Starting phenix.real_space_refine on Fri May 16 02:03:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rot_19404/05_2025/8rot_19404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rot_19404/05_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_19404/05_2025/8rot_19404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rot_19404/05_2025/8rot_19404.map" model { file = "/net/cci-nas-00/data/ceres_data/8rot_19404/05_2025/8rot_19404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rot_19404/05_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-5687/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: 12.47, per 1000 atoms: 0.90 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: 3.03 Conformation dependent library (CDL) restraints added in 1.9 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: 1.43 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: 4.71 Time building geometry restraints manager: 3.63 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: 32.850 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: 0.000 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.250 Find NCS groups from input model: 0.410 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.980 ------------------------------------------------------------------------------- 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 : 1.376 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: 0.3410 time to fit residues: 74.2265 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 : 1.579 ------------------------------------------------------------------------------- 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 = 0.160139 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 = 16388.524| |-----------------------------------------------------------------------------| 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: 0.3146 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- 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 3.97835 ( 2406) SS BOND : bond 0.00398 ( 4) SS BOND : angle 2.12394 ( 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 : 1.396 Fit side-chains REVERT: B 572 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: B 696 ARG cc_start: 0.8046 (mpt180) cc_final: 0.7647 (mmt180) REVERT: A 98 ARG cc_start: 0.8062 (ptm160) cc_final: 0.7791 (ptt180) REVERT: A 945 ASP cc_start: 0.6925 (t0) cc_final: 0.6696 (t0) outliers start: 30 outliers final: 12 residues processed: 180 average time/residue: 0.3517 time to fit residues: 86.9569 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 : 1.388 ------------------------------------------------------------------------------- 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: 0.9990 chunk 54 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 A 805 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.157120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121712 restraints weight = 16503.311| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.92 r_work: 0.3202 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14118 Z= 0.192 Angle : 0.589 9.967 19212 Z= 0.288 Chirality : 0.040 0.180 2160 Planarity : 0.005 0.059 2558 Dihedral : 4.202 33.522 2016 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.73 % Allowed : 18.87 % Favored : 78.41 % 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: 1.05 (0.20), residues: 1790 helix: 1.56 (0.16), residues: 1088 sheet: -1.51 (0.41), residues: 143 loop : -0.29 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 437 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 0.006 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 806) hydrogen bonds : angle 3.95397 ( 2406) SS BOND : bond 0.00460 ( 4) SS BOND : angle 2.65225 ( 8) covalent geometry : bond 0.00470 (14114) covalent geometry : angle 0.58644 (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 192 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.574 Fit side-chains REVERT: B 241 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8614 (p) REVERT: B 572 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: A 827 ARG cc_start: 0.8445 (mpt180) cc_final: 0.8233 (mpt-90) REVERT: A 908 GLU cc_start: 0.6348 (tm-30) cc_final: 0.6083 (tm-30) REVERT: A 945 ASP cc_start: 0.7035 (t0) cc_final: 0.6754 (t0) outliers start: 38 outliers final: 23 residues processed: 183 average time/residue: 0.3127 time to fit residues: 79.5504 Evaluate side-chains 170 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.951 ------------------------------------------------------------------------------- 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 713 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 748 MET 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 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 334 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 939 HIS 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: 0.5980 chunk 174 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 169 optimal weight: 0.0050 chunk 88 optimal weight: 2.9990 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 = 0.3878 r_free = 0.3878 target = 0.161838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124576 restraints weight = 16362.720| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.08 r_work: 0.3238 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14118 Z= 0.119 Angle : 0.528 9.822 19212 Z= 0.258 Chirality : 0.038 0.170 2160 Planarity : 0.004 0.053 2558 Dihedral : 4.065 34.535 2016 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.65 % Allowed : 19.66 % Favored : 77.69 % 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: 1.27 (0.20), residues: 1790 helix: 1.73 (0.16), residues: 1090 sheet: -1.45 (0.41), residues: 147 loop : -0.17 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 437 HIS 0.003 0.001 HIS B 593 PHE 0.017 0.001 PHE A 634 TYR 0.011 0.001 TYR B 123 ARG 0.006 0.000 ARG B 696 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 806) hydrogen bonds : angle 3.78874 ( 2406) SS BOND : bond 0.00325 ( 4) SS BOND : angle 2.30023 ( 8) covalent geometry : bond 0.00275 (14114) covalent geometry : angle 0.52591 (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 186 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.448 Fit side-chains REVERT: B 241 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8636 (p) REVERT: B 475 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7565 (mp) REVERT: B 572 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: B 738 LEU cc_start: 0.8923 (tt) cc_final: 0.8658 (mp) REVERT: B 840 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7480 (mp) REVERT: A 151 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7969 (tt0) REVERT: A 152 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8381 (ttpt) REVERT: A 377 GLU cc_start: 0.8126 (tt0) cc_final: 0.7596 (tm-30) REVERT: A 700 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: A 908 GLU cc_start: 0.6221 (tm-30) cc_final: 0.5884 (tm-30) REVERT: A 945 ASP cc_start: 0.6999 (t0) cc_final: 0.6727 (t0) outliers start: 37 outliers final: 19 residues processed: 176 average time/residue: 0.3178 time to fit residues: 78.5212 Evaluate side-chains 164 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 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 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 131 MET Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 308 LEU 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 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: 1.9990 chunk 158 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 72 optimal weight: 0.0040 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.160903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123501 restraints weight = 16547.594| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.10 r_work: 0.3167 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14118 Z= 0.146 Angle : 0.540 10.046 19212 Z= 0.263 Chirality : 0.038 0.170 2160 Planarity : 0.004 0.055 2558 Dihedral : 4.060 33.878 2016 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.30 % Allowed : 19.37 % 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: 1.28 (0.20), residues: 1790 helix: 1.73 (0.16), residues: 1090 sheet: -1.37 (0.41), residues: 147 loop : -0.17 (0.27), residues: 553 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 0.002 PHE A 634 TYR 0.010 0.001 TYR B 123 ARG 0.008 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 806) hydrogen bonds : angle 3.75385 ( 2406) SS BOND : bond 0.00433 ( 4) SS BOND : angle 2.57715 ( 8) covalent geometry : bond 0.00352 (14114) covalent geometry : angle 0.53749 (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 195 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 1.397 Fit side-chains REVERT: B 241 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8644 (p) REVERT: B 475 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7542 (mp) REVERT: B 572 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: B 738 LEU cc_start: 0.8928 (tt) cc_final: 0.8679 (mp) REVERT: B 840 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7500 (mp) REVERT: A 141 ASN cc_start: 0.5737 (OUTLIER) cc_final: 0.4374 (t0) REVERT: A 151 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7962 (tt0) REVERT: A 152 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8393 (ttpt) REVERT: A 700 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: A 816 GLU cc_start: 0.7792 (pm20) cc_final: 0.6902 (pm20) REVERT: A 908 GLU cc_start: 0.6325 (tm-30) cc_final: 0.6037 (tm-30) REVERT: A 927 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7285 (mp) REVERT: A 945 ASP cc_start: 0.7030 (t0) cc_final: 0.6745 (t0) outliers start: 46 outliers final: 27 residues processed: 181 average time/residue: 0.3271 time to fit residues: 86.2285 Evaluate side-chains 180 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 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 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 881 ASP Chi-restraints excluded: chain A residue 927 LEU 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: 0.5980 chunk 155 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 170 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.162064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124820 restraints weight = 16638.218| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.09 r_work: 0.3211 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1255 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 : 0.523 9.875 19212 Z= 0.254 Chirality : 0.038 0.168 2160 Planarity : 0.004 0.051 2558 Dihedral : 3.986 33.395 2016 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.65 % Allowed : 20.16 % Favored : 77.19 % 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: 1.38 (0.20), residues: 1790 helix: 1.83 (0.16), residues: 1089 sheet: -1.34 (0.41), residues: 147 loop : -0.16 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS A 262 PHE 0.010 0.001 PHE A 634 TYR 0.010 0.001 TYR B 123 ARG 0.006 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 806) hydrogen bonds : angle 3.69857 ( 2406) SS BOND : bond 0.00353 ( 4) SS BOND : angle 2.75494 ( 8) covalent geometry : bond 0.00281 (14114) covalent geometry : angle 0.51970 (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 195 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.410 Fit side-chains REVERT: B 152 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8328 (ttmt) REVERT: B 241 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 458 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: B 475 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7527 (mp) REVERT: B 572 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: B 686 ASP cc_start: 0.8438 (t0) cc_final: 0.7960 (m-30) REVERT: B 704 GLU cc_start: 0.8688 (tt0) cc_final: 0.8477 (tt0) REVERT: B 840 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7501 (mp) REVERT: A 141 ASN cc_start: 0.5709 (OUTLIER) cc_final: 0.4346 (t0) REVERT: A 149 GLU cc_start: 0.7765 (tp30) cc_final: 0.7546 (tp30) REVERT: A 151 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7939 (tt0) REVERT: A 152 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8363 (ttpt) REVERT: A 700 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: A 816 GLU cc_start: 0.7742 (pm20) cc_final: 0.6900 (pm20) REVERT: A 908 GLU cc_start: 0.6415 (tm-30) cc_final: 0.6140 (tm-30) REVERT: A 927 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7261 (mp) REVERT: A 945 ASP cc_start: 0.7003 (t0) cc_final: 0.6714 (t0) outliers start: 37 outliers final: 22 residues processed: 185 average time/residue: 0.3116 time to fit residues: 80.6613 Evaluate side-chains 181 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 845 THR 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: 0.8980 chunk 110 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 171 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 80 optimal weight: 0.2980 chunk 112 optimal weight: 0.6980 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128259 restraints weight = 16693.965| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.94 r_work: 0.3199 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14118 Z= 0.128 Angle : 0.528 10.219 19212 Z= 0.255 Chirality : 0.038 0.168 2160 Planarity : 0.004 0.052 2558 Dihedral : 3.960 32.934 2016 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.08 % Allowed : 19.87 % 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: 1.44 (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 0.009 0.001 PHE A 990 TYR 0.015 0.001 TYR B 379 ARG 0.007 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 806) hydrogen bonds : angle 3.68979 ( 2406) SS BOND : bond 0.00319 ( 4) SS BOND : angle 2.55291 ( 8) covalent geometry : bond 0.00304 (14114) covalent geometry : angle 0.52545 (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 200 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 1.440 Fit side-chains REVERT: B 152 LYS cc_start: 0.8528 (ttpp) cc_final: 0.8302 (ttmt) REVERT: B 241 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8636 (p) REVERT: B 475 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7517 (mp) REVERT: B 572 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: B 686 ASP cc_start: 0.8370 (t0) cc_final: 0.7924 (m-30) REVERT: B 704 GLU cc_start: 0.8628 (tt0) cc_final: 0.8414 (tt0) REVERT: B 840 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7472 (mp) REVERT: A 141 ASN cc_start: 0.5574 (OUTLIER) cc_final: 0.4325 (t0) REVERT: A 152 LYS cc_start: 0.8637 (ttpt) cc_final: 0.8355 (ttpt) REVERT: A 700 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: A 816 GLU cc_start: 0.7782 (pm20) cc_final: 0.6927 (pm20) REVERT: A 827 ARG cc_start: 0.8351 (mpt-90) cc_final: 0.7879 (mmt90) REVERT: A 908 GLU cc_start: 0.6398 (tm-30) cc_final: 0.6187 (tm-30) REVERT: A 927 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7288 (mp) REVERT: A 945 ASP cc_start: 0.6950 (t0) cc_final: 0.6665 (t0) outliers start: 43 outliers final: 28 residues processed: 186 average time/residue: 0.3124 time to fit residues: 80.5037 Evaluate side-chains 184 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 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 740 SER 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 334 SER 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 845 THR 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: 3.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 17 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.150990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119443 restraints weight = 16326.513| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.63 r_work: 0.3003 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14118 Z= 0.167 Angle : 0.564 10.038 19212 Z= 0.272 Chirality : 0.039 0.167 2160 Planarity : 0.005 0.051 2558 Dihedral : 4.054 32.333 2016 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.94 % Allowed : 19.94 % Favored : 77.12 % 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: 1.32 (0.20), residues: 1790 helix: 1.73 (0.16), residues: 1090 sheet: -1.22 (0.42), residues: 148 loop : -0.12 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 437 HIS 0.004 0.001 HIS B 593 PHE 0.012 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 0.04013 ( 806) hydrogen bonds : angle 3.75130 ( 2406) SS BOND : bond 0.00512 ( 4) SS BOND : angle 3.21372 ( 8) covalent geometry : bond 0.00408 (14114) covalent geometry : angle 0.56058 (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 193 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 1.595 Fit side-chains REVERT: B 152 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8312 (ttmt) REVERT: B 241 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8578 (p) REVERT: B 458 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: B 572 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: B 704 GLU cc_start: 0.8540 (tt0) cc_final: 0.8327 (tt0) REVERT: B 840 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7508 (mp) REVERT: A 141 ASN cc_start: 0.5557 (OUTLIER) cc_final: 0.4346 (t0) REVERT: A 149 GLU cc_start: 0.7754 (tp30) cc_final: 0.7508 (tp30) REVERT: A 152 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8295 (ttpt) REVERT: A 700 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: A 816 GLU cc_start: 0.7803 (pm20) cc_final: 0.6913 (pm20) REVERT: A 823 GLN cc_start: 0.7161 (mp10) cc_final: 0.6947 (mp10) REVERT: A 827 ARG cc_start: 0.8337 (mpt-90) cc_final: 0.7888 (mmt90) REVERT: A 927 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7276 (mp) REVERT: A 945 ASP cc_start: 0.6826 (t0) cc_final: 0.6574 (t0) outliers start: 41 outliers final: 28 residues processed: 181 average time/residue: 0.3180 time to fit residues: 79.4768 Evaluate side-chains 182 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 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 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 845 THR Chi-restraints excluded: chain A residue 927 LEU 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: 0.6980 chunk 130 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 106 optimal weight: 0.5980 chunk 84 optimal weight: 0.0270 chunk 163 optimal weight: 4.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN B 809 ASN A 262 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.152228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120808 restraints weight = 16215.502| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.67 r_work: 0.3024 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14118 Z= 0.131 Angle : 0.546 10.154 19212 Z= 0.264 Chirality : 0.038 0.180 2160 Planarity : 0.005 0.050 2558 Dihedral : 3.978 31.154 2016 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.87 % Allowed : 20.01 % Favored : 77.12 % 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: 1.42 (0.20), residues: 1790 helix: 1.82 (0.16), residues: 1090 sheet: -1.24 (0.42), residues: 150 loop : -0.08 (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 0.009 0.001 PHE A 990 TYR 0.012 0.001 TYR B 123 ARG 0.009 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 806) hydrogen bonds : angle 3.69351 ( 2406) SS BOND : bond 0.00417 ( 4) SS BOND : angle 3.17761 ( 8) covalent geometry : bond 0.00312 (14114) covalent geometry : angle 0.54205 (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 190 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 1.661 Fit side-chains REVERT: B 152 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8313 (ttmt) REVERT: B 241 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8591 (p) REVERT: B 458 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: B 572 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: B 686 ASP cc_start: 0.8269 (t0) cc_final: 0.7865 (m-30) REVERT: B 704 GLU cc_start: 0.8534 (tt0) cc_final: 0.8324 (tt0) REVERT: B 739 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8188 (mtm180) REVERT: B 840 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7509 (mp) REVERT: A 141 ASN cc_start: 0.5499 (OUTLIER) cc_final: 0.4284 (t0) REVERT: A 149 GLU cc_start: 0.7724 (tp30) cc_final: 0.7423 (tp30) REVERT: A 152 LYS cc_start: 0.8642 (ttpt) cc_final: 0.8303 (ttpt) REVERT: A 700 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: A 816 GLU cc_start: 0.7784 (pm20) cc_final: 0.6935 (pm20) REVERT: A 823 GLN cc_start: 0.7180 (mp10) cc_final: 0.6975 (mp10) REVERT: A 827 ARG cc_start: 0.8316 (mpt-90) cc_final: 0.7882 (mmt90) REVERT: A 927 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7302 (mp) REVERT: A 945 ASP cc_start: 0.6772 (t0) cc_final: 0.6493 (t0) outliers start: 40 outliers final: 28 residues processed: 180 average time/residue: 0.3354 time to fit residues: 83.2169 Evaluate side-chains 182 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 881 ASP Chi-restraints excluded: chain A residue 927 LEU 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: 0.9990 chunk 46 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 113 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 159 optimal weight: 0.0870 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3725 r_free = 0.3725 target = 0.153035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121014 restraints weight = 16243.602| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.65 r_work: 0.3047 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1535 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= 0.121 Angle : 0.539 10.163 19212 Z= 0.261 Chirality : 0.037 0.180 2160 Planarity : 0.005 0.050 2558 Dihedral : 3.936 31.381 2016 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.51 % Allowed : 20.16 % 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: 1.52 (0.20), residues: 1790 helix: 1.89 (0.16), residues: 1090 sheet: -1.20 (0.42), residues: 150 loop : -0.03 (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 B 697 TYR 0.009 0.001 TYR B 123 ARG 0.009 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 806) hydrogen bonds : angle 3.65863 ( 2406) SS BOND : bond 0.00352 ( 4) SS BOND : angle 3.00507 ( 8) covalent geometry : bond 0.00285 (14114) covalent geometry : angle 0.53601 (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 185 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.602 Fit side-chains REVERT: B 152 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8345 (ttmt) REVERT: B 241 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8588 (p) REVERT: B 371 ARG cc_start: 0.7946 (ptp-170) cc_final: 0.7576 (ttp80) REVERT: B 458 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: B 475 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7466 (mp) REVERT: B 572 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: B 686 ASP cc_start: 0.8244 (t0) cc_final: 0.7878 (m-30) REVERT: B 704 GLU cc_start: 0.8525 (tt0) cc_final: 0.8319 (tt0) REVERT: B 739 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8188 (mtm180) REVERT: B 840 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7497 (mp) REVERT: A 141 ASN cc_start: 0.5537 (OUTLIER) cc_final: 0.4257 (t0) REVERT: A 149 GLU cc_start: 0.7624 (tp30) cc_final: 0.7288 (tp30) REVERT: A 152 LYS cc_start: 0.8642 (ttpt) cc_final: 0.8269 (ttpt) REVERT: A 700 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: A 816 GLU cc_start: 0.7809 (pm20) cc_final: 0.6955 (pm20) REVERT: A 823 GLN cc_start: 0.7258 (mp10) cc_final: 0.6921 (mm-40) REVERT: A 827 ARG cc_start: 0.8311 (mpt-90) cc_final: 0.7878 (mmt90) REVERT: A 927 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7288 (mp) REVERT: A 945 ASP cc_start: 0.6741 (t0) cc_final: 0.6476 (t0) outliers start: 35 outliers final: 24 residues processed: 178 average time/residue: 0.3351 time to fit residues: 81.9314 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 : 2.205 ------------------------------------------------------------------------------- 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 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 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 881 ASP Chi-restraints excluded: chain A residue 927 LEU 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: 0.0980 chunk 168 optimal weight: 0.9980 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: 0.9990 chunk 88 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 363 GLN A 262 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.152823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121408 restraints weight = 16347.380| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.62 r_work: 0.3051 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1571 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= 0.130 Angle : 0.547 10.262 19212 Z= 0.266 Chirality : 0.038 0.180 2160 Planarity : 0.005 0.052 2558 Dihedral : 3.935 31.033 2016 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.73 % Allowed : 20.16 % Favored : 77.12 % 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: 1.54 (0.20), residues: 1790 helix: 1.88 (0.16), residues: 1090 sheet: -1.03 (0.42), residues: 156 loop : 0.00 (0.28), residues: 544 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 0.013 0.001 PHE A 949 TYR 0.010 0.001 TYR B 123 ARG 0.014 0.000 ARG B 696 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 806) hydrogen bonds : angle 3.66540 ( 2406) SS BOND : bond 0.00491 ( 4) SS BOND : angle 2.95072 ( 8) covalent geometry : bond 0.00309 (14114) covalent geometry : angle 0.54389 (19204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8306.42 seconds wall clock time: 144 minutes 57.18 seconds (8697.18 seconds total)