Starting phenix.real_space_refine on Thu Mar 5 10:15:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r4i_53567/03_2026/9r4i_53567_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r4i_53567/03_2026/9r4i_53567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r4i_53567/03_2026/9r4i_53567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r4i_53567/03_2026/9r4i_53567.map" model { file = "/net/cci-nas-00/data/ceres_data/9r4i_53567/03_2026/9r4i_53567_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r4i_53567/03_2026/9r4i_53567_trim.cif" } resolution = 2.92 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= 0.002 sd= 1.077 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: 8 Type Number sf(0) Gaussians K 4 8.98 5 Zn 2 6.06 5 P 12 5.49 5 S 66 5.16 5 C 6638 2.51 5 N 1791 2.21 5 O 1962 1.98 5 H 10188 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20663 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5878 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "B" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 3029 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 15, 'TRANS': 170} Chain breaks: 2 Chain: "C" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1531 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain breaks: 1 Chain: "D" Number of atoms: 5878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5878 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2738 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 12, 'TRANS': 155} Chain breaks: 1 Chain: "F" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1531 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain breaks: 1 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' K': 2, ' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.66, per 1000 atoms: 0.18 Number of scatterers: 20663 At special positions: 0 Unit cell: (120.1, 144.12, 136.914, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 4 19.00 S 66 16.00 P 12 15.00 O 1962 8.00 N 1791 7.00 C 6638 6.00 H 10188 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 544.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 178 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 178 " 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 3 sheets defined 51.2% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 removed outlier: 3.936A pdb=" N TYR A 22 " --> pdb=" O VAL A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.637A pdb=" N ARG A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.756A pdb=" N MET A 51 " --> pdb=" O TYR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 69 through 79 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 105 through 126 Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.858A pdb=" N LEU A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 233 through 252 Proline residue: A 243 - end of helix Processing helix chain 'A' and resid 277 through 290 removed outlier: 4.061A pdb=" N CYS A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 321 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 355 through 372 removed outlier: 3.751A pdb=" N MET A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 744 Processing helix chain 'B' and resid 762 through 777 removed outlier: 4.065A pdb=" N GLN B 766 " --> pdb=" O SER B 762 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS B 777 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 798 Processing helix chain 'B' and resid 801 through 811 Processing helix chain 'B' and resid 834 through 849 Processing helix chain 'B' and resid 851 through 859 Processing helix chain 'B' and resid 863 through 874 Processing helix chain 'C' and resid 62 through 105 removed outlier: 3.732A pdb=" N ASP C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Proline residue: C 76 - end of helix removed outlier: 3.856A pdb=" N LYS C 88 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS C 91 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N PHE C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE C 93 " --> pdb=" O TYR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 125 removed outlier: 4.379A pdb=" N LEU C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 removed outlier: 4.052A pdb=" N ASP C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 22 removed outlier: 4.047A pdb=" N TYR D 22 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 46 removed outlier: 3.929A pdb=" N ARG D 36 " --> pdb=" O PRO D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.902A pdb=" N MET D 51 " --> pdb=" O TYR D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 removed outlier: 4.045A pdb=" N MET D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 79 Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.934A pdb=" N MET D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 95 Processing helix chain 'D' and resid 105 through 126 Processing helix chain 'D' and resid 154 through 165 removed outlier: 3.637A pdb=" N LEU D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 187 removed outlier: 3.664A pdb=" N GLU D 184 " --> pdb=" O GLY D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 Proline residue: D 243 - end of helix Processing helix chain 'D' and resid 262 through 266 removed outlier: 4.228A pdb=" N SER D 265 " --> pdb=" O GLY D 262 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 266 " --> pdb=" O SER D 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 262 through 266' Processing helix chain 'D' and resid 277 through 290 removed outlier: 3.804A pdb=" N CYS D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 285 " --> pdb=" O HIS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 321 Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 355 through 372 removed outlier: 4.019A pdb=" N MET D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 744 Processing helix chain 'E' and resid 762 through 776 removed outlier: 4.085A pdb=" N GLN E 766 " --> pdb=" O SER E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 785 removed outlier: 4.587A pdb=" N GLY E 785 " --> pdb=" O PRO E 782 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 798 Processing helix chain 'E' and resid 801 through 811 Processing helix chain 'E' and resid 834 through 849 Processing helix chain 'E' and resid 851 through 859 Processing helix chain 'E' and resid 863 through 874 Processing helix chain 'F' and resid 62 through 89 Proline residue: F 76 - end of helix removed outlier: 3.670A pdb=" N GLU F 80 " --> pdb=" O PRO F 76 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS F 88 " --> pdb=" O THR F 84 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR F 89 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 105 Processing helix chain 'F' and resid 109 through 131 removed outlier: 3.523A pdb=" N LEU F 113 " --> pdb=" O ASP F 109 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU F 128 " --> pdb=" O GLN F 124 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE F 129 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 228 removed outlier: 8.065A pdb=" N VAL A 224 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N TYR A 226 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 197 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 228 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N HIS A 199 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 170 " --> pdb=" O MET A 194 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL A 196 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR A 172 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE A 198 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP A 174 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N LYS A 200 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 257 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU A 298 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU A 259 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA A 132 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N CYS A 12 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 11 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N TYR A 54 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR A 13 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A 53 " --> pdb=" O VAL B 752 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 223 through 228 removed outlier: 8.378A pdb=" N VAL D 224 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR D 195 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N TYR D 226 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER D 197 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU D 228 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N HIS D 199 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL D 257 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU D 298 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU D 259 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA D 132 " --> pdb=" O MET D 297 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS D 12 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL D 11 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR D 54 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR D 13 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE D 53 " --> pdb=" O VAL E 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 46 through 47 removed outlier: 3.810A pdb=" N MET F 56 " --> pdb=" O GLN F 46 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10162 1.03 - 1.23: 29 1.23 - 1.42: 4581 1.42 - 1.62: 6020 1.62 - 1.81: 118 Bond restraints: 20910 Sorted by residual: bond pdb=" C ARG B 816 " pdb=" O ARG B 816 " ideal model delta sigma weight residual 1.249 1.237 0.011 8.50e-03 1.38e+04 1.83e+00 bond pdb=" CA THR B 655 " pdb=" CB THR B 655 " ideal model delta sigma weight residual 1.528 1.543 -0.015 1.68e-02 3.54e+03 7.72e-01 bond pdb=" CG1 ILE D 53 " pdb=" CD1 ILE D 53 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.91e-01 bond pdb=" CA VAL C 108 " pdb=" CB VAL C 108 " ideal model delta sigma weight residual 1.528 1.538 -0.011 1.34e-02 5.57e+03 6.16e-01 bond pdb=" CA VAL D 96 " pdb=" CB VAL D 96 " ideal model delta sigma weight residual 1.533 1.542 -0.010 1.26e-02 6.30e+03 5.70e-01 ... (remaining 20905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 35329 1.08 - 2.15: 2196 2.15 - 3.23: 111 3.23 - 4.31: 42 4.31 - 5.38: 6 Bond angle restraints: 37684 Sorted by residual: angle pdb=" N VAL E 752 " pdb=" CA VAL E 752 " pdb=" C VAL E 752 " ideal model delta sigma weight residual 112.96 109.31 3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" N ALA E 823 " pdb=" CA ALA E 823 " pdb=" C ALA E 823 " ideal model delta sigma weight residual 113.97 109.37 4.60 1.28e+00 6.10e-01 1.29e+01 angle pdb=" N VAL B 752 " pdb=" CA VAL B 752 " pdb=" C VAL B 752 " ideal model delta sigma weight residual 112.96 109.48 3.48 1.00e+00 1.00e+00 1.21e+01 angle pdb=" N THR A 208 " pdb=" CA THR A 208 " pdb=" C THR A 208 " ideal model delta sigma weight residual 114.56 111.24 3.32 1.27e+00 6.20e-01 6.84e+00 angle pdb=" C MET D 249 " pdb=" CA MET D 249 " pdb=" CB MET D 249 " ideal model delta sigma weight residual 110.90 106.83 4.07 1.58e+00 4.01e-01 6.63e+00 ... (remaining 37679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9042 17.99 - 35.98: 671 35.98 - 53.98: 172 53.98 - 71.97: 51 71.97 - 89.96: 15 Dihedral angle restraints: 9951 sinusoidal: 5398 harmonic: 4553 Sorted by residual: dihedral pdb=" CA THR A 304 " pdb=" C THR A 304 " pdb=" N ILE A 305 " pdb=" CA ILE A 305 " ideal model delta harmonic sigma weight residual 180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA TYR A 204 " pdb=" C TYR A 204 " pdb=" N PHE A 205 " pdb=" CA PHE A 205 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP F 109 " pdb=" CB ASP F 109 " pdb=" CG ASP F 109 " pdb=" OD1 ASP F 109 " ideal model delta sinusoidal sigma weight residual -30.00 -90.22 60.22 1 2.00e+01 2.50e-03 1.21e+01 ... (remaining 9948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 930 0.026 - 0.052: 388 0.052 - 0.078: 136 0.078 - 0.105: 48 0.105 - 0.131: 30 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CA ILE B 723 " pdb=" N ILE B 723 " pdb=" C ILE B 723 " pdb=" CB ILE B 723 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE E 859 " pdb=" N ILE E 859 " pdb=" C ILE E 859 " pdb=" CB ILE E 859 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE D 131 " pdb=" N ILE D 131 " pdb=" C ILE D 131 " pdb=" CB ILE D 131 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1529 not shown) Planarity restraints: 3073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 657 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO E 658 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 658 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 658 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 62 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO C 63 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 63 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 63 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 31 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 32 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.022 5.00e-02 4.00e+02 ... (remaining 3070 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.26: 2677 2.26 - 2.98: 55311 2.98 - 3.70: 75002 3.70 - 4.42: 118405 4.42 - 5.14: 186618 Nonbonded interactions: 438013 Sorted by model distance: nonbonded pdb=" OE1 GLU A 98 " pdb=" H GLU A 98 " model vdw 1.535 2.450 nonbonded pdb=" OD1 ASN D 21 " pdb="HH12 ARG D 36 " model vdw 1.556 2.450 nonbonded pdb=" OE1 GLU D 98 " pdb=" H GLU D 98 " model vdw 1.595 2.450 nonbonded pdb=" O ASP E 801 " pdb=" HG1 THR E 805 " model vdw 1.632 2.450 nonbonded pdb=" HZ1 LYS A 126 " pdb=" O ASP B 745 " model vdw 1.639 2.450 ... (remaining 438008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 376 or resid 503)) selection = (chain 'D' and (resid 7 through 376 or resid 503)) } ncs_group { reference = (chain 'B' and (resid 653 through 662 or resid 719 through 796 or (resid 797 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or \ resid 798 through 823 or (resid 824 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG2 \ 1 or name HG22 or name HG23)) or resid 825 through 876)) selection = (chain 'E' and (resid 653 through 815 or (resid 816 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22) \ ) or resid 817 through 876)) } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 1.480 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.550 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.009 0.896 10725 Z= 0.875 Angle : 0.537 5.384 14506 Z= 0.300 Chirality : 0.037 0.131 1532 Planarity : 0.004 0.058 1865 Dihedral : 14.465 89.959 4075 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.12 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1262 helix: 1.00 (0.23), residues: 594 sheet: 0.92 (0.52), residues: 104 loop : -1.45 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 838 TYR 0.021 0.001 TYR A 204 PHE 0.010 0.001 PHE A 252 TRP 0.005 0.001 TRP E 756 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00278 (10722) covalent geometry : angle 0.53672 (14506) hydrogen bonds : bond 0.17162 ( 428) hydrogen bonds : angle 6.60016 ( 1212) metal coordination : bond 0.00173 ( 2) Misc. bond : bond 0.89637 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9242 (mtp) cc_final: 0.9005 (mtm) REVERT: B 631 GLN cc_start: 0.7176 (pp30) cc_final: 0.6932 (pp30) REVERT: B 819 ASN cc_start: 0.8599 (t0) cc_final: 0.8328 (t0) REVERT: C 56 MET cc_start: 0.7946 (ppp) cc_final: 0.7610 (ppp) REVERT: C 102 ASP cc_start: 0.9055 (m-30) cc_final: 0.8817 (m-30) REVERT: D 155 ASP cc_start: 0.8648 (p0) cc_final: 0.8131 (p0) REVERT: E 654 TYR cc_start: 0.8327 (t80) cc_final: 0.7735 (t80) REVERT: E 732 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8400 (mp0) REVERT: E 733 ILE cc_start: 0.9371 (pt) cc_final: 0.9150 (mp) REVERT: E 768 GLN cc_start: 0.8781 (mt0) cc_final: 0.8447 (mt0) REVERT: E 770 GLU cc_start: 0.8871 (tp30) cc_final: 0.8604 (mm-30) REVERT: E 804 GLU cc_start: 0.9010 (tp30) cc_final: 0.8601 (tp30) REVERT: E 851 ASP cc_start: 0.8524 (t70) cc_final: 0.8162 (t0) REVERT: E 869 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8548 (tm-30) REVERT: F 46 GLN cc_start: 0.7882 (pp30) cc_final: 0.6443 (pp30) REVERT: F 81 GLU cc_start: 0.8783 (mm-30) cc_final: 0.7972 (mm-30) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.3402 time to fit residues: 231.8415 Evaluate side-chains 113 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN D 275 ASN E 866 GLN F 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.073722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.054010 restraints weight = 78747.371| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.12 r_work: 0.2732 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10725 Z= 0.199 Angle : 0.566 7.071 14506 Z= 0.294 Chirality : 0.038 0.136 1532 Planarity : 0.005 0.053 1865 Dihedral : 5.621 59.826 1499 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.99 % Favored : 94.85 % Rotamer: Outliers : 0.44 % Allowed : 7.73 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.24), residues: 1262 helix: 1.24 (0.22), residues: 602 sheet: 0.89 (0.52), residues: 104 loop : -1.44 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 763 TYR 0.015 0.001 TYR D 48 PHE 0.016 0.001 PHE A 291 TRP 0.004 0.001 TRP C 38 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00450 (10722) covalent geometry : angle 0.56608 (14506) hydrogen bonds : bond 0.05146 ( 428) hydrogen bonds : angle 4.69254 ( 1212) metal coordination : bond 0.00393 ( 2) Misc. bond : bond 0.00621 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9247 (mtp) cc_final: 0.8847 (mtm) REVERT: A 162 GLU cc_start: 0.8709 (tp30) cc_final: 0.8419 (mm-30) REVERT: B 631 GLN cc_start: 0.7041 (pp30) cc_final: 0.6689 (pp30) REVERT: B 819 ASN cc_start: 0.9029 (t0) cc_final: 0.8803 (t0) REVERT: C 80 GLU cc_start: 0.8423 (pp20) cc_final: 0.8177 (pp20) REVERT: C 81 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8581 (mt-10) REVERT: C 102 ASP cc_start: 0.8881 (m-30) cc_final: 0.8565 (m-30) REVERT: D 91 MET cc_start: 0.9392 (mtm) cc_final: 0.9188 (mtm) REVERT: D 155 ASP cc_start: 0.8629 (p0) cc_final: 0.8201 (p0) REVERT: E 654 TYR cc_start: 0.8576 (t80) cc_final: 0.7889 (t80) REVERT: E 732 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8567 (mp0) REVERT: E 767 ARG cc_start: 0.7813 (tmm-80) cc_final: 0.7422 (tmm-80) REVERT: E 768 GLN cc_start: 0.8618 (mt0) cc_final: 0.8213 (mt0) REVERT: E 770 GLU cc_start: 0.9153 (tp30) cc_final: 0.8841 (mm-30) REVERT: E 804 GLU cc_start: 0.9263 (tp30) cc_final: 0.8702 (tp30) REVERT: E 835 MET cc_start: 0.7538 (mmm) cc_final: 0.7279 (mmm) REVERT: E 851 ASP cc_start: 0.8257 (t70) cc_final: 0.7884 (t0) REVERT: E 869 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8571 (tm-30) REVERT: F 46 GLN cc_start: 0.7331 (pp30) cc_final: 0.6933 (pp30) outliers start: 5 outliers final: 3 residues processed: 117 average time/residue: 1.2693 time to fit residues: 160.1915 Evaluate side-chains 110 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 151 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 0.9990 chunk 104 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** D 260 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 = 0.3357 r_free = 0.3357 target = 0.074076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.054300 restraints weight = 78193.348| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.15 r_work: 0.2738 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10725 Z= 0.126 Angle : 0.510 7.328 14506 Z= 0.261 Chirality : 0.037 0.132 1532 Planarity : 0.004 0.047 1865 Dihedral : 5.461 59.196 1499 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.20 % Favored : 95.56 % Rotamer: Outliers : 0.36 % Allowed : 8.79 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1262 helix: 1.73 (0.22), residues: 588 sheet: 0.86 (0.52), residues: 104 loop : -1.45 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 728 TYR 0.014 0.001 TYR D 48 PHE 0.010 0.001 PHE A 291 TRP 0.004 0.000 TRP B 753 HIS 0.002 0.000 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00296 (10722) covalent geometry : angle 0.51047 (14506) hydrogen bonds : bond 0.04269 ( 428) hydrogen bonds : angle 4.31850 ( 1212) metal coordination : bond 0.00137 ( 2) Misc. bond : bond 0.00201 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9252 (mtp) cc_final: 0.8755 (mtm) REVERT: A 349 ASN cc_start: 0.8900 (p0) cc_final: 0.8674 (p0) REVERT: B 631 GLN cc_start: 0.7012 (pp30) cc_final: 0.6676 (pp30) REVERT: B 819 ASN cc_start: 0.9023 (t0) cc_final: 0.8799 (t0) REVERT: C 80 GLU cc_start: 0.8456 (pp20) cc_final: 0.8197 (pp20) REVERT: C 81 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8454 (mt-10) REVERT: C 102 ASP cc_start: 0.8884 (m-30) cc_final: 0.8560 (m-30) REVERT: D 30 MET cc_start: 0.9087 (tpt) cc_final: 0.8356 (tpp) REVERT: D 91 MET cc_start: 0.9370 (mtm) cc_final: 0.9149 (mtm) REVERT: D 155 ASP cc_start: 0.8558 (p0) cc_final: 0.8192 (p0) REVERT: E 654 TYR cc_start: 0.8555 (t80) cc_final: 0.7898 (t80) REVERT: E 732 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8594 (mp0) REVERT: E 768 GLN cc_start: 0.8641 (mt0) cc_final: 0.8209 (mt0) REVERT: E 770 GLU cc_start: 0.9141 (tp30) cc_final: 0.8871 (mm-30) REVERT: E 804 GLU cc_start: 0.9268 (tp30) cc_final: 0.8726 (tp30) REVERT: E 851 ASP cc_start: 0.8184 (t70) cc_final: 0.7742 (t0) REVERT: E 869 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 46 GLN cc_start: 0.7192 (pp30) cc_final: 0.6748 (pp30) outliers start: 4 outliers final: 2 residues processed: 118 average time/residue: 1.2818 time to fit residues: 163.1782 Evaluate side-chains 108 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain F residue 62 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 1 optimal weight: 0.0770 chunk 37 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** D 260 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 = 0.3354 r_free = 0.3354 target = 0.073853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.054033 restraints weight = 78276.772| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.16 r_work: 0.2734 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10725 Z= 0.124 Angle : 0.505 7.783 14506 Z= 0.256 Chirality : 0.037 0.135 1532 Planarity : 0.004 0.047 1865 Dihedral : 5.399 58.803 1499 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 0.44 % Allowed : 9.15 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1262 helix: 1.85 (0.22), residues: 588 sheet: 0.82 (0.51), residues: 104 loop : -1.47 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 728 TYR 0.011 0.001 TYR A 330 PHE 0.009 0.001 PHE A 252 TRP 0.004 0.000 TRP B 753 HIS 0.002 0.000 HIS E 796 Details of bonding type rmsd covalent geometry : bond 0.00291 (10722) covalent geometry : angle 0.50468 (14506) hydrogen bonds : bond 0.03916 ( 428) hydrogen bonds : angle 4.16719 ( 1212) metal coordination : bond 0.00198 ( 2) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASN cc_start: 0.8913 (p0) cc_final: 0.8687 (p0) REVERT: B 631 GLN cc_start: 0.6956 (pp30) cc_final: 0.6614 (pp30) REVERT: B 819 ASN cc_start: 0.9032 (t0) cc_final: 0.8811 (t0) REVERT: C 80 GLU cc_start: 0.8493 (pp20) cc_final: 0.8256 (pp20) REVERT: C 81 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8501 (mt-10) REVERT: C 102 ASP cc_start: 0.8883 (m-30) cc_final: 0.8561 (m-30) REVERT: D 30 MET cc_start: 0.9046 (tpt) cc_final: 0.8417 (tpp) REVERT: D 91 MET cc_start: 0.9369 (mtm) cc_final: 0.9166 (mtm) REVERT: D 155 ASP cc_start: 0.8531 (p0) cc_final: 0.8194 (p0) REVERT: E 654 TYR cc_start: 0.8568 (t80) cc_final: 0.7927 (t80) REVERT: E 732 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8598 (mp0) REVERT: E 768 GLN cc_start: 0.8615 (mt0) cc_final: 0.8235 (mt0) REVERT: E 770 GLU cc_start: 0.9133 (tp30) cc_final: 0.8824 (mm-30) REVERT: E 804 GLU cc_start: 0.9274 (tp30) cc_final: 0.8727 (tp30) REVERT: E 851 ASP cc_start: 0.8118 (t70) cc_final: 0.7661 (t0) REVERT: E 869 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8390 (tm-30) REVERT: F 46 GLN cc_start: 0.6987 (pp30) cc_final: 0.6513 (pp30) outliers start: 5 outliers final: 1 residues processed: 107 average time/residue: 1.3293 time to fit residues: 153.3079 Evaluate side-chains 101 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** D 260 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 = 0.3324 r_free = 0.3324 target = 0.072349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.052558 restraints weight = 78188.487| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.14 r_work: 0.2702 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10725 Z= 0.171 Angle : 0.523 8.053 14506 Z= 0.267 Chirality : 0.037 0.128 1532 Planarity : 0.004 0.045 1865 Dihedral : 5.467 59.788 1499 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.60 % Favored : 95.17 % Rotamer: Outliers : 0.71 % Allowed : 8.88 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1262 helix: 1.73 (0.22), residues: 600 sheet: 0.80 (0.50), residues: 104 loop : -1.51 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 728 TYR 0.013 0.001 TYR A 330 PHE 0.010 0.001 PHE D 291 TRP 0.005 0.001 TRP B 753 HIS 0.003 0.001 HIS E 820 Details of bonding type rmsd covalent geometry : bond 0.00394 (10722) covalent geometry : angle 0.52294 (14506) hydrogen bonds : bond 0.04116 ( 428) hydrogen bonds : angle 4.12386 ( 1212) metal coordination : bond 0.00337 ( 2) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9228 (mtm) cc_final: 0.8953 (mtm) REVERT: A 162 GLU cc_start: 0.8674 (tp30) cc_final: 0.8374 (mm-30) REVERT: A 249 MET cc_start: 0.7989 (mtp) cc_final: 0.7396 (tmt) REVERT: A 349 ASN cc_start: 0.8935 (p0) cc_final: 0.8708 (p0) REVERT: B 631 GLN cc_start: 0.7056 (pp30) cc_final: 0.6727 (pp30) REVERT: B 819 ASN cc_start: 0.9037 (t0) cc_final: 0.8820 (t0) REVERT: C 80 GLU cc_start: 0.8510 (pp20) cc_final: 0.8278 (pp20) REVERT: C 81 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8548 (mt-10) REVERT: C 102 ASP cc_start: 0.8911 (m-30) cc_final: 0.8710 (m-30) REVERT: D 30 MET cc_start: 0.8985 (tpt) cc_final: 0.8359 (tpp) REVERT: D 51 MET cc_start: 0.9074 (ptp) cc_final: 0.8710 (ptp) REVERT: D 91 MET cc_start: 0.9364 (mtm) cc_final: 0.9158 (mtm) REVERT: D 155 ASP cc_start: 0.8585 (p0) cc_final: 0.8275 (p0) REVERT: E 654 TYR cc_start: 0.8606 (t80) cc_final: 0.7987 (t80) REVERT: E 732 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8741 (mm-30) REVERT: E 768 GLN cc_start: 0.8648 (mt0) cc_final: 0.8263 (mt0) REVERT: E 770 GLU cc_start: 0.9143 (tp30) cc_final: 0.8804 (mm-30) REVERT: E 804 GLU cc_start: 0.9276 (tp30) cc_final: 0.8759 (tp30) REVERT: E 851 ASP cc_start: 0.8131 (t70) cc_final: 0.7661 (t0) REVERT: E 869 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8435 (tm-30) REVERT: F 46 GLN cc_start: 0.6795 (pp30) cc_final: 0.6414 (pp30) outliers start: 8 outliers final: 5 residues processed: 112 average time/residue: 1.3054 time to fit residues: 157.5724 Evaluate side-chains 107 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain E residue 822 LEU Chi-restraints excluded: chain F residue 62 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** D 260 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 = 0.3313 r_free = 0.3313 target = 0.071807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.052075 restraints weight = 78160.627| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.11 r_work: 0.2688 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10725 Z= 0.186 Angle : 0.537 8.216 14506 Z= 0.274 Chirality : 0.038 0.130 1532 Planarity : 0.004 0.046 1865 Dihedral : 5.513 59.304 1499 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.68 % Favored : 95.09 % Rotamer: Outliers : 0.62 % Allowed : 9.33 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1262 helix: 1.71 (0.22), residues: 600 sheet: 0.71 (0.50), residues: 104 loop : -1.55 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 728 TYR 0.017 0.001 TYR D 48 PHE 0.011 0.001 PHE A 252 TRP 0.005 0.001 TRP B 753 HIS 0.002 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00431 (10722) covalent geometry : angle 0.53705 (14506) hydrogen bonds : bond 0.04138 ( 428) hydrogen bonds : angle 4.13321 ( 1212) metal coordination : bond 0.00398 ( 2) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9253 (mtm) cc_final: 0.9025 (mtm) REVERT: A 162 GLU cc_start: 0.8677 (tp30) cc_final: 0.8357 (mm-30) REVERT: A 249 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7486 (tmt) REVERT: A 349 ASN cc_start: 0.8935 (p0) cc_final: 0.8706 (p0) REVERT: B 631 GLN cc_start: 0.7079 (pp30) cc_final: 0.6623 (pp30) REVERT: B 819 ASN cc_start: 0.9047 (t0) cc_final: 0.8843 (t0) REVERT: C 80 GLU cc_start: 0.8522 (pp20) cc_final: 0.8290 (pp20) REVERT: C 81 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8459 (mt-10) REVERT: D 30 MET cc_start: 0.8953 (tpt) cc_final: 0.8303 (tpp) REVERT: D 91 MET cc_start: 0.9365 (mtm) cc_final: 0.9153 (mtm) REVERT: D 155 ASP cc_start: 0.8611 (p0) cc_final: 0.8305 (p0) REVERT: E 654 TYR cc_start: 0.8635 (t80) cc_final: 0.8018 (t80) REVERT: E 732 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8756 (mm-30) REVERT: E 768 GLN cc_start: 0.8637 (mt0) cc_final: 0.8270 (mt0) REVERT: E 770 GLU cc_start: 0.9138 (tp30) cc_final: 0.8854 (mm-30) REVERT: E 804 GLU cc_start: 0.9277 (tp30) cc_final: 0.8755 (tp30) REVERT: E 845 ILE cc_start: 0.8837 (tt) cc_final: 0.8590 (tp) REVERT: E 851 ASP cc_start: 0.8086 (t70) cc_final: 0.7629 (t0) REVERT: E 869 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8408 (tm-30) REVERT: F 46 GLN cc_start: 0.6776 (pp30) cc_final: 0.6387 (pp30) REVERT: F 111 GLU cc_start: 0.8725 (mp0) cc_final: 0.8442 (pm20) outliers start: 7 outliers final: 5 residues processed: 111 average time/residue: 1.3085 time to fit residues: 156.4964 Evaluate side-chains 106 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain E residue 822 LEU Chi-restraints excluded: chain F residue 62 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** D 260 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 = 0.3307 r_free = 0.3307 target = 0.071435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.051703 restraints weight = 78113.127| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.13 r_work: 0.2681 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10725 Z= 0.180 Angle : 0.536 8.055 14506 Z= 0.275 Chirality : 0.038 0.134 1532 Planarity : 0.004 0.047 1865 Dihedral : 5.561 59.132 1499 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.91 % Favored : 94.85 % Rotamer: Outliers : 0.71 % Allowed : 9.77 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1262 helix: 1.74 (0.22), residues: 600 sheet: 0.59 (0.49), residues: 104 loop : -1.57 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 728 TYR 0.019 0.001 TYR D 48 PHE 0.011 0.001 PHE A 252 TRP 0.005 0.001 TRP B 753 HIS 0.003 0.001 HIS E 796 Details of bonding type rmsd covalent geometry : bond 0.00416 (10722) covalent geometry : angle 0.53621 (14506) hydrogen bonds : bond 0.04104 ( 428) hydrogen bonds : angle 4.08273 ( 1212) metal coordination : bond 0.00423 ( 2) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9238 (mtm) cc_final: 0.9000 (mtm) REVERT: A 74 LYS cc_start: 0.8472 (tptp) cc_final: 0.8260 (ttmm) REVERT: A 162 GLU cc_start: 0.8674 (tp30) cc_final: 0.8363 (mm-30) REVERT: A 249 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7462 (tmt) REVERT: A 349 ASN cc_start: 0.8945 (p0) cc_final: 0.8655 (p0) REVERT: B 631 GLN cc_start: 0.7281 (pp30) cc_final: 0.6873 (pp30) REVERT: B 819 ASN cc_start: 0.9022 (t0) cc_final: 0.8812 (t0) REVERT: C 80 GLU cc_start: 0.8502 (pp20) cc_final: 0.8258 (pp20) REVERT: C 81 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8394 (mt-10) REVERT: C 102 ASP cc_start: 0.8922 (m-30) cc_final: 0.8635 (m-30) REVERT: D 30 MET cc_start: 0.8920 (tpt) cc_final: 0.8376 (tpp) REVERT: D 155 ASP cc_start: 0.8581 (p0) cc_final: 0.8277 (p0) REVERT: E 654 TYR cc_start: 0.8646 (t80) cc_final: 0.8057 (t80) REVERT: E 732 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8764 (mm-30) REVERT: E 768 GLN cc_start: 0.8653 (mt0) cc_final: 0.8364 (mt0) REVERT: E 770 GLU cc_start: 0.9139 (tp30) cc_final: 0.8853 (mm-30) REVERT: E 804 GLU cc_start: 0.9236 (tp30) cc_final: 0.8739 (tp30) REVERT: E 845 ILE cc_start: 0.8850 (tt) cc_final: 0.8622 (tp) REVERT: E 851 ASP cc_start: 0.8030 (t70) cc_final: 0.7564 (t0) REVERT: E 869 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8451 (tm-30) REVERT: F 46 GLN cc_start: 0.6753 (pp30) cc_final: 0.6365 (pp30) REVERT: F 111 GLU cc_start: 0.8745 (mp0) cc_final: 0.8416 (pm20) outliers start: 8 outliers final: 5 residues processed: 113 average time/residue: 1.3523 time to fit residues: 164.6186 Evaluate side-chains 108 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain E residue 822 LEU Chi-restraints excluded: chain F residue 62 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 260 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 = 0.3307 r_free = 0.3307 target = 0.071482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.051757 restraints weight = 78087.433| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.14 r_work: 0.2678 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10725 Z= 0.163 Angle : 0.538 8.053 14506 Z= 0.273 Chirality : 0.037 0.128 1532 Planarity : 0.004 0.046 1865 Dihedral : 5.586 59.288 1499 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.60 % Favored : 95.17 % Rotamer: Outliers : 0.71 % Allowed : 9.86 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1262 helix: 1.74 (0.22), residues: 600 sheet: 0.47 (0.49), residues: 106 loop : -1.55 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 728 TYR 0.014 0.001 TYR D 48 PHE 0.011 0.001 PHE D 291 TRP 0.005 0.001 TRP B 753 HIS 0.002 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00380 (10722) covalent geometry : angle 0.53760 (14506) hydrogen bonds : bond 0.04011 ( 428) hydrogen bonds : angle 4.05537 ( 1212) metal coordination : bond 0.00347 ( 2) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9227 (mtm) cc_final: 0.8923 (mtm) REVERT: A 74 LYS cc_start: 0.8472 (tptp) cc_final: 0.8261 (ttmm) REVERT: A 162 GLU cc_start: 0.8671 (tp30) cc_final: 0.8362 (mm-30) REVERT: A 249 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7459 (tmt) REVERT: A 349 ASN cc_start: 0.8940 (p0) cc_final: 0.8652 (p0) REVERT: B 631 GLN cc_start: 0.7334 (pp30) cc_final: 0.6981 (pp30) REVERT: B 819 ASN cc_start: 0.9024 (t0) cc_final: 0.8815 (t0) REVERT: C 80 GLU cc_start: 0.8504 (pp20) cc_final: 0.8249 (pp20) REVERT: C 81 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8324 (mt-10) REVERT: D 30 MET cc_start: 0.8909 (tpt) cc_final: 0.8357 (tpp) REVERT: D 37 MET cc_start: 0.9107 (mtp) cc_final: 0.8888 (mtp) REVERT: D 91 MET cc_start: 0.9384 (mtm) cc_final: 0.9155 (mtm) REVERT: D 155 ASP cc_start: 0.8575 (p0) cc_final: 0.8261 (p0) REVERT: E 654 TYR cc_start: 0.8655 (t80) cc_final: 0.8099 (t80) REVERT: E 732 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8770 (mm-30) REVERT: E 768 GLN cc_start: 0.8689 (mt0) cc_final: 0.8357 (mt0) REVERT: E 770 GLU cc_start: 0.9132 (tp30) cc_final: 0.8845 (mm-30) REVERT: E 804 GLU cc_start: 0.9238 (tp30) cc_final: 0.8740 (tp30) REVERT: E 845 ILE cc_start: 0.8864 (tt) cc_final: 0.8613 (tp) REVERT: E 851 ASP cc_start: 0.8035 (t70) cc_final: 0.7589 (t0) REVERT: E 869 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8403 (tm-30) REVERT: F 46 GLN cc_start: 0.6725 (pp30) cc_final: 0.6337 (pp30) REVERT: F 111 GLU cc_start: 0.8735 (mp0) cc_final: 0.8416 (pm20) outliers start: 8 outliers final: 6 residues processed: 110 average time/residue: 1.3878 time to fit residues: 164.0800 Evaluate side-chains 107 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain E residue 822 LEU Chi-restraints excluded: chain F residue 62 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 0.0870 chunk 53 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 260 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 = 0.3319 r_free = 0.3319 target = 0.072094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.052400 restraints weight = 78265.717| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.14 r_work: 0.2696 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10725 Z= 0.119 Angle : 0.527 8.211 14506 Z= 0.267 Chirality : 0.037 0.130 1532 Planarity : 0.004 0.050 1865 Dihedral : 5.540 59.609 1499 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.28 % Favored : 95.48 % Rotamer: Outliers : 0.71 % Allowed : 10.04 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1262 helix: 1.95 (0.22), residues: 588 sheet: 0.63 (0.49), residues: 104 loop : -1.55 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 728 TYR 0.015 0.001 TYR D 48 PHE 0.009 0.001 PHE A 252 TRP 0.004 0.000 TRP B 753 HIS 0.002 0.000 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00284 (10722) covalent geometry : angle 0.52705 (14506) hydrogen bonds : bond 0.03755 ( 428) hydrogen bonds : angle 3.96770 ( 1212) metal coordination : bond 0.00166 ( 2) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9221 (mtm) cc_final: 0.8923 (mtm) REVERT: A 74 LYS cc_start: 0.8463 (tptp) cc_final: 0.8252 (ttmm) REVERT: A 162 GLU cc_start: 0.8679 (tp30) cc_final: 0.8383 (mm-30) REVERT: A 249 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7445 (tmt) REVERT: A 349 ASN cc_start: 0.8921 (p0) cc_final: 0.8626 (p0) REVERT: B 631 GLN cc_start: 0.7327 (pp30) cc_final: 0.6971 (pp30) REVERT: B 819 ASN cc_start: 0.9017 (t0) cc_final: 0.8808 (t0) REVERT: C 80 GLU cc_start: 0.8513 (pp20) cc_final: 0.8252 (pp20) REVERT: C 81 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8376 (mt-10) REVERT: C 102 ASP cc_start: 0.8855 (m-30) cc_final: 0.8568 (m-30) REVERT: D 30 MET cc_start: 0.8883 (tpt) cc_final: 0.8314 (tpp) REVERT: D 91 MET cc_start: 0.9377 (mtm) cc_final: 0.9147 (mtm) REVERT: D 155 ASP cc_start: 0.8537 (p0) cc_final: 0.8229 (p0) REVERT: E 654 TYR cc_start: 0.8642 (t80) cc_final: 0.8092 (t80) REVERT: E 732 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8770 (mm-30) REVERT: E 768 GLN cc_start: 0.8679 (mt0) cc_final: 0.8344 (mt0) REVERT: E 770 GLU cc_start: 0.9115 (tp30) cc_final: 0.8832 (mm-30) REVERT: E 804 GLU cc_start: 0.9233 (tp30) cc_final: 0.8734 (tp30) REVERT: E 845 ILE cc_start: 0.8883 (tt) cc_final: 0.8632 (tp) REVERT: E 851 ASP cc_start: 0.7956 (t70) cc_final: 0.7521 (t0) REVERT: E 869 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8412 (tm-30) REVERT: F 46 GLN cc_start: 0.6728 (pp30) cc_final: 0.6332 (pp30) REVERT: F 68 ASP cc_start: 0.9056 (t0) cc_final: 0.8742 (t0) REVERT: F 111 GLU cc_start: 0.8742 (mp0) cc_final: 0.8390 (pm20) outliers start: 8 outliers final: 3 residues processed: 111 average time/residue: 1.3059 time to fit residues: 156.1614 Evaluate side-chains 106 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain F residue 62 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 38 optimal weight: 0.0870 chunk 44 optimal weight: 0.6980 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 260 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 = 0.3319 r_free = 0.3319 target = 0.072112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.052458 restraints weight = 78472.690| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.14 r_work: 0.2695 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10725 Z= 0.126 Angle : 0.536 8.933 14506 Z= 0.269 Chirality : 0.037 0.129 1532 Planarity : 0.004 0.052 1865 Dihedral : 5.527 59.910 1499 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.68 % Favored : 95.17 % Rotamer: Outliers : 0.36 % Allowed : 10.57 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.24), residues: 1262 helix: 1.99 (0.22), residues: 588 sheet: 0.51 (0.49), residues: 106 loop : -1.53 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 728 TYR 0.015 0.001 TYR D 48 PHE 0.008 0.001 PHE E 852 TRP 0.004 0.000 TRP B 753 HIS 0.002 0.000 HIS E 796 Details of bonding type rmsd covalent geometry : bond 0.00301 (10722) covalent geometry : angle 0.53565 (14506) hydrogen bonds : bond 0.03710 ( 428) hydrogen bonds : angle 3.93320 ( 1212) metal coordination : bond 0.00244 ( 2) Misc. bond : bond 0.00061 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9239 (mtm) cc_final: 0.8943 (mtm) REVERT: A 74 LYS cc_start: 0.8495 (tptp) cc_final: 0.8279 (ttmm) REVERT: A 162 GLU cc_start: 0.8685 (tp30) cc_final: 0.8383 (mm-30) REVERT: A 249 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7451 (tmt) REVERT: A 349 ASN cc_start: 0.8912 (p0) cc_final: 0.8616 (p0) REVERT: B 631 GLN cc_start: 0.7410 (pp30) cc_final: 0.7068 (pp30) REVERT: B 819 ASN cc_start: 0.9010 (t0) cc_final: 0.8803 (t0) REVERT: C 80 GLU cc_start: 0.8505 (pp20) cc_final: 0.8250 (pp20) REVERT: C 81 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8466 (mt-10) REVERT: C 102 ASP cc_start: 0.8863 (m-30) cc_final: 0.8547 (m-30) REVERT: D 30 MET cc_start: 0.8868 (tpt) cc_final: 0.8287 (tpp) REVERT: D 91 MET cc_start: 0.9377 (mtm) cc_final: 0.9146 (mtm) REVERT: D 155 ASP cc_start: 0.8518 (p0) cc_final: 0.8220 (p0) REVERT: E 654 TYR cc_start: 0.8644 (t80) cc_final: 0.8095 (t80) REVERT: E 732 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8784 (mm-30) REVERT: E 768 GLN cc_start: 0.8682 (mt0) cc_final: 0.8361 (mt0) REVERT: E 770 GLU cc_start: 0.9117 (tp30) cc_final: 0.8840 (mm-30) REVERT: E 804 GLU cc_start: 0.9231 (tp30) cc_final: 0.8733 (tp30) REVERT: E 845 ILE cc_start: 0.8892 (tt) cc_final: 0.8639 (tp) REVERT: E 851 ASP cc_start: 0.7966 (t70) cc_final: 0.7547 (t0) REVERT: E 869 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8436 (tm-30) REVERT: F 46 GLN cc_start: 0.6740 (pp30) cc_final: 0.6341 (pp30) REVERT: F 68 ASP cc_start: 0.9059 (t0) cc_final: 0.8747 (t0) REVERT: F 111 GLU cc_start: 0.8754 (mp0) cc_final: 0.8390 (pm20) outliers start: 4 outliers final: 3 residues processed: 103 average time/residue: 1.3366 time to fit residues: 148.5435 Evaluate side-chains 106 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain E residue 655 THR Chi-restraints excluded: chain F residue 62 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 121 optimal weight: 0.2980 chunk 58 optimal weight: 0.1980 chunk 47 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 260 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 = 0.3327 r_free = 0.3327 target = 0.072522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.052849 restraints weight = 78267.063| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.16 r_work: 0.2703 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10725 Z= 0.111 Angle : 0.528 9.186 14506 Z= 0.266 Chirality : 0.036 0.130 1532 Planarity : 0.004 0.055 1865 Dihedral : 5.486 59.540 1499 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.68 % Favored : 95.17 % Rotamer: Outliers : 0.27 % Allowed : 10.75 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1262 helix: 1.92 (0.22), residues: 602 sheet: 0.53 (0.50), residues: 106 loop : -1.56 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 728 TYR 0.011 0.001 TYR D 330 PHE 0.008 0.001 PHE D 291 TRP 0.004 0.000 TRP B 753 HIS 0.002 0.000 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00267 (10722) covalent geometry : angle 0.52805 (14506) hydrogen bonds : bond 0.03557 ( 428) hydrogen bonds : angle 3.86083 ( 1212) metal coordination : bond 0.00144 ( 2) Misc. bond : bond 0.00061 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6162.65 seconds wall clock time: 105 minutes 4.85 seconds (6304.85 seconds total)