Starting phenix.real_space_refine on Thu Jul 31 22:09:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rot_19404/07_2025/8rot_19404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rot_19404/07_2025/8rot_19404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rot_19404/07_2025/8rot_19404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rot_19404/07_2025/8rot_19404.map" model { file = "/net/cci-nas-00/data/ceres_data/8rot_19404/07_2025/8rot_19404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rot_19404/07_2025/8rot_19404.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 8656 2.51 5 N 2574 2.21 5 O 2568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13838 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 6919 Classifications: {'peptide': 897} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 847} Chain: "A" Number of atoms: 6919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 6919 Classifications: {'peptide': 897} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 847} Time building chain proxies: 11.66, per 1000 atoms: 0.84 Number of scatterers: 13838 At special positions: 0 Unit cell: (96.2838, 107.915, 129.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 2568 8.00 N 2574 7.00 C 8656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 479 " distance=2.04 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 763 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 763 " 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: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 6 sheets defined 63.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'B' and resid 143 through 154 Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.572A pdb=" N THR B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 183 removed outlier: 4.384A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 208 through 230 removed outlier: 4.206A pdb=" N GLU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 266 through 281 Processing helix chain 'B' and resid 283 through 304 removed outlier: 3.713A pdb=" N LYS B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.649A pdb=" N LEU B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 352 removed outlier: 3.879A pdb=" N VAL B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 365 Processing helix chain 'B' and resid 368 through 385 Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 388 through 402 removed outlier: 4.202A pdb=" N ASP B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 422 through 430 Processing helix chain 'B' and resid 435 through 453 removed outlier: 3.725A pdb=" N GLN B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 474 removed outlier: 3.613A pdb=" N LEU B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 493 removed outlier: 3.663A pdb=" N CYS B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 481 " --> pdb=" O TYR B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 511 Processing helix chain 'B' and resid 515 through 532 Processing helix chain 'B' and resid 534 through 549 Processing helix chain 'B' and resid 553 through 570 removed outlier: 3.713A pdb=" N ARG B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.662A pdb=" N THR B 586 " --> pdb=" O ARG B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 609 through 621 Processing helix chain 'B' and resid 625 through 644 removed outlier: 4.418A pdb=" N GLU B 642 " --> pdb=" O ARG B 638 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 643 " --> pdb=" O ILE B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 660 Processing helix chain 'B' and resid 666 through 687 removed outlier: 3.578A pdb=" N THR B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 701 removed outlier: 3.758A pdb=" N ALA B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 694 " --> pdb=" O PHE B 690 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 762 removed outlier: 3.972A pdb=" N ALA B 762 " --> pdb=" O ALA B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 818 removed outlier: 3.529A pdb=" N ARG B 817 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 818 " --> pdb=" O GLU B 815 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 814 through 818' Processing helix chain 'B' and resid 838 through 842 removed outlier: 3.774A pdb=" N ALA B 842 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 852 removed outlier: 3.774A pdb=" N SER B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 894 Processing helix chain 'B' and resid 921 through 930 Processing helix chain 'B' and resid 945 through 960 Processing helix chain 'B' and resid 962 through 977 Processing helix chain 'B' and resid 980 through 985 removed outlier: 3.651A pdb=" N VAL B 984 " --> pdb=" O ASP B 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.700A pdb=" N THR A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.501A pdb=" N ALA A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 205 removed outlier: 3.580A pdb=" N LYS A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 230 removed outlier: 4.308A pdb=" N GLU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 266 through 281 Processing helix chain 'A' and resid 282 through 304 removed outlier: 4.163A pdb=" N ARG A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 318 through 329 removed outlier: 4.506A pdb=" N ARG A 322 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 357 through 367 removed outlier: 3.565A pdb=" N ARG A 367 " --> pdb=" O GLN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 384 removed outlier: 3.887A pdb=" N ARG A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Proline residue: A 374 - end of helix removed outlier: 3.617A pdb=" N GLN A 378 " --> pdb=" O PRO A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 401 removed outlier: 4.116A pdb=" N ASP A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.658A pdb=" N ALA A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 435 through 453 removed outlier: 3.610A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 459 through 474 removed outlier: 3.915A pdb=" N LEU A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 493 removed outlier: 3.687A pdb=" N CYS A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 481 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 511 Processing helix chain 'A' and resid 515 through 532 Processing helix chain 'A' and resid 534 through 549 Processing helix chain 'A' and resid 554 through 570 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 609 through 621 Processing helix chain 'A' and resid 625 through 641 Processing helix chain 'A' and resid 644 through 660 Processing helix chain 'A' and resid 666 through 688 Processing helix chain 'A' and resid 690 through 702 removed outlier: 4.072A pdb=" N LEU A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 843 through 852 removed outlier: 3.825A pdb=" N SER A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 894 Processing helix chain 'A' and resid 921 through 930 Processing helix chain 'A' and resid 945 through 960 Processing helix chain 'A' and resid 962 through 977 Processing helix chain 'A' and resid 980 through 985 removed outlier: 4.043A pdb=" N VAL A 984 " --> pdb=" O ASP A 980 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 731 through 736 removed outlier: 3.559A pdb=" N VAL B 710 " --> pdb=" O ARG B 725 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 711 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 833 through 836 removed outlier: 4.453A pdb=" N GLU B 856 " --> pdb=" O THR B 804 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 857 " --> pdb=" O LEU B 901 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 902 " --> pdb=" O LEU B 935 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA B 937 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B 904 " --> pdb=" O ALA B 937 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 862 through 865 removed outlier: 4.305A pdb=" N HIS B 862 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 731 through 736 removed outlier: 6.655A pdb=" N LEU A 711 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 833 through 839 removed outlier: 6.595A pdb=" N HIS A 805 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU A 837 " --> pdb=" O HIS A 805 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 807 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP A 839 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASN A 809 " --> pdb=" O ASP A 839 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU A 856 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 857 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 902 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA A 937 " --> pdb=" O VAL A 902 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 904 " --> pdb=" O ALA A 937 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 865 removed outlier: 4.286A pdb=" N HIS A 862 " --> pdb=" O LEU A 875 " (cutoff:3.500A) 806 hydrogen bonds defined for protein. 2406 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: 4.73 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4877 1.34 - 1.47: 3004 1.47 - 1.59: 6165 1.59 - 1.71: 0 1.71 - 1.83: 68 Bond restraints: 14114 Sorted by residual: bond pdb=" CB CYS A 470 " pdb=" SG CYS A 470 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.89e+00 bond pdb=" CB GLU A 908 " pdb=" CG GLU A 908 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" CB PHE A 949 " pdb=" CG PHE A 949 " ideal model delta sigma weight residual 1.502 1.527 -0.025 2.30e-02 1.89e+03 1.19e+00 bond pdb=" C ARG A 911 " pdb=" N PRO A 912 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.17e+00 bond pdb=" CA ARG A 474 " pdb=" C ARG A 474 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.34e-02 5.57e+03 1.11e+00 ... (remaining 14109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 18914 1.92 - 3.84: 232 3.84 - 5.76: 39 5.76 - 7.68: 11 7.68 - 9.61: 8 Bond angle restraints: 19204 Sorted by residual: angle pdb=" CB GLU A 908 " pdb=" CG GLU A 908 " pdb=" CD GLU A 908 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CA GLU A 908 " pdb=" CB GLU A 908 " pdb=" CG GLU A 908 " ideal model delta sigma weight residual 114.10 119.81 -5.71 2.00e+00 2.50e-01 8.15e+00 angle pdb=" CA LEU A 312 " pdb=" CB LEU A 312 " pdb=" CG LEU A 312 " ideal model delta sigma weight residual 116.30 125.89 -9.59 3.50e+00 8.16e-02 7.51e+00 angle pdb=" CA LEU A 475 " pdb=" CB LEU A 475 " pdb=" CG LEU A 475 " ideal model delta sigma weight residual 116.30 125.83 -9.53 3.50e+00 8.16e-02 7.41e+00 angle pdb=" CA GLU A 704 " pdb=" CB GLU A 704 " pdb=" CG GLU A 704 " ideal model delta sigma weight residual 114.10 119.39 -5.29 2.00e+00 2.50e-01 6.99e+00 ... (remaining 19199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7368 17.91 - 35.83: 940 35.83 - 53.74: 238 53.74 - 71.65: 46 71.65 - 89.56: 18 Dihedral angle restraints: 8610 sinusoidal: 3406 harmonic: 5204 Sorted by residual: dihedral pdb=" CB CYS B 470 " pdb=" SG CYS B 470 " pdb=" SG CYS B 479 " pdb=" CB CYS B 479 " ideal model delta sinusoidal sigma weight residual 93.00 17.75 75.25 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CA ARG A 911 " pdb=" C ARG A 911 " pdb=" N PRO A 912 " pdb=" CA PRO A 912 " ideal model delta harmonic sigma weight residual -180.00 -143.33 -36.67 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CA GLY A 139 " pdb=" C GLY A 139 " pdb=" N PRO A 140 " pdb=" CA PRO A 140 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 8607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1642 0.042 - 0.084: 411 0.084 - 0.126: 103 0.126 - 0.168: 1 0.168 - 0.210: 3 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CG LEU A 312 " pdb=" CB LEU A 312 " pdb=" CD1 LEU A 312 " pdb=" CD2 LEU A 312 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO A 912 " pdb=" N PRO A 912 " pdb=" C PRO A 912 " pdb=" CB PRO A 912 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA PRO B 912 " pdb=" N PRO B 912 " pdb=" C PRO B 912 " pdb=" CB PRO B 912 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 2157 not shown) Planarity restraints: 2558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 911 " -0.051 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO A 912 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 912 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 912 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 795 " -0.036 5.00e-02 4.00e+02 5.54e-02 4.92e+00 pdb=" N PRO B 796 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 796 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 796 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 341 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO B 342 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 342 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 342 " 0.025 5.00e-02 4.00e+02 ... (remaining 2555 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 688 2.73 - 3.27: 14008 3.27 - 3.82: 23477 3.82 - 4.36: 27691 4.36 - 4.90: 48510 Nonbonded interactions: 114374 Sorted by model distance: nonbonded pdb=" NH2 ARG B 142 " pdb=" O VAL B 168 " model vdw 2.188 3.120 nonbonded pdb=" OH TYR A 325 " pdb=" OD2 ASP A 435 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR B 325 " pdb=" OD2 ASP B 435 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLU B 856 " pdb=" NH1 ARG B 954 " model vdw 2.247 3.120 nonbonded pdb=" O ALA A 672 " pdb=" OG SER A 676 " model vdw 2.249 3.040 ... (remaining 114369 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.970 Find NCS groups from input model: 0.450 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 0.065 14118 Z= 0.146 Angle : 0.592 9.605 19212 Z= 0.292 Chirality : 0.039 0.210 2160 Planarity : 0.005 0.078 2558 Dihedral : 17.092 89.564 5226 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.22 % Allowed : 19.80 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1790 helix: 1.64 (0.16), residues: 1080 sheet: -1.79 (0.40), residues: 132 loop : -0.37 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 437 HIS 0.003 0.001 HIS A 805 PHE 0.009 0.002 PHE A 634 TYR 0.010 0.001 TYR B 123 ARG 0.006 0.000 ARG A 620 Details of bonding type rmsd hydrogen bonds : bond 0.11304 ( 806) hydrogen bonds : angle 4.96330 ( 2406) SS BOND : bond 0.00557 ( 4) SS BOND : angle 3.46885 ( 8) covalent geometry : bond 0.00341 (14114) covalent geometry : angle 0.58801 (19204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 3.680 Fit side-chains revert: symmetry clash REVERT: A 307 GLU cc_start: 0.8218 (mp0) cc_final: 0.7653 (mt-10) REVERT: A 945 ASP cc_start: 0.6864 (t0) cc_final: 0.6573 (t0) outliers start: 3 outliers final: 1 residues processed: 161 average time/residue: 0.4262 time to fit residues: 94.2072 Evaluate side-chains 151 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 696 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 161 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN A 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.160141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127628 restraints weight = 16388.508| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.89 r_work: 0.3301 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14118 Z= 0.136 Angle : 0.555 9.370 19212 Z= 0.273 Chirality : 0.039 0.179 2160 Planarity : 0.005 0.060 2558 Dihedral : 4.302 45.115 2020 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.15 % Allowed : 18.29 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1790 helix: 1.66 (0.16), residues: 1095 sheet: -1.55 (0.41), residues: 136 loop : -0.22 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 974 HIS 0.003 0.001 HIS A 805 PHE 0.012 0.002 PHE A 990 TYR 0.010 0.001 TYR B 123 ARG 0.005 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 806) hydrogen bonds : angle 3.97833 ( 2406) SS BOND : bond 0.00398 ( 4) SS BOND : angle 2.12381 ( 8) covalent geometry : bond 0.00314 (14114) covalent geometry : angle 0.55325 (19204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.853 Fit side-chains REVERT: B 572 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: B 696 ARG cc_start: 0.8045 (mpt180) cc_final: 0.7647 (mmt180) REVERT: A 98 ARG cc_start: 0.8064 (ptm160) cc_final: 0.7792 (ptt180) REVERT: A 945 ASP cc_start: 0.6920 (t0) cc_final: 0.6693 (t0) outliers start: 30 outliers final: 12 residues processed: 180 average time/residue: 0.4585 time to fit residues: 118.7703 Evaluate side-chains 156 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 881 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 124 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 0.0060 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 GLN A 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.125806 restraints weight = 16478.197| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.89 r_work: 0.3282 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14118 Z= 0.166 Angle : 0.563 9.641 19212 Z= 0.275 Chirality : 0.039 0.179 2160 Planarity : 0.005 0.061 2558 Dihedral : 4.119 33.962 2016 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.58 % Allowed : 18.65 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1790 helix: 1.63 (0.16), residues: 1090 sheet: -1.50 (0.41), residues: 143 loop : -0.24 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.003 0.001 HIS A 805 PHE 0.011 0.002 PHE A 990 TYR 0.010 0.001 TYR B 123 ARG 0.007 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 806) hydrogen bonds : angle 3.91343 ( 2406) SS BOND : bond 0.00395 ( 4) SS BOND : angle 2.24271 ( 8) covalent geometry : bond 0.00404 (14114) covalent geometry : angle 0.56079 (19204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.676 Fit side-chains REVERT: B 241 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8633 (p) REVERT: B 572 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7837 (mt-10) REVERT: B 696 ARG cc_start: 0.8059 (mpt180) cc_final: 0.7638 (mmt180) REVERT: A 152 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8448 (ttpt) REVERT: A 945 ASP cc_start: 0.6931 (t0) cc_final: 0.6663 (t0) outliers start: 36 outliers final: 22 residues processed: 177 average time/residue: 0.3241 time to fit residues: 80.1423 Evaluate side-chains 166 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 881 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 155 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 169 optimal weight: 0.0770 chunk 88 optimal weight: 3.9990 overall best weight: 0.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS A 805 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.161322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123980 restraints weight = 16392.461| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.07 r_work: 0.3204 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14118 Z= 0.136 Angle : 0.541 9.849 19212 Z= 0.264 Chirality : 0.038 0.172 2160 Planarity : 0.004 0.055 2558 Dihedral : 4.065 33.996 2016 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.94 % Allowed : 19.44 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1790 helix: 1.72 (0.16), residues: 1090 sheet: -1.40 (0.41), residues: 147 loop : -0.19 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.003 0.001 HIS A 805 PHE 0.015 0.002 PHE A 634 TYR 0.011 0.001 TYR B 123 ARG 0.003 0.000 ARG B 303 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 806) hydrogen bonds : angle 3.81050 ( 2406) SS BOND : bond 0.00349 ( 4) SS BOND : angle 2.34480 ( 8) covalent geometry : bond 0.00323 (14114) covalent geometry : angle 0.53882 (19204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 2.471 Fit side-chains REVERT: B 241 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8643 (p) REVERT: B 475 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7551 (mp) REVERT: B 572 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: B 738 LEU cc_start: 0.8928 (tt) cc_final: 0.8651 (mp) REVERT: B 840 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7477 (mp) REVERT: A 149 GLU cc_start: 0.7809 (tp30) cc_final: 0.7592 (tp30) REVERT: A 152 LYS cc_start: 0.8693 (ttpt) cc_final: 0.8380 (ttpt) REVERT: A 700 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: A 945 ASP cc_start: 0.7018 (t0) cc_final: 0.6745 (t0) outliers start: 41 outliers final: 23 residues processed: 182 average time/residue: 0.3455 time to fit residues: 88.9702 Evaluate side-chains 170 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 939 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.158698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122039 restraints weight = 16602.124| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.98 r_work: 0.3192 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14118 Z= 0.207 Angle : 0.592 10.308 19212 Z= 0.288 Chirality : 0.041 0.175 2160 Planarity : 0.005 0.055 2558 Dihedral : 4.206 33.565 2016 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.37 % Allowed : 18.87 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1790 helix: 1.58 (0.16), residues: 1088 sheet: -1.41 (0.41), residues: 147 loop : -0.25 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 437 HIS 0.005 0.001 HIS B 593 PHE 0.014 0.002 PHE A 990 TYR 0.010 0.001 TYR B 123 ARG 0.007 0.000 ARG B 696 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 806) hydrogen bonds : angle 3.88116 ( 2406) SS BOND : bond 0.00634 ( 4) SS BOND : angle 2.90048 ( 8) covalent geometry : bond 0.00508 (14114) covalent geometry : angle 0.58913 (19204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 1.633 Fit side-chains REVERT: B 152 LYS cc_start: 0.8526 (ttpp) cc_final: 0.8298 (ttmt) REVERT: B 211 ARG cc_start: 0.8891 (mtm-85) cc_final: 0.8675 (mtm-85) REVERT: B 241 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8631 (p) REVERT: B 572 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: B 738 LEU cc_start: 0.8964 (tt) cc_final: 0.8669 (mp) REVERT: B 840 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7542 (mp) REVERT: A 141 ASN cc_start: 0.5784 (OUTLIER) cc_final: 0.4417 (t0) REVERT: A 152 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8476 (ttpt) REVERT: A 700 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: A 945 ASP cc_start: 0.7045 (t0) cc_final: 0.6777 (t0) outliers start: 47 outliers final: 28 residues processed: 186 average time/residue: 0.3030 time to fit residues: 78.6221 Evaluate side-chains 174 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 939 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 75 optimal weight: 0.1980 chunk 155 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126164 restraints weight = 16524.047| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.86 r_work: 0.3296 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14118 Z= 0.137 Angle : 0.541 9.840 19212 Z= 0.264 Chirality : 0.038 0.176 2160 Planarity : 0.005 0.051 2558 Dihedral : 4.109 33.312 2016 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.01 % Allowed : 19.66 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1790 helix: 1.70 (0.16), residues: 1090 sheet: -1.35 (0.41), residues: 146 loop : -0.18 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS B 593 PHE 0.010 0.001 PHE A 634 TYR 0.011 0.001 TYR B 123 ARG 0.007 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 806) hydrogen bonds : angle 3.77679 ( 2406) SS BOND : bond 0.00328 ( 4) SS BOND : angle 3.05325 ( 8) covalent geometry : bond 0.00325 (14114) covalent geometry : angle 0.53801 (19204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 1.453 Fit side-chains REVERT: B 152 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8339 (ttmt) REVERT: B 211 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.8647 (mtm-85) REVERT: B 241 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8637 (p) REVERT: B 475 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7541 (mp) REVERT: B 572 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: B 738 LEU cc_start: 0.8937 (tt) cc_final: 0.8705 (mp) REVERT: B 840 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7585 (mp) REVERT: A 141 ASN cc_start: 0.5763 (OUTLIER) cc_final: 0.4425 (t0) REVERT: A 152 LYS cc_start: 0.8693 (ttpt) cc_final: 0.8448 (ttpt) REVERT: A 700 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: A 927 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7447 (mp) REVERT: A 945 ASP cc_start: 0.6916 (t0) cc_final: 0.6648 (t0) outliers start: 42 outliers final: 28 residues processed: 184 average time/residue: 0.3297 time to fit residues: 84.1517 Evaluate side-chains 181 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 939 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 56 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 171 optimal weight: 0.0980 chunk 163 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 80 optimal weight: 0.0050 chunk 112 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.161926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128218 restraints weight = 16640.798| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.96 r_work: 0.3281 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14118 Z= 0.119 Angle : 0.531 9.913 19212 Z= 0.258 Chirality : 0.037 0.176 2160 Planarity : 0.004 0.050 2558 Dihedral : 4.012 33.084 2016 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.73 % Allowed : 20.23 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1790 helix: 1.82 (0.16), residues: 1090 sheet: -1.37 (0.41), residues: 148 loop : -0.12 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 593 PHE 0.009 0.001 PHE A 634 TYR 0.015 0.001 TYR B 379 ARG 0.010 0.000 ARG B 696 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 806) hydrogen bonds : angle 3.69771 ( 2406) SS BOND : bond 0.00486 ( 4) SS BOND : angle 2.91984 ( 8) covalent geometry : bond 0.00277 (14114) covalent geometry : angle 0.52817 (19204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.469 Fit side-chains REVERT: B 152 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8333 (ttmt) REVERT: B 211 ARG cc_start: 0.8859 (mtm-85) cc_final: 0.8644 (mtm-85) REVERT: B 241 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8652 (p) REVERT: B 458 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: B 475 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7501 (mp) REVERT: B 572 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: B 686 ASP cc_start: 0.8438 (t0) cc_final: 0.7963 (m-30) REVERT: B 704 GLU cc_start: 0.8678 (tt0) cc_final: 0.8471 (tt0) REVERT: B 840 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7562 (mp) REVERT: A 141 ASN cc_start: 0.5720 (OUTLIER) cc_final: 0.4405 (t0) REVERT: A 149 GLU cc_start: 0.7729 (tp30) cc_final: 0.7502 (tp30) REVERT: A 152 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8416 (ttpt) REVERT: A 700 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: A 827 ARG cc_start: 0.8335 (mpt-90) cc_final: 0.7874 (mmt90) REVERT: A 927 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7427 (mp) REVERT: A 945 ASP cc_start: 0.6948 (t0) cc_final: 0.6670 (t0) outliers start: 38 outliers final: 26 residues processed: 184 average time/residue: 0.3272 time to fit residues: 84.9917 Evaluate side-chains 181 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 939 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 157 optimal weight: 0.0060 chunk 143 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126890 restraints weight = 16543.803| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.19 r_work: 0.3219 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14118 Z= 0.120 Angle : 0.538 10.073 19212 Z= 0.259 Chirality : 0.038 0.172 2160 Planarity : 0.004 0.050 2558 Dihedral : 3.962 32.495 2016 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.80 % Allowed : 20.52 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.20), residues: 1790 helix: 1.85 (0.16), residues: 1090 sheet: -1.29 (0.42), residues: 150 loop : -0.08 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 593 PHE 0.008 0.001 PHE A 634 TYR 0.010 0.001 TYR B 123 ARG 0.008 0.000 ARG B 696 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 806) hydrogen bonds : angle 3.67414 ( 2406) SS BOND : bond 0.00347 ( 4) SS BOND : angle 2.92823 ( 8) covalent geometry : bond 0.00282 (14114) covalent geometry : angle 0.53461 (19204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.459 Fit side-chains REVERT: B 152 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8346 (ttmt) REVERT: B 211 ARG cc_start: 0.8861 (mtm-85) cc_final: 0.8596 (mtt90) REVERT: B 241 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8654 (p) REVERT: B 458 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: B 475 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7485 (mp) REVERT: B 572 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: B 686 ASP cc_start: 0.8410 (t0) cc_final: 0.7946 (m-30) REVERT: B 704 GLU cc_start: 0.8694 (tt0) cc_final: 0.8487 (tt0) REVERT: B 840 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7536 (mp) REVERT: A 141 ASN cc_start: 0.5621 (OUTLIER) cc_final: 0.4311 (t0) REVERT: A 149 GLU cc_start: 0.7728 (tp30) cc_final: 0.7490 (tp30) REVERT: A 152 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8373 (ttpt) REVERT: A 700 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: A 827 ARG cc_start: 0.8355 (mpt-90) cc_final: 0.7875 (mmt90) REVERT: A 945 ASP cc_start: 0.7019 (t0) cc_final: 0.6731 (t0) outliers start: 39 outliers final: 26 residues processed: 182 average time/residue: 0.3835 time to fit residues: 98.5605 Evaluate side-chains 183 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 939 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 0.0370 chunk 163 optimal weight: 4.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN A 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124870 restraints weight = 16490.090| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.10 r_work: 0.3215 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14118 Z= 0.120 Angle : 0.533 10.126 19212 Z= 0.257 Chirality : 0.037 0.173 2160 Planarity : 0.004 0.049 2558 Dihedral : 3.937 32.597 2016 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.01 % Allowed : 20.16 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1790 helix: 1.87 (0.16), residues: 1090 sheet: -1.20 (0.42), residues: 150 loop : -0.05 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 593 PHE 0.009 0.001 PHE A 990 TYR 0.009 0.001 TYR B 123 ARG 0.009 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 806) hydrogen bonds : angle 3.65736 ( 2406) SS BOND : bond 0.00306 ( 4) SS BOND : angle 2.66968 ( 8) covalent geometry : bond 0.00283 (14114) covalent geometry : angle 0.53057 (19204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.549 Fit side-chains REVERT: B 152 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8376 (ttmt) REVERT: B 211 ARG cc_start: 0.8870 (mtm-85) cc_final: 0.8612 (mtt90) REVERT: B 241 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8652 (p) REVERT: B 458 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: B 475 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7538 (mp) REVERT: B 572 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: B 686 ASP cc_start: 0.8416 (t0) cc_final: 0.7969 (m-30) REVERT: B 704 GLU cc_start: 0.8690 (tt0) cc_final: 0.8485 (tt0) REVERT: B 840 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7549 (mp) REVERT: A 141 ASN cc_start: 0.5650 (OUTLIER) cc_final: 0.4321 (t0) REVERT: A 149 GLU cc_start: 0.7742 (tp30) cc_final: 0.7460 (tp30) REVERT: A 152 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8363 (ttpt) REVERT: A 700 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: A 827 ARG cc_start: 0.8363 (mpt-90) cc_final: 0.7869 (mmt90) REVERT: A 945 ASP cc_start: 0.7040 (t0) cc_final: 0.6755 (t0) outliers start: 42 outliers final: 28 residues processed: 181 average time/residue: 0.3461 time to fit residues: 88.7217 Evaluate side-chains 175 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 939 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 132 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 159 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN A 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.152412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120661 restraints weight = 16336.397| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.67 r_work: 0.3016 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14118 Z= 0.160 Angle : 0.564 10.407 19212 Z= 0.272 Chirality : 0.039 0.172 2160 Planarity : 0.005 0.050 2558 Dihedral : 4.014 32.015 2016 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.80 % Allowed : 20.44 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.20), residues: 1790 helix: 1.76 (0.16), residues: 1090 sheet: -1.21 (0.42), residues: 150 loop : -0.09 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS B 593 PHE 0.011 0.002 PHE A 990 TYR 0.010 0.001 TYR B 123 ARG 0.009 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 806) hydrogen bonds : angle 3.72586 ( 2406) SS BOND : bond 0.00615 ( 4) SS BOND : angle 3.07019 ( 8) covalent geometry : bond 0.00389 (14114) covalent geometry : angle 0.56027 (19204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 2.851 Fit side-chains REVERT: B 152 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8333 (ttmt) REVERT: B 211 ARG cc_start: 0.8810 (mtm-85) cc_final: 0.8552 (mtt90) REVERT: B 241 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8588 (p) REVERT: B 458 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: B 475 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7471 (mp) REVERT: B 572 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: B 686 ASP cc_start: 0.8282 (t0) cc_final: 0.7858 (m-30) REVERT: B 704 GLU cc_start: 0.8538 (tt0) cc_final: 0.8332 (tt0) REVERT: B 739 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8206 (mtm180) REVERT: B 840 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7558 (mp) REVERT: A 141 ASN cc_start: 0.5565 (OUTLIER) cc_final: 0.4249 (t0) REVERT: A 149 GLU cc_start: 0.7714 (tp30) cc_final: 0.7476 (tp30) REVERT: A 152 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8368 (ttpt) REVERT: A 700 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: A 827 ARG cc_start: 0.8356 (mpt-90) cc_final: 0.7906 (mmt90) REVERT: A 945 ASP cc_start: 0.6824 (t0) cc_final: 0.6582 (t0) outliers start: 39 outliers final: 27 residues processed: 180 average time/residue: 0.4899 time to fit residues: 125.3155 Evaluate side-chains 179 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 739 ARG Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 939 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN A 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118806 restraints weight = 16377.630| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.64 r_work: 0.2987 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 14118 Z= 0.154 Angle : 0.564 10.148 19212 Z= 0.274 Chirality : 0.039 0.173 2160 Planarity : 0.005 0.049 2558 Dihedral : 4.040 32.187 2016 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.58 % Allowed : 20.73 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.20), residues: 1790 helix: 1.76 (0.16), residues: 1090 sheet: -1.19 (0.42), residues: 150 loop : -0.07 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS B 593 PHE 0.011 0.002 PHE A 990 TYR 0.010 0.001 TYR B 123 ARG 0.009 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 806) hydrogen bonds : angle 3.72485 ( 2406) SS BOND : bond 0.00724 ( 4) SS BOND : angle 3.71139 ( 8) covalent geometry : bond 0.00371 (14114) covalent geometry : angle 0.55907 (19204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10273.42 seconds wall clock time: 186 minutes 45.28 seconds (11205.28 seconds total)