Starting phenix.real_space_refine on Thu Sep 18 04:00:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rot_19404/09_2025/8rot_19404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rot_19404/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rot_19404/09_2025/8rot_19404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rot_19404/09_2025/8rot_19404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rot_19404/09_2025/8rot_19404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rot_19404/09_2025/8rot_19404.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.35, per 1000 atoms: 0.24 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: 1.10 Conformation dependent library (CDL) restraints added in 630.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.54 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: 2.35 Time building geometry restraints manager: 1.50 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: 0.03 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: 21.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.030 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.400 ------------------------------------------------------------------------------- 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 : 5.28 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.006 0.000 ARG A 620 TYR 0.010 0.001 TYR B 123 PHE 0.009 0.002 PHE A 634 TRP 0.012 0.001 TRP A 437 HIS 0.003 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00341 (14114) covalent geometry : angle 0.58801 (19204) SS BOND : bond 0.00557 ( 4) SS BOND : angle 3.46885 ( 8) hydrogen bonds : bond 0.11304 ( 806) hydrogen bonds : angle 4.96330 ( 2406) *********************** 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 : 0.529 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: 0.1715 time to fit residues: 37.3686 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 : 0.526 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN B 561 GLN B 913 ASN A 262 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127728 restraints weight = 16654.628| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.89 r_work: 0.3255 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14118 Z= 0.159 Angle : 0.571 9.716 19212 Z= 0.280 Chirality : 0.039 0.175 2160 Planarity : 0.005 0.063 2558 Dihedral : 4.350 45.018 2020 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.44 % Allowed : 18.08 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.20), residues: 1790 helix: 1.64 (0.16), residues: 1088 sheet: -1.58 (0.40), residues: 140 loop : -0.29 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 310 TYR 0.010 0.001 TYR B 123 PHE 0.014 0.002 PHE A 990 TRP 0.013 0.001 TRP B 974 HIS 0.003 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00378 (14114) covalent geometry : angle 0.56910 (19204) SS BOND : bond 0.00415 ( 4) SS BOND : angle 2.22836 ( 8) hydrogen bonds : bond 0.04332 ( 806) hydrogen bonds : angle 4.06353 ( 2406) *********************** 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 189 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.502 Fit side-chains REVERT: B 241 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8598 (p) REVERT: B 572 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: B 696 ARG cc_start: 0.7906 (mpt180) cc_final: 0.7632 (mmt180) REVERT: A 98 ARG cc_start: 0.8050 (ptm160) cc_final: 0.7762 (ptt180) outliers start: 34 outliers final: 14 residues processed: 183 average time/residue: 0.1562 time to fit residues: 39.3974 Evaluate side-chains 161 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 572 GLU Chi-restraints excluded: chain B residue 714 THR 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 913 ASN 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 161 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.156954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121834 restraints weight = 16622.104| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.91 r_work: 0.3206 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14118 Z= 0.194 Angle : 0.586 10.156 19212 Z= 0.287 Chirality : 0.040 0.180 2160 Planarity : 0.005 0.060 2558 Dihedral : 4.209 34.322 2016 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.87 % Allowed : 18.51 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.20), residues: 1790 helix: 1.55 (0.16), residues: 1088 sheet: -1.53 (0.41), residues: 143 loop : -0.32 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 310 TYR 0.011 0.001 TYR B 123 PHE 0.013 0.002 PHE A 990 TRP 0.014 0.001 TRP A 437 HIS 0.003 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00474 (14114) covalent geometry : angle 0.58461 (19204) SS BOND : bond 0.00740 ( 4) SS BOND : angle 2.31535 ( 8) hydrogen bonds : bond 0.04472 ( 806) hydrogen bonds : angle 3.96948 ( 2406) *********************** 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: 40 poor density : 152 time to evaluate : 0.409 Fit side-chains REVERT: B 241 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8643 (p) REVERT: B 572 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: B 840 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7421 (mp) REVERT: A 945 ASP cc_start: 0.6920 (t0) cc_final: 0.6699 (t0) outliers start: 40 outliers final: 24 residues processed: 181 average time/residue: 0.1559 time to fit residues: 38.6954 Evaluate side-chains 168 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 722 LEU 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 840 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 881 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 A 805 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.158137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122782 restraints weight = 16565.002| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.93 r_work: 0.3274 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14118 Z= 0.152 Angle : 0.557 9.914 19212 Z= 0.272 Chirality : 0.039 0.174 2160 Planarity : 0.005 0.055 2558 Dihedral : 4.152 34.179 2016 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.73 % Allowed : 19.44 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.20), residues: 1790 helix: 1.62 (0.16), residues: 1089 sheet: -1.43 (0.41), residues: 147 loop : -0.24 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 696 TYR 0.011 0.001 TYR B 123 PHE 0.011 0.002 PHE A 990 TRP 0.013 0.001 TRP A 437 HIS 0.003 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00366 (14114) covalent geometry : angle 0.55427 (19204) SS BOND : bond 0.00382 ( 4) SS BOND : angle 2.62749 ( 8) hydrogen bonds : bond 0.04046 ( 806) hydrogen bonds : angle 3.84915 ( 2406) *********************** 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 185 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.498 Fit side-chains REVERT: B 241 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8655 (p) REVERT: B 572 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: B 738 LEU cc_start: 0.8939 (tt) cc_final: 0.8654 (mp) REVERT: A 151 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7912 (tt0) REVERT: A 700 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: A 775 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: A 945 ASP cc_start: 0.6883 (t0) cc_final: 0.6620 (t0) outliers start: 38 outliers final: 21 residues processed: 175 average time/residue: 0.1360 time to fit residues: 33.3640 Evaluate side-chains 163 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 THR 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 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 614 VAL 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 944 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 939 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 95 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.159635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122794 restraints weight = 16734.675| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.01 r_work: 0.3226 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14118 Z= 0.168 Angle : 0.566 10.123 19212 Z= 0.275 Chirality : 0.039 0.174 2160 Planarity : 0.005 0.055 2558 Dihedral : 4.165 33.638 2016 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.37 % Allowed : 19.08 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.20), residues: 1790 helix: 1.61 (0.16), residues: 1089 sheet: -1.40 (0.41), residues: 147 loop : -0.24 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 696 TYR 0.011 0.001 TYR B 123 PHE 0.014 0.002 PHE A 634 TRP 0.014 0.001 TRP B 437 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00409 (14114) covalent geometry : angle 0.56323 (19204) SS BOND : bond 0.00415 ( 4) SS BOND : angle 2.63131 ( 8) hydrogen bonds : bond 0.04142 ( 806) hydrogen bonds : angle 3.83373 ( 2406) *********************** 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 198 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.521 Fit side-chains REVERT: B 211 ARG cc_start: 0.8901 (mtm-85) cc_final: 0.8680 (mtm-85) REVERT: B 241 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8665 (p) REVERT: B 572 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: B 696 ARG cc_start: 0.8291 (mmt90) cc_final: 0.8065 (mmt90) REVERT: B 738 LEU cc_start: 0.8958 (tt) cc_final: 0.8685 (mp) REVERT: B 840 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7519 (mp) REVERT: A 700 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: A 945 ASP cc_start: 0.6928 (t0) cc_final: 0.6645 (t0) outliers start: 47 outliers final: 31 residues processed: 187 average time/residue: 0.1449 time to fit residues: 37.5927 Evaluate side-chains 176 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 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 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 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 700 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 881 ASP 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 60 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 155 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.161349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124002 restraints weight = 16537.021| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.10 r_work: 0.3232 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1254 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= 0.126 Angle : 0.536 9.893 19212 Z= 0.261 Chirality : 0.038 0.174 2160 Planarity : 0.004 0.051 2558 Dihedral : 4.070 33.441 2016 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.20), residues: 1790 helix: 1.75 (0.16), residues: 1090 sheet: -1.43 (0.41), residues: 148 loop : -0.13 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 310 TYR 0.010 0.001 TYR B 123 PHE 0.012 0.001 PHE A 634 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00297 (14114) covalent geometry : angle 0.53288 (19204) SS BOND : bond 0.00392 ( 4) SS BOND : angle 2.77578 ( 8) hydrogen bonds : bond 0.03684 ( 806) hydrogen bonds : angle 3.72789 ( 2406) *********************** 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 189 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.540 Fit side-chains REVERT: B 211 ARG cc_start: 0.8879 (mtm-85) cc_final: 0.8651 (mtm-85) REVERT: B 458 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: B 475 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7511 (mp) REVERT: B 572 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: B 696 ARG cc_start: 0.8267 (mmt90) cc_final: 0.8047 (mmt90) REVERT: B 738 LEU cc_start: 0.8947 (tt) cc_final: 0.8742 (mp) REVERT: B 840 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7503 (mp) REVERT: A 141 ASN cc_start: 0.5777 (OUTLIER) cc_final: 0.4400 (t0) REVERT: A 700 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: A 927 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7438 (mp) REVERT: A 945 ASP cc_start: 0.6965 (t0) cc_final: 0.6669 (t0) outliers start: 37 outliers final: 23 residues processed: 180 average time/residue: 0.1497 time to fit residues: 37.2407 Evaluate side-chains 173 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 740 SER 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 334 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 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 146 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 37 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 52 optimal weight: 0.0370 chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 150 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 913 ASN A 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.162882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129141 restraints weight = 16619.275| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.97 r_work: 0.3207 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14118 Z= 0.107 Angle : 0.519 10.056 19212 Z= 0.252 Chirality : 0.037 0.175 2160 Planarity : 0.004 0.050 2558 Dihedral : 3.936 33.097 2016 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.20), residues: 1790 helix: 1.90 (0.16), residues: 1091 sheet: -1.31 (0.41), residues: 150 loop : -0.06 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 310 TYR 0.016 0.001 TYR B 379 PHE 0.011 0.001 PHE A 634 TRP 0.012 0.001 TRP B 437 HIS 0.005 0.000 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00245 (14114) covalent geometry : angle 0.51695 (19204) SS BOND : bond 0.00272 ( 4) SS BOND : angle 2.33578 ( 8) hydrogen bonds : bond 0.03402 ( 806) hydrogen bonds : angle 3.64430 ( 2406) *********************** 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 195 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.574 Fit side-chains REVERT: B 211 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.8584 (mtm-85) REVERT: B 363 GLN cc_start: 0.7977 (mm110) cc_final: 0.7750 (tt0) REVERT: B 475 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7436 (mp) REVERT: B 572 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: B 686 ASP cc_start: 0.8288 (t0) cc_final: 0.7823 (m-30) REVERT: B 704 GLU cc_start: 0.8666 (tt0) cc_final: 0.8463 (tt0) REVERT: B 739 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8207 (mtm180) REVERT: B 840 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7475 (mp) REVERT: A 141 ASN cc_start: 0.5662 (OUTLIER) cc_final: 0.4370 (t0) REVERT: A 700 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: A 827 ARG cc_start: 0.8359 (mpt-90) cc_final: 0.7877 (mmt90) REVERT: A 927 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7250 (mp) REVERT: A 945 ASP cc_start: 0.6935 (t0) cc_final: 0.6655 (t0) outliers start: 38 outliers final: 21 residues processed: 187 average time/residue: 0.1455 time to fit residues: 37.7966 Evaluate side-chains 175 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 739 ARG Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.161150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127106 restraints weight = 16569.466| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.08 r_work: 0.3226 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14118 Z= 0.144 Angle : 0.551 10.112 19212 Z= 0.267 Chirality : 0.038 0.173 2160 Planarity : 0.005 0.051 2558 Dihedral : 3.988 32.531 2016 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.80 % Allowed : 20.52 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.20), residues: 1790 helix: 1.83 (0.16), residues: 1089 sheet: -1.18 (0.42), residues: 148 loop : -0.11 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 696 TYR 0.010 0.001 TYR B 123 PHE 0.009 0.001 PHE A 990 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00348 (14114) covalent geometry : angle 0.54763 (19204) SS BOND : bond 0.00571 ( 4) SS BOND : angle 3.11689 ( 8) hydrogen bonds : bond 0.03753 ( 806) hydrogen bonds : angle 3.68612 ( 2406) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.522 Fit side-chains REVERT: B 211 ARG cc_start: 0.8847 (mtm-85) cc_final: 0.8578 (mtt90) REVERT: B 241 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8654 (p) REVERT: B 458 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: B 572 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: B 686 ASP cc_start: 0.8399 (t0) cc_final: 0.7942 (m-30) REVERT: B 704 GLU cc_start: 0.8676 (tt0) cc_final: 0.8468 (tt0) REVERT: B 739 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8197 (mtm180) REVERT: B 840 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7519 (mp) REVERT: A 141 ASN cc_start: 0.5625 (OUTLIER) cc_final: 0.4335 (t0) REVERT: A 700 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: A 827 ARG cc_start: 0.8366 (mpt-90) cc_final: 0.7881 (mmt90) REVERT: A 945 ASP cc_start: 0.6958 (t0) cc_final: 0.6681 (t0) outliers start: 39 outliers final: 26 residues processed: 182 average time/residue: 0.1541 time to fit residues: 38.8396 Evaluate side-chains 183 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 739 ARG Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 939 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 118 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 0.0470 chunk 64 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 128 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 135 optimal weight: 0.5980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.162221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127013 restraints weight = 16667.653| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.18 r_work: 0.3227 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1501 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= 0.116 Angle : 0.534 10.066 19212 Z= 0.258 Chirality : 0.037 0.173 2160 Planarity : 0.004 0.050 2558 Dihedral : 3.927 32.661 2016 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.73 % Allowed : 20.44 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.20), residues: 1790 helix: 1.90 (0.16), residues: 1089 sheet: -1.16 (0.41), residues: 159 loop : -0.00 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 310 TYR 0.009 0.001 TYR B 123 PHE 0.009 0.001 PHE A 990 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00271 (14114) covalent geometry : angle 0.53035 (19204) SS BOND : bond 0.00330 ( 4) SS BOND : angle 3.02294 ( 8) hydrogen bonds : bond 0.03488 ( 806) hydrogen bonds : angle 3.65224 ( 2406) *********************** 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 187 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.568 Fit side-chains REVERT: B 211 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8591 (mtt90) REVERT: B 241 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8645 (p) REVERT: B 458 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: B 475 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7519 (mp) REVERT: B 572 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: B 686 ASP cc_start: 0.8405 (t0) cc_final: 0.7966 (m-30) REVERT: B 704 GLU cc_start: 0.8701 (tt0) cc_final: 0.8497 (tt0) REVERT: B 739 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8247 (mtm180) REVERT: B 840 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7530 (mp) REVERT: A 141 ASN cc_start: 0.5648 (OUTLIER) cc_final: 0.4314 (t0) REVERT: A 700 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: A 827 ARG cc_start: 0.8370 (mpt-90) cc_final: 0.7886 (mmt90) REVERT: A 945 ASP cc_start: 0.6947 (t0) cc_final: 0.6666 (t0) outliers start: 38 outliers final: 24 residues processed: 181 average time/residue: 0.1629 time to fit residues: 40.6141 Evaluate side-chains 174 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 740 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 939 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 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 = 0.3850 r_free = 0.3850 target = 0.158998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122404 restraints weight = 16564.586| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.98 r_work: 0.3245 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14118 Z= 0.212 Angle : 0.613 10.716 19212 Z= 0.297 Chirality : 0.041 0.174 2160 Planarity : 0.005 0.051 2558 Dihedral : 4.168 32.024 2016 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.87 % Allowed : 20.16 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.20), residues: 1790 helix: 1.60 (0.16), residues: 1089 sheet: -1.19 (0.42), residues: 148 loop : -0.16 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 310 TYR 0.012 0.001 TYR B 123 PHE 0.016 0.002 PHE A 990 TRP 0.014 0.002 TRP B 437 HIS 0.004 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00522 (14114) covalent geometry : angle 0.60839 (19204) SS BOND : bond 0.00688 ( 4) SS BOND : angle 3.64395 ( 8) hydrogen bonds : bond 0.04460 ( 806) hydrogen bonds : angle 3.83762 ( 2406) ********************** 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 191 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.557 Fit side-chains REVERT: B 241 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8665 (p) REVERT: B 458 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: B 572 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: B 696 ARG cc_start: 0.8224 (mmt90) cc_final: 0.7987 (mmt90) REVERT: B 704 GLU cc_start: 0.8707 (tt0) cc_final: 0.8493 (tt0) REVERT: B 739 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8260 (mtm180) REVERT: B 840 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7569 (mp) REVERT: A 141 ASN cc_start: 0.5714 (OUTLIER) cc_final: 0.4278 (t0) REVERT: A 700 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: A 827 ARG cc_start: 0.8407 (mpt-90) cc_final: 0.7894 (mmt90) REVERT: A 945 ASP cc_start: 0.7027 (t0) cc_final: 0.6721 (t0) outliers start: 40 outliers final: 28 residues processed: 182 average time/residue: 0.1681 time to fit residues: 41.2958 Evaluate side-chains 177 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 740 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 939 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.151171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119311 restraints weight = 16364.666| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.64 r_work: 0.2994 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14118 Z= 0.176 Angle : 0.583 10.501 19212 Z= 0.284 Chirality : 0.040 0.173 2160 Planarity : 0.005 0.049 2558 Dihedral : 4.137 32.601 2016 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.58 % Allowed : 20.59 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.20), residues: 1790 helix: 1.64 (0.16), residues: 1089 sheet: -1.32 (0.40), residues: 155 loop : -0.09 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 310 TYR 0.012 0.001 TYR B 123 PHE 0.013 0.002 PHE A 990 TRP 0.014 0.001 TRP B 437 HIS 0.004 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00430 (14114) covalent geometry : angle 0.57952 (19204) SS BOND : bond 0.00506 ( 4) SS BOND : angle 3.30833 ( 8) hydrogen bonds : bond 0.04094 ( 806) hydrogen bonds : angle 3.79483 ( 2406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4229.32 seconds wall clock time: 72 minutes 48.60 seconds (4368.60 seconds total)