Starting phenix.real_space_refine on Sat Aug 23 06:42:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8se9_40407/08_2025/8se9_40407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8se9_40407/08_2025/8se9_40407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8se9_40407/08_2025/8se9_40407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8se9_40407/08_2025/8se9_40407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8se9_40407/08_2025/8se9_40407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8se9_40407/08_2025/8se9_40407.map" } resolution = 3.2 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= 0.023 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 38 5.16 5 C 6480 2.51 5 N 1790 2.21 5 O 1886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10195 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7693 Classifications: {'peptide': 989} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 923} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 633 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "D" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.29, per 1000 atoms: 0.22 Number of scatterers: 10195 At special positions: 0 Unit cell: (91.652, 105.816, 117.481, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 1 15.00 O 1886 8.00 N 1790 7.00 C 6480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS C 86 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 454.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 44.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.533A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.909A pdb=" N ASP A 71 " --> pdb=" O CYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.919A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.837A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 197 through 203 removed outlier: 4.268A pdb=" N HIS A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 357 through 378 Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.528A pdb=" N CYS A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 423 through 432 Processing helix chain 'A' and resid 441 through 455 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.921A pdb=" N ARG A 479 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 480 " --> pdb=" O LEU A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 480' Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.557A pdb=" N ASP A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.835A pdb=" N GLU A 521 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.359A pdb=" N ASP A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.602A pdb=" N THR A 600 " --> pdb=" O PRO A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 624 Processing helix chain 'A' and resid 624 through 631 removed outlier: 4.043A pdb=" N GLU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 644 through 653 removed outlier: 4.302A pdb=" N THR A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 removed outlier: 4.771A pdb=" N HIS A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 722 through 740 removed outlier: 3.638A pdb=" N TYR A 727 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 756 Processing helix chain 'A' and resid 760 through 763 removed outlier: 3.512A pdb=" N GLN A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 760 through 763' Processing helix chain 'A' and resid 764 through 770 removed outlier: 3.611A pdb=" N ILE A 768 " --> pdb=" O GLN A 764 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 798 Processing helix chain 'A' and resid 816 through 832 removed outlier: 3.553A pdb=" N PHE A 820 " --> pdb=" O PHE A 816 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 821 " --> pdb=" O HIS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 844 Processing helix chain 'A' and resid 853 through 874 removed outlier: 3.678A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 927 through 939 Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.589A pdb=" N LEU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 removed outlier: 3.605A pdb=" N GLY B 141 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.616A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.610A pdb=" N LEU C 48 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 49 " --> pdb=" O TYR C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 49' Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.642A pdb=" N VAL C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'D' and resid 103 through 116 removed outlier: 4.677A pdb=" N GLN D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 141 removed outlier: 3.991A pdb=" N GLU D 139 " --> pdb=" O PRO D 136 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY D 141 " --> pdb=" O GLY D 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.869A pdb=" N HIS A 62 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 37 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU A 36 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.630A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.404A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 254 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS A 183 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 509 through 512 removed outlier: 6.853A pdb=" N LEU A 464 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU A 512 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 466 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 437 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 559 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA7, first strand: chain 'A' and resid 917 through 920 removed outlier: 6.354A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A 945 " --> pdb=" O SER A 995 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ARG A 944 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA A 955 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.689A pdb=" N LEU B 85 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N MET B 150 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG B 87 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU B 152 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.025A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 85 through 86 removed outlier: 7.757A pdb=" N LEU D 85 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N MET D 150 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN D 151 " --> pdb=" O TRP D 123 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP D 123 " --> pdb=" O ASN D 151 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1146 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: 1.18 Time building geometry restraints manager: 1.16 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: 3379 1.34 - 1.46: 1342 1.46 - 1.57: 5665 1.57 - 1.69: 4 1.69 - 1.81: 57 Bond restraints: 10447 Sorted by residual: bond pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.426 1.624 -0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " ideal model delta sigma weight residual 1.524 1.363 0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" C6 AMP B1101 " pdb=" N6 AMP B1101 " ideal model delta sigma weight residual 1.355 1.499 -0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.426 1.294 0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C4 AMP B1101 " pdb=" C5 AMP B1101 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.30e+01 ... (remaining 10442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 14179 3.39 - 6.78: 38 6.78 - 10.18: 2 10.18 - 13.57: 3 13.57 - 16.96: 2 Bond angle restraints: 14224 Sorted by residual: angle pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" N9 AMP B1101 " ideal model delta sigma weight residual 109.47 126.43 -16.96 3.00e+00 1.11e-01 3.20e+01 angle pdb=" N9 AMP B1101 " pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 109.47 94.58 14.89 3.00e+00 1.11e-01 2.46e+01 angle pdb=" O2P AMP B1101 " pdb=" P AMP B1101 " pdb=" O3P AMP B1101 " ideal model delta sigma weight residual 119.90 106.91 12.99 3.00e+00 1.11e-01 1.87e+01 angle pdb=" C GLY A 187 " pdb=" N SER A 188 " pdb=" CA SER A 188 " ideal model delta sigma weight residual 121.80 132.20 -10.40 2.44e+00 1.68e-01 1.82e+01 angle pdb=" O1P AMP B1101 " pdb=" P AMP B1101 " pdb=" O2P AMP B1101 " ideal model delta sigma weight residual 119.60 106.93 12.67 3.00e+00 1.11e-01 1.78e+01 ... (remaining 14219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5886 17.67 - 35.35: 322 35.35 - 53.02: 65 53.02 - 70.70: 14 70.70 - 88.37: 8 Dihedral angle restraints: 6295 sinusoidal: 2548 harmonic: 3747 Sorted by residual: dihedral pdb=" CA SER A 188 " pdb=" C SER A 188 " pdb=" N PRO A 189 " pdb=" CA PRO A 189 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLN A 923 " pdb=" C GLN A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA GLN A 385 " pdb=" C GLN A 385 " pdb=" N TRP A 386 " pdb=" CA TRP A 386 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.53e+00 ... (remaining 6292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 987 0.029 - 0.058: 416 0.058 - 0.087: 105 0.087 - 0.116: 69 0.116 - 0.145: 11 Chirality restraints: 1588 Sorted by residual: chirality pdb=" C3' AMP B1101 " pdb=" C2' AMP B1101 " pdb=" C4' AMP B1101 " pdb=" O3' AMP B1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.14 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" C3' AMP B1101 " pdb=" O2' AMP B1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.37 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 945 " pdb=" N ILE A 945 " pdb=" C ILE A 945 " pdb=" CB ILE A 945 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1585 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 517 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 518 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 188 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 189 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 923 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 924 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 924 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 924 " -0.015 5.00e-02 4.00e+02 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 941 2.74 - 3.28: 10079 3.28 - 3.82: 16340 3.82 - 4.36: 18988 4.36 - 4.90: 33477 Nonbonded interactions: 79825 Sorted by model distance: nonbonded pdb=" OE1 GLU A 925 " pdb=" OG1 THR A 972 " model vdw 2.204 3.040 nonbonded pdb=" O TYR A 514 " pdb=" OH TYR A 524 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR C 46 " pdb=" O TYR C 75 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASP A 468 " pdb=" O2' AMP B1101 " model vdw 2.239 3.040 nonbonded pdb=" NE2 GLN C 15 " pdb=" O LEU C 25 " model vdw 2.289 3.120 ... (remaining 79820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 82 through 157) selection = chain 'D' } 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: 2.740 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.810 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.005 0.198 10450 Z= 0.260 Angle : 0.592 16.960 14226 Z= 0.271 Chirality : 0.038 0.145 1588 Planarity : 0.004 0.048 1865 Dihedral : 11.993 88.369 3868 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.41 % Favored : 96.43 % Rotamer: Outliers : 2.00 % Allowed : 7.45 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.24), residues: 1289 helix: 1.53 (0.24), residues: 457 sheet: -0.62 (0.40), residues: 171 loop : -0.21 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 118 TYR 0.008 0.001 TYR C 61 PHE 0.008 0.001 PHE A 146 TRP 0.006 0.001 TRP C 95 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00485 (10447) covalent geometry : angle 0.59229 (14224) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.71986 ( 2) hydrogen bonds : bond 0.16395 ( 411) hydrogen bonds : angle 6.83715 ( 1146) Misc. bond : bond 0.08991 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 225 PRO cc_start: 0.8058 (Cg_exo) cc_final: 0.7802 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7357 (tm-30) cc_final: 0.6963 (tm-30) REVERT: A 373 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8519 (mm) REVERT: A 508 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7171 (mt0) REVERT: A 531 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7513 (ptp-110) REVERT: A 638 THR cc_start: 0.3737 (OUTLIER) cc_final: 0.3269 (m) REVERT: A 738 MET cc_start: 0.3515 (ppp) cc_final: 0.0512 (mmm) REVERT: C 5 MET cc_start: 0.8894 (tpt) cc_final: 0.8506 (tpt) REVERT: C 43 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 70 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: D 99 ARG cc_start: 0.8030 (mmp-170) cc_final: 0.7529 (mmm160) outliers start: 22 outliers final: 10 residues processed: 152 average time/residue: 0.1060 time to fit residues: 22.1173 Evaluate side-chains 120 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0020 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 140 HIS A 199 ASN A 634 GLN A 637 HIS A 786 GLN A 817 HIS A 939 HIS A1009 HIS B 106 HIS B 110 GLN C 103 GLN D 106 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.201511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151788 restraints weight = 12418.360| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.69 r_work: 0.3199 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10450 Z= 0.119 Angle : 0.566 10.411 14226 Z= 0.272 Chirality : 0.039 0.213 1588 Planarity : 0.004 0.054 1865 Dihedral : 5.929 59.560 1432 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 2.09 % Allowed : 10.55 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.24), residues: 1289 helix: 1.59 (0.24), residues: 470 sheet: -0.61 (0.40), residues: 170 loop : -0.28 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 258 TYR 0.019 0.001 TYR B 140 PHE 0.015 0.001 PHE A 481 TRP 0.017 0.001 TRP A 677 HIS 0.007 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00269 (10447) covalent geometry : angle 0.56621 (14224) SS BOND : bond 0.00256 ( 1) SS BOND : angle 0.44445 ( 2) hydrogen bonds : bond 0.03990 ( 411) hydrogen bonds : angle 5.26521 ( 1146) Misc. bond : bond 0.00067 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8640 (mp) REVERT: A 225 PRO cc_start: 0.8425 (Cg_exo) cc_final: 0.8198 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 373 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8720 (mm) REVERT: A 508 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7367 (mt0) REVERT: A 531 ARG cc_start: 0.7944 (mtm110) cc_final: 0.7684 (ptp-110) REVERT: A 568 TRP cc_start: 0.8704 (m100) cc_final: 0.8434 (m100) REVERT: A 638 THR cc_start: 0.3937 (OUTLIER) cc_final: 0.3640 (m) REVERT: A 738 MET cc_start: 0.3672 (ppp) cc_final: 0.0733 (mmm) REVERT: C 5 MET cc_start: 0.8781 (tpt) cc_final: 0.8410 (tpt) REVERT: C 70 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8064 (m-80) REVERT: D 99 ARG cc_start: 0.8190 (mmp-170) cc_final: 0.7674 (mmm160) REVERT: D 110 GLN cc_start: 0.1936 (OUTLIER) cc_final: 0.1480 (mp10) outliers start: 23 outliers final: 11 residues processed: 130 average time/residue: 0.0912 time to fit residues: 16.4351 Evaluate side-chains 125 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 0.1980 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 HIS C 103 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.199624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125525 restraints weight = 12483.754| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.50 r_work: 0.3248 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10450 Z= 0.155 Angle : 0.573 10.355 14226 Z= 0.272 Chirality : 0.040 0.131 1588 Planarity : 0.004 0.055 1865 Dihedral : 5.946 59.936 1430 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 2.64 % Allowed : 11.00 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.24), residues: 1289 helix: 1.52 (0.24), residues: 469 sheet: -0.63 (0.40), residues: 170 loop : -0.37 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 137 TYR 0.012 0.001 TYR B 140 PHE 0.013 0.001 PHE A 481 TRP 0.019 0.001 TRP A 677 HIS 0.005 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00376 (10447) covalent geometry : angle 0.57335 (14224) SS BOND : bond 0.00278 ( 1) SS BOND : angle 0.52729 ( 2) hydrogen bonds : bond 0.03662 ( 411) hydrogen bonds : angle 5.01001 ( 1146) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8812 (mp) REVERT: A 225 PRO cc_start: 0.8515 (Cg_exo) cc_final: 0.8257 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6710 (ttm170) cc_final: 0.6467 (ttm170) REVERT: A 273 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7474 (tm-30) REVERT: A 373 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8755 (mm) REVERT: A 508 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7340 (mt0) REVERT: A 531 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7691 (ptp-110) REVERT: A 568 TRP cc_start: 0.8818 (m100) cc_final: 0.8549 (m100) REVERT: A 638 THR cc_start: 0.4237 (OUTLIER) cc_final: 0.3997 (m) REVERT: A 738 MET cc_start: 0.3996 (ppp) cc_final: 0.1251 (mmm) REVERT: C 5 MET cc_start: 0.8869 (tpt) cc_final: 0.8472 (tpt) REVERT: C 70 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: C 128 LEU cc_start: 0.8341 (mp) cc_final: 0.7992 (tt) REVERT: D 99 ARG cc_start: 0.8297 (mmp-170) cc_final: 0.7785 (mmm160) REVERT: D 110 GLN cc_start: 0.2068 (OUTLIER) cc_final: 0.1794 (mp10) outliers start: 29 outliers final: 17 residues processed: 131 average time/residue: 0.0911 time to fit residues: 16.8853 Evaluate side-chains 131 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 84 optimal weight: 0.2980 chunk 127 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.199281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.124930 restraints weight = 12593.471| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.24 r_work: 0.3293 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10450 Z= 0.160 Angle : 0.573 10.341 14226 Z= 0.272 Chirality : 0.040 0.136 1588 Planarity : 0.004 0.055 1865 Dihedral : 5.988 59.347 1430 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 3.09 % Allowed : 11.55 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.24), residues: 1289 helix: 1.48 (0.24), residues: 471 sheet: -0.71 (0.39), residues: 170 loop : -0.39 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 23 TYR 0.020 0.001 TYR B 140 PHE 0.013 0.001 PHE A 481 TRP 0.022 0.001 TRP A 677 HIS 0.003 0.001 HIS A1009 Details of bonding type rmsd covalent geometry : bond 0.00392 (10447) covalent geometry : angle 0.57302 (14224) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.39454 ( 2) hydrogen bonds : bond 0.03489 ( 411) hydrogen bonds : angle 4.87762 ( 1146) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8824 (mp) REVERT: A 225 PRO cc_start: 0.8476 (Cg_exo) cc_final: 0.8212 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6737 (ttm170) cc_final: 0.6501 (ttm170) REVERT: A 273 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7332 (tm-30) REVERT: A 508 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7326 (pt0) REVERT: A 531 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7638 (ptp-110) REVERT: A 568 TRP cc_start: 0.8788 (m100) cc_final: 0.8518 (m100) REVERT: A 610 HIS cc_start: 0.6951 (m90) cc_final: 0.6739 (m90) REVERT: A 638 THR cc_start: 0.4229 (OUTLIER) cc_final: 0.3991 (m) REVERT: A 713 GLN cc_start: 0.9043 (tt0) cc_final: 0.8685 (pp30) REVERT: A 738 MET cc_start: 0.3901 (ppp) cc_final: 0.1190 (mmm) REVERT: A 864 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8569 (mt) REVERT: C 5 MET cc_start: 0.8833 (tpt) cc_final: 0.8470 (tpt) REVERT: C 70 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8064 (m-80) REVERT: C 128 LEU cc_start: 0.8302 (mp) cc_final: 0.7922 (tt) REVERT: D 99 ARG cc_start: 0.8247 (mmp-170) cc_final: 0.7738 (mmm160) REVERT: D 110 GLN cc_start: 0.2526 (OUTLIER) cc_final: 0.2317 (mp10) outliers start: 34 outliers final: 20 residues processed: 136 average time/residue: 0.0909 time to fit residues: 17.4478 Evaluate side-chains 133 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 55 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 78 optimal weight: 0.0060 chunk 93 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.200606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125860 restraints weight = 12508.478| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.21 r_work: 0.3308 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10450 Z= 0.112 Angle : 0.555 10.336 14226 Z= 0.261 Chirality : 0.039 0.212 1588 Planarity : 0.004 0.054 1865 Dihedral : 5.768 59.289 1428 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 2.36 % Allowed : 13.09 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.24), residues: 1289 helix: 1.58 (0.24), residues: 473 sheet: -0.77 (0.40), residues: 164 loop : -0.33 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 137 TYR 0.008 0.001 TYR A 547 PHE 0.015 0.001 PHE A 481 TRP 0.020 0.001 TRP A 677 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00266 (10447) covalent geometry : angle 0.55470 (14224) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.28279 ( 2) hydrogen bonds : bond 0.03236 ( 411) hydrogen bonds : angle 4.71742 ( 1146) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8776 (mp) REVERT: A 225 PRO cc_start: 0.8462 (Cg_exo) cc_final: 0.8182 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6726 (ttm170) cc_final: 0.6459 (ttm170) REVERT: A 273 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 373 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8745 (mm) REVERT: A 508 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7508 (pt0) REVERT: A 531 ARG cc_start: 0.7970 (mtm110) cc_final: 0.7640 (ptp-110) REVERT: A 638 THR cc_start: 0.4212 (OUTLIER) cc_final: 0.3987 (m) REVERT: A 713 GLN cc_start: 0.9063 (tt0) cc_final: 0.8706 (pp30) REVERT: A 738 MET cc_start: 0.3879 (ppp) cc_final: 0.1184 (mmm) REVERT: A 864 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8524 (mt) REVERT: C 5 MET cc_start: 0.8809 (tpt) cc_final: 0.8362 (tpt) REVERT: C 70 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: C 128 LEU cc_start: 0.8308 (mp) cc_final: 0.7912 (tt) REVERT: D 110 GLN cc_start: 0.2502 (OUTLIER) cc_final: 0.2295 (mp10) outliers start: 26 outliers final: 14 residues processed: 128 average time/residue: 0.0860 time to fit residues: 15.7099 Evaluate side-chains 127 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.199147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124282 restraints weight = 12609.190| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.49 r_work: 0.3265 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10450 Z= 0.131 Angle : 0.556 10.334 14226 Z= 0.262 Chirality : 0.039 0.148 1588 Planarity : 0.004 0.054 1865 Dihedral : 5.727 59.799 1428 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.27 % Allowed : 14.27 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.24), residues: 1289 helix: 1.62 (0.24), residues: 472 sheet: -0.78 (0.40), residues: 164 loop : -0.33 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 137 TYR 0.014 0.001 TYR B 140 PHE 0.017 0.001 PHE A 481 TRP 0.022 0.001 TRP A 677 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00320 (10447) covalent geometry : angle 0.55577 (14224) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.30311 ( 2) hydrogen bonds : bond 0.03223 ( 411) hydrogen bonds : angle 4.66097 ( 1146) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8791 (mp) REVERT: A 225 PRO cc_start: 0.8513 (Cg_exo) cc_final: 0.8222 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6736 (ttm170) cc_final: 0.5898 (ttm170) REVERT: A 273 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7456 (tm-30) REVERT: A 373 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8782 (mm) REVERT: A 508 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7560 (pt0) REVERT: A 738 MET cc_start: 0.3940 (ppp) cc_final: 0.1283 (mmm) REVERT: A 864 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8523 (mt) REVERT: C 5 MET cc_start: 0.8803 (tpt) cc_final: 0.8392 (tpt) REVERT: C 43 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7716 (tm-30) REVERT: C 70 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: C 128 LEU cc_start: 0.8326 (mp) cc_final: 0.7931 (tt) REVERT: D 99 ARG cc_start: 0.8291 (mmp-170) cc_final: 0.7682 (mmm160) REVERT: D 110 GLN cc_start: 0.2632 (OUTLIER) cc_final: 0.2425 (mp10) outliers start: 25 outliers final: 17 residues processed: 128 average time/residue: 0.0913 time to fit residues: 16.4978 Evaluate side-chains 126 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 17 optimal weight: 7.9990 chunk 89 optimal weight: 0.2980 chunk 85 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.199570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126107 restraints weight = 12510.421| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.22 r_work: 0.3330 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10450 Z= 0.106 Angle : 0.539 10.348 14226 Z= 0.253 Chirality : 0.038 0.130 1588 Planarity : 0.004 0.052 1865 Dihedral : 5.518 59.256 1427 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 2.00 % Allowed : 14.64 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1289 helix: 1.70 (0.24), residues: 472 sheet: -0.72 (0.40), residues: 164 loop : -0.28 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.012 0.001 TYR B 140 PHE 0.014 0.001 PHE A 481 TRP 0.022 0.001 TRP A 677 HIS 0.003 0.000 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00253 (10447) covalent geometry : angle 0.53929 (14224) SS BOND : bond 0.00232 ( 1) SS BOND : angle 0.29575 ( 2) hydrogen bonds : bond 0.03029 ( 411) hydrogen bonds : angle 4.55392 ( 1146) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PRO cc_start: 0.8463 (Cg_exo) cc_final: 0.8190 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6673 (ttm170) cc_final: 0.5848 (ttm170) REVERT: A 373 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8715 (mm) REVERT: A 508 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7525 (pt0) REVERT: A 531 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7600 (ptp-110) REVERT: A 568 TRP cc_start: 0.8709 (m100) cc_final: 0.8408 (m-90) REVERT: A 738 MET cc_start: 0.3822 (ppp) cc_final: 0.1248 (mmm) REVERT: A 864 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8505 (mt) REVERT: C 70 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: C 128 LEU cc_start: 0.8298 (mp) cc_final: 0.7903 (tt) REVERT: D 110 GLN cc_start: 0.2553 (OUTLIER) cc_final: 0.2353 (mp10) outliers start: 22 outliers final: 14 residues processed: 128 average time/residue: 0.1011 time to fit residues: 18.2611 Evaluate side-chains 123 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.199124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126631 restraints weight = 12533.350| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.33 r_work: 0.3274 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10450 Z= 0.158 Angle : 0.577 10.283 14226 Z= 0.273 Chirality : 0.040 0.134 1588 Planarity : 0.004 0.054 1865 Dihedral : 5.434 59.122 1425 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.18 % Allowed : 14.82 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.24), residues: 1289 helix: 1.57 (0.24), residues: 472 sheet: -0.65 (0.40), residues: 161 loop : -0.34 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 137 TYR 0.024 0.001 TYR A 603 PHE 0.010 0.001 PHE A 481 TRP 0.019 0.001 TRP A 677 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00392 (10447) covalent geometry : angle 0.57671 (14224) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.38193 ( 2) hydrogen bonds : bond 0.03357 ( 411) hydrogen bonds : angle 4.64381 ( 1146) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.6715 (ttm170) cc_final: 0.5900 (ttm170) REVERT: A 470 ASP cc_start: 0.8224 (m-30) cc_final: 0.7882 (m-30) REVERT: A 508 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7380 (pt0) REVERT: A 738 MET cc_start: 0.3850 (ppp) cc_final: 0.1328 (mmm) REVERT: A 864 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8589 (mt) REVERT: C 43 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7707 (tm-30) REVERT: C 70 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: C 128 LEU cc_start: 0.8257 (mp) cc_final: 0.7879 (tt) outliers start: 24 outliers final: 17 residues processed: 121 average time/residue: 0.0863 time to fit residues: 14.6982 Evaluate side-chains 119 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 118 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.199968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126713 restraints weight = 12468.650| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.43 r_work: 0.3278 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10450 Z= 0.129 Angle : 0.570 10.281 14226 Z= 0.269 Chirality : 0.039 0.130 1588 Planarity : 0.004 0.053 1865 Dihedral : 5.181 59.592 1422 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.41 % Favored : 96.51 % Rotamer: Outliers : 2.09 % Allowed : 15.18 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.24), residues: 1289 helix: 1.61 (0.24), residues: 471 sheet: -0.64 (0.40), residues: 161 loop : -0.33 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 99 TYR 0.020 0.001 TYR A 603 PHE 0.022 0.001 PHE A 481 TRP 0.023 0.001 TRP A 677 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00312 (10447) covalent geometry : angle 0.56991 (14224) SS BOND : bond 0.00215 ( 1) SS BOND : angle 0.37411 ( 2) hydrogen bonds : bond 0.03258 ( 411) hydrogen bonds : angle 4.57726 ( 1146) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.6691 (ttm170) cc_final: 0.5866 (ttm170) REVERT: A 470 ASP cc_start: 0.8237 (m-30) cc_final: 0.7897 (m-30) REVERT: A 508 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7385 (pt0) REVERT: A 738 MET cc_start: 0.3871 (ppp) cc_final: 0.1391 (mmm) REVERT: A 864 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8564 (mt) REVERT: C 43 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7711 (tm-30) REVERT: C 70 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: C 128 LEU cc_start: 0.8260 (mp) cc_final: 0.7899 (tt) REVERT: D 99 ARG cc_start: 0.8007 (mmp-170) cc_final: 0.7388 (mmp80) outliers start: 23 outliers final: 17 residues processed: 121 average time/residue: 0.0959 time to fit residues: 16.4138 Evaluate side-chains 120 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.0040 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 0.0000 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.199971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128754 restraints weight = 12363.238| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.34 r_work: 0.3308 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10450 Z= 0.106 Angle : 0.557 10.312 14226 Z= 0.265 Chirality : 0.039 0.144 1588 Planarity : 0.004 0.052 1865 Dihedral : 5.046 58.048 1422 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 2.18 % Allowed : 15.09 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1289 helix: 1.67 (0.24), residues: 471 sheet: -0.57 (0.40), residues: 161 loop : -0.30 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 137 TYR 0.020 0.001 TYR A 603 PHE 0.021 0.001 PHE A 481 TRP 0.030 0.001 TRP A 677 HIS 0.003 0.000 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00251 (10447) covalent geometry : angle 0.55720 (14224) SS BOND : bond 0.00242 ( 1) SS BOND : angle 0.35214 ( 2) hydrogen bonds : bond 0.03063 ( 411) hydrogen bonds : angle 4.50440 ( 1146) Misc. bond : bond 0.00020 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7297 (mt0) REVERT: A 568 TRP cc_start: 0.8585 (m100) cc_final: 0.8094 (m-90) REVERT: A 713 GLN cc_start: 0.9050 (tt0) cc_final: 0.8725 (pp30) REVERT: A 738 MET cc_start: 0.3810 (ppp) cc_final: 0.1323 (mmm) REVERT: A 864 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8557 (mt) REVERT: C 43 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7653 (tm-30) REVERT: C 128 LEU cc_start: 0.8301 (mp) cc_final: 0.7932 (tt) REVERT: D 99 ARG cc_start: 0.7935 (mmp-170) cc_final: 0.7601 (mmp80) outliers start: 24 outliers final: 16 residues processed: 124 average time/residue: 0.0996 time to fit residues: 17.3746 Evaluate side-chains 121 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.197682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128112 restraints weight = 12526.257| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.24 r_work: 0.3242 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10450 Z= 0.210 Angle : 0.626 10.239 14226 Z= 0.299 Chirality : 0.041 0.129 1588 Planarity : 0.004 0.055 1865 Dihedral : 5.288 57.746 1420 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 1.82 % Allowed : 15.73 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.24), residues: 1289 helix: 1.41 (0.24), residues: 472 sheet: -0.64 (0.41), residues: 154 loop : -0.47 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 137 TYR 0.015 0.001 TYR A 603 PHE 0.018 0.001 PHE A 481 TRP 0.024 0.001 TRP A 677 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00523 (10447) covalent geometry : angle 0.62647 (14224) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.47339 ( 2) hydrogen bonds : bond 0.03686 ( 411) hydrogen bonds : angle 4.70034 ( 1146) Misc. bond : bond 0.00051 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3128.58 seconds wall clock time: 53 minutes 54.46 seconds (3234.46 seconds total)