.7171 (OUTLIER) cc_final: 0.6821 (m-40) REVERT: B 511 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5902 (tt) REVERT: B 603 ASN cc_start: 0.7498 (m-40) cc_final: 0.7163 (t0) REVERT: B 694 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 883 GLU cc_start: 0.7536 (pm20) cc_final: 0.7275 (pm20) outliers start: 45 outliers final: 33 residues processed: 177 average time/residue: 0.2860 time to fit residues: 71.5585 Evaluate side-chains 172 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 139 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 808 ASN B 360 ASN B 430 GLN B 776 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.136278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.111270 restraints weight = 94474.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.113072 restraints weight = 51371.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.113952 restraints weight = 40497.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.114064 restraints weight = 35692.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.114259 restraints weight = 34223.278| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13021 Z= 0.137 Angle : 0.543 11.990 17606 Z= 0.296 Chirality : 0.058 1.499 1964 Planarity : 0.003 0.031 2243 Dihedral : 5.984 59.026 1754 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.50 % Favored : 92.43 % Rotamer: Outliers : 3.63 % Allowed : 13.31 % Favored : 83.06 % 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 aren not related in a simple way. whole: -0.08 (0.22), residues: 1573 helix: 1.74 (0.19), residues: 756 sheet: -1.49 (0.38), residues: 163 loop : -1.90 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 300 TYR 0.018 0.001 TYR B 167 PHE 0.015 0.001 PHE B 541 TRP 0.008 0.001 TRP A 509 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00302 (13020) covalent geometry : angle 0.54108 (17604) SS BOND : bond 0.00848 ( 1) SS BOND : angle 4.48556 ( 2) hydrogen bonds : bond 0.03593 ( 600) hydrogen bonds : angle 4.91991 ( 1761) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7247 (tmm) cc_final: 0.7006 (tmm) REVERT: A 302 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6961 (pmm-80) REVERT: A 359 LEU cc_start: 0.8978 (tp) cc_final: 0.8701 (tt) REVERT: A 420 LYS cc_start: 0.7867 (tttt) cc_final: 0.7537 (tttm) REVERT: A 471 LYS cc_start: 0.8333 (ttpp) cc_final: 0.8108 (tmtt) REVERT: A 493 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7838 (mmt90) REVERT: A 543 MET cc_start: 0.7719 (mmm) cc_final: 0.7132 (mmp) REVERT: A 605 SER cc_start: 0.8175 (m) cc_final: 0.7656 (t) REVERT: B 168 HIS cc_start: 0.5481 (OUTLIER) cc_final: 0.5250 (p-80) REVERT: B 434 ASN cc_start: 0.7223 (OUTLIER) cc_final: 0.6838 (m-40) REVERT: B 511 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5946 (tt) REVERT: B 603 ASN cc_start: 0.7795 (m-40) cc_final: 0.7385 (t0) REVERT: B 694 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8187 (p) REVERT: B 883 GLU cc_start: 0.7710 (pm20) cc_final: 0.7391 (pm20) outliers start: 51 outliers final: 34 residues processed: 180 average time/residue: 0.2631 time to fit residues: 66.5925 Evaluate side-chains 171 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN A 808 ASN B 360 ASN B 430 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.136922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.112357 restraints weight = 93491.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.114452 restraints weight = 57434.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.115756 restraints weight = 37328.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.116091 restraints weight = 31272.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.116430 restraints weight = 30420.146| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13021 Z= 0.119 Angle : 0.533 11.931 17606 Z= 0.289 Chirality : 0.058 1.501 1964 Planarity : 0.003 0.033 2243 Dihedral : 5.694 59.058 1750 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.18 % Favored : 92.75 % Rotamer: Outliers : 2.99 % Allowed : 14.23 % Favored : 82.78 % 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 aren not related in a simple way. whole: 0.01 (0.22), residues: 1573 helix: 1.82 (0.19), residues: 756 sheet: -1.52 (0.38), residues: 164 loop : -1.84 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 300 TYR 0.017 0.001 TYR B 167 PHE 0.014 0.001 PHE B 541 TRP 0.007 0.001 TRP A 509 HIS 0.003 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00265 (13020) covalent geometry : angle 0.53194 (17604) SS BOND : bond 0.00912 ( 1) SS BOND : angle 2.96323 ( 2) hydrogen bonds : bond 0.03441 ( 600) hydrogen bonds : angle 4.82115 ( 1761) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6897 (pmm-80) REVERT: A 359 LEU cc_start: 0.8940 (tp) cc_final: 0.8670 (tt) REVERT: A 420 LYS cc_start: 0.7807 (tttt) cc_final: 0.7498 (tttm) REVERT: A 471 LYS cc_start: 0.8309 (ttpp) cc_final: 0.8081 (tmtt) REVERT: A 493 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7811 (mpt-90) REVERT: A 605 SER cc_start: 0.8106 (m) cc_final: 0.7567 (t) REVERT: B 434 ASN cc_start: 0.7219 (OUTLIER) cc_final: 0.6823 (m-40) REVERT: B 511 LEU cc_start: 0.6286 (OUTLIER) cc_final: 0.6053 (tt) REVERT: B 603 ASN cc_start: 0.7669 (m-40) cc_final: 0.7276 (t0) REVERT: B 694 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8173 (p) REVERT: B 883 GLU cc_start: 0.7680 (pm20) cc_final: 0.7411 (pm20) outliers start: 42 outliers final: 31 residues processed: 175 average time/residue: 0.2590 time to fit residues: 63.5346 Evaluate side-chains 166 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 148 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 808 ASN B 131 HIS B 360 ASN B 430 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.135375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.110830 restraints weight = 93853.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.112808 restraints weight = 58566.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.114194 restraints weight = 38049.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.114502 restraints weight = 31710.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.114856 restraints weight = 32240.851| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13021 Z= 0.165 Angle : 0.571 12.040 17606 Z= 0.311 Chirality : 0.058 1.500 1964 Planarity : 0.004 0.040 2243 Dihedral : 5.799 59.084 1750 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.50 % Favored : 92.43 % Rotamer: Outliers : 3.56 % Allowed : 13.67 % Favored : 82.78 % 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 aren not related in a simple way. whole: -0.20 (0.22), residues: 1573 helix: 1.65 (0.19), residues: 755 sheet: -1.55 (0.38), residues: 165 loop : -1.97 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.020 0.001 TYR B 167 PHE 0.015 0.002 PHE B 541 TRP 0.008 0.001 TRP A 509 HIS 0.005 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00367 (13020) covalent geometry : angle 0.57007 (17604) SS BOND : bond 0.00815 ( 1) SS BOND : angle 2.39077 ( 2) hydrogen bonds : bond 0.03656 ( 600) hydrogen bonds : angle 4.97120 ( 1761) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LEU cc_start: 0.8973 (tp) cc_final: 0.8698 (tt) REVERT: A 420 LYS cc_start: 0.7906 (tttt) cc_final: 0.7552 (tttm) REVERT: A 493 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7851 (mmt90) REVERT: A 605 SER cc_start: 0.8130 (m) cc_final: 0.7590 (t) REVERT: B 434 ASN cc_start: 0.7323 (OUTLIER) cc_final: 0.6883 (m-40) REVERT: B 511 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6190 (tt) REVERT: B 694 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8202 (p) REVERT: B 883 GLU cc_start: 0.7693 (pm20) cc_final: 0.7426 (pm20) outliers start: 50 outliers final: 37 residues processed: 184 average time/residue: 0.2539 time to fit residues: 66.4675 Evaluate side-chains 175 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 808 ASN B 131 HIS B 360 ASN B 430 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.136598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.111905 restraints weight = 93489.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.113693 restraints weight = 52807.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.113828 restraints weight = 41263.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.114464 restraints weight = 39877.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.114665 restraints weight = 35912.390| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13021 Z= 0.114 Angle : 0.547 11.973 17606 Z= 0.296 Chirality : 0.058 1.505 1964 Planarity : 0.004 0.036 2243 Dihedral : 5.668 59.370 1750 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.69 % Rotamer: Outliers : 2.85 % Allowed : 14.66 % Favored : 82.49 % 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 aren not related in a simple way. whole: -0.04 (0.22), residues: 1573 helix: 1.78 (0.19), residues: 756 sheet: -1.54 (0.38), residues: 166 loop : -1.87 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 300 TYR 0.017 0.001 TYR B 167 PHE 0.014 0.001 PHE B 541 TRP 0.008 0.001 TRP A 509 HIS 0.007 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00256 (13020) covalent geometry : angle 0.54659 (17604) SS BOND : bond 0.00765 ( 1) SS BOND : angle 2.23485 ( 2) hydrogen bonds : bond 0.03412 ( 600) hydrogen bonds : angle 4.81368 ( 1761) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LEU cc_start: 0.8968 (tp) cc_final: 0.8711 (tt) REVERT: A 420 LYS cc_start: 0.7877 (tttt) cc_final: 0.7528 (tttm) REVERT: A 471 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8131 (tmtt) REVERT: A 493 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7821 (mmt90) REVERT: A 605 SER cc_start: 0.8101 (m) cc_final: 0.7558 (t) REVERT: A 744 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6145 (p90) REVERT: B 434 ASN cc_start: 0.7280 (OUTLIER) cc_final: 0.6661 (m-40) REVERT: B 511 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6158 (tt) REVERT: B 603 ASN cc_start: 0.7750 (m-40) cc_final: 0.7307 (t0) REVERT: B 694 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8214 (p) REVERT: B 883 GLU cc_start: 0.7778 (pm20) cc_final: 0.7520 (pm20) outliers start: 40 outliers final: 31 residues processed: 172 average time/residue: 0.2431 time to fit residues: 59.0614 Evaluate side-chains 165 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 808 ASN B 360 ASN B 430 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.137197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.111642 restraints weight = 92612.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.114468 restraints weight = 53021.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.115274 restraints weight = 37425.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.116033 restraints weight = 32656.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.116130 restraints weight = 31737.741| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13021 Z= 0.106 Angle : 0.545 11.841 17606 Z= 0.293 Chirality : 0.058 1.519 1964 Planarity : 0.004 0.055 2243 Dihedral : 5.537 59.457 1748 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.80 % Favored : 93.13 % Rotamer: Outliers : 2.70 % Allowed : 15.02 % Favored : 82.28 % 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 aren not related in a simple way. whole: 0.07 (0.22), residues: 1573 helix: 1.88 (0.19), residues: 756 sheet: -1.48 (0.38), residues: 166 loop : -1.83 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 395 TYR 0.017 0.001 TYR B 167 PHE 0.014 0.001 PHE B 604 TRP 0.007 0.001 TRP A 509 HIS 0.010 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00238 (13020) covalent geometry : angle 0.54429 (17604) SS BOND : bond 0.00699 ( 1) SS BOND : angle 2.00245 ( 2) hydrogen bonds : bond 0.03306 ( 600) hydrogen bonds : angle 4.72941 ( 1761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3996.39 seconds wall clock time: 68 minutes 59.54 seconds (4139.54 seconds total)