Starting phenix.real_space_refine on Tue Nov 18 10:17:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e87_31011/11_2025/7e87_31011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e87_31011/11_2025/7e87_31011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e87_31011/11_2025/7e87_31011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e87_31011/11_2025/7e87_31011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e87_31011/11_2025/7e87_31011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e87_31011/11_2025/7e87_31011.map" } resolution = 3.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 8642 2.51 5 N 2242 2.21 5 O 2350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13304 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3122 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "J" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "I" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "C" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3122 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "D" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "E" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "F" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Time building chain proxies: 3.21, per 1000 atoms: 0.24 Number of scatterers: 13304 At special positions: 0 Unit cell: (109, 111, 129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2350 8.00 N 2242 7.00 C 8642 6.00 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=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 628.6 milliseconds 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3160 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 4 sheets defined 73.0% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.718A pdb=" N PHE B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.573A pdb=" N HIS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.618A pdb=" N PHE B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 147 removed outlier: 3.976A pdb=" N ARG B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 228 through 250 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 260 through 282 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.542A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 401 through 434 removed outlier: 3.990A pdb=" N ASP B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.661A pdb=" N PHE A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N HIS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.603A pdb=" N ILE A 128 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 129' Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.508A pdb=" N ARG A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 167 through 177 removed outlier: 3.690A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 228 through 250 removed outlier: 4.462A pdb=" N ILE A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 282 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.709A pdb=" N PHE A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.978A pdb=" N ARG A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 320 Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 401 through 434 Processing helix chain 'J' and resid 32 through 56 removed outlier: 3.509A pdb=" N ILE J 36 " --> pdb=" O LYS J 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 56 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.717A pdb=" N PHE C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.573A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.618A pdb=" N PHE C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.976A pdb=" N ARG C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 228 through 250 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 260 through 282 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.542A pdb=" N ARG C 305 " --> pdb=" O LYS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 401 through 434 removed outlier: 3.989A pdb=" N ASP C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS C 421 " --> pdb=" O GLN C 417 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 88 through 101 removed outlier: 3.661A pdb=" N PHE D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N HIS D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.603A pdb=" N ILE D 128 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 129 " --> pdb=" O PRO D 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 129' Processing helix chain 'D' and resid 131 through 150 removed outlier: 3.506A pdb=" N ARG D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 167 through 177 removed outlier: 3.690A pdb=" N ASN D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 205 Processing helix chain 'D' and resid 228 through 250 removed outlier: 4.463A pdb=" N ILE D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 282 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 295 removed outlier: 3.708A pdb=" N PHE D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 305 removed outlier: 3.978A pdb=" N ARG D 299 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 302 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 320 through 346 Processing helix chain 'D' and resid 356 through 369 Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 401 through 434 Processing helix chain 'E' and resid 32 through 56 removed outlier: 3.509A pdb=" N ILE E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 56 Processing sheet with id=AA1, first strand: chain 'B' and resid 51 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.803A pdb=" N THR A 54 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 43 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 55 Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.802A pdb=" N THR D 54 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 43 " --> pdb=" O THR D 54 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2532 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2917 1.33 - 1.45: 3108 1.45 - 1.57: 7483 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 13612 Sorted by residual: bond pdb=" C LEU C 400 " pdb=" N PRO C 401 " ideal model delta sigma weight residual 1.332 1.354 -0.022 8.20e-03 1.49e+04 7.08e+00 bond pdb=" C LEU B 400 " pdb=" N PRO B 401 " ideal model delta sigma weight residual 1.332 1.353 -0.021 8.20e-03 1.49e+04 6.60e+00 bond pdb=" C THR I 56 " pdb=" N PRO I 57 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.68e+00 bond pdb=" C THR F 56 " pdb=" N PRO F 57 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.68e+00 bond pdb=" CG LEU C 271 " pdb=" CD1 LEU C 271 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 ... (remaining 13607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 18001 1.71 - 3.43: 345 3.43 - 5.14: 81 5.14 - 6.86: 17 6.86 - 8.57: 10 Bond angle restraints: 18454 Sorted by residual: angle pdb=" N GLN A 417 " pdb=" CA GLN A 417 " pdb=" CB GLN A 417 " ideal model delta sigma weight residual 110.28 116.69 -6.41 1.55e+00 4.16e-01 1.71e+01 angle pdb=" N GLN D 417 " pdb=" CA GLN D 417 " pdb=" CB GLN D 417 " ideal model delta sigma weight residual 110.28 116.65 -6.37 1.55e+00 4.16e-01 1.69e+01 angle pdb=" N ILE B 112 " pdb=" CA ILE B 112 " pdb=" C ILE B 112 " ideal model delta sigma weight residual 112.12 109.32 2.80 8.40e-01 1.42e+00 1.11e+01 angle pdb=" N ILE C 112 " pdb=" CA ILE C 112 " pdb=" C ILE C 112 " ideal model delta sigma weight residual 112.12 109.36 2.76 8.40e-01 1.42e+00 1.08e+01 angle pdb=" N LEU A 271 " pdb=" CA LEU A 271 " pdb=" C LEU A 271 " ideal model delta sigma weight residual 109.81 116.98 -7.17 2.21e+00 2.05e-01 1.05e+01 ... (remaining 18449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 7091 16.05 - 32.10: 749 32.10 - 48.15: 168 48.15 - 64.20: 26 64.20 - 80.25: 8 Dihedral angle restraints: 8042 sinusoidal: 3154 harmonic: 4888 Sorted by residual: dihedral pdb=" CA VAL D 297 " pdb=" C VAL D 297 " pdb=" N PHE D 298 " pdb=" CA PHE D 298 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA VAL A 297 " pdb=" C VAL A 297 " pdb=" N PHE A 298 " pdb=" CA PHE A 298 " ideal model delta harmonic sigma weight residual 180.00 157.29 22.71 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PRO B 89 " pdb=" C PRO B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 8039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1448 0.040 - 0.080: 511 0.080 - 0.119: 138 0.119 - 0.159: 11 0.159 - 0.199: 8 Chirality restraints: 2116 Sorted by residual: chirality pdb=" CA LEU C 271 " pdb=" N LEU C 271 " pdb=" C LEU C 271 " pdb=" CB LEU C 271 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA LEU A 271 " pdb=" N LEU A 271 " pdb=" C LEU A 271 " pdb=" CB LEU A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA LEU B 271 " pdb=" N LEU B 271 " pdb=" C LEU B 271 " pdb=" CB LEU B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 2113 not shown) Planarity restraints: 2306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 235 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ALA C 235 " 0.029 2.00e-02 2.50e+03 pdb=" O ALA C 235 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS C 236 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 235 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C ALA B 235 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA B 235 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS B 236 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 238 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C MET C 238 " -0.027 2.00e-02 2.50e+03 pdb=" O MET C 238 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE C 239 " 0.009 2.00e-02 2.50e+03 ... (remaining 2303 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 268 2.67 - 3.23: 14220 3.23 - 3.78: 21300 3.78 - 4.34: 27696 4.34 - 4.90: 44582 Nonbonded interactions: 108066 Sorted by model distance: nonbonded pdb=" OG SER A 69 " pdb=" OE1 GLU A 71 " model vdw 2.111 3.040 nonbonded pdb=" OG SER D 69 " pdb=" OE1 GLU D 71 " model vdw 2.112 3.040 nonbonded pdb=" OD1 ASN C 97 " pdb=" NH1 ARG C 100 " model vdw 2.150 3.120 nonbonded pdb=" OD1 ASN B 97 " pdb=" NH1 ARG B 100 " model vdw 2.150 3.120 nonbonded pdb=" O MET A 238 " pdb=" OG1 THR A 241 " model vdw 2.174 3.040 ... (remaining 108061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'B' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'C' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'D' and (resid 40 through 158 or resid 167 through 436)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } 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: 3.040 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.020 Find NCS groups from input model: 0.290 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13612 Z= 0.161 Angle : 0.648 8.571 18454 Z= 0.345 Chirality : 0.044 0.199 2116 Planarity : 0.005 0.039 2306 Dihedral : 13.861 80.250 4882 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -0.03 (0.21), residues: 1632 helix: 0.84 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -1.98 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 142 TYR 0.019 0.001 TYR A 83 PHE 0.017 0.002 PHE D 187 TRP 0.019 0.002 TRP F 31 HIS 0.004 0.001 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00343 (13612) covalent geometry : angle 0.64819 (18454) hydrogen bonds : bond 0.13336 ( 868) hydrogen bonds : angle 5.45668 ( 2532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.516 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: B 97 ASN cc_start: 0.8210 (t0) cc_final: 0.7790 (t0) REVERT: B 98 PHE cc_start: 0.8324 (t80) cc_final: 0.7862 (t80) REVERT: B 110 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 224 ARG cc_start: 0.4502 (pmt170) cc_final: 0.4296 (ptm160) REVERT: B 238 MET cc_start: 0.8048 (mmp) cc_final: 0.7808 (mmp) REVERT: B 308 GLN cc_start: 0.7033 (pm20) cc_final: 0.6823 (pm20) REVERT: B 315 TYR cc_start: 0.7165 (m-10) cc_final: 0.6844 (m-10) REVERT: B 318 LYS cc_start: 0.7209 (mptt) cc_final: 0.6870 (mptt) REVERT: B 418 ARG cc_start: 0.6524 (ptm-80) cc_final: 0.6301 (ptt90) REVERT: A 53 GLN cc_start: 0.7820 (mp10) cc_final: 0.7582 (mp10) REVERT: A 66 LEU cc_start: 0.7587 (tt) cc_final: 0.7168 (tt) REVERT: A 71 GLU cc_start: 0.7421 (mp0) cc_final: 0.7108 (mp0) REVERT: A 81 GLN cc_start: 0.6461 (mp10) cc_final: 0.5839 (mp10) REVERT: A 136 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 138 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7851 (mmmm) REVERT: A 149 GLN cc_start: 0.6885 (pp30) cc_final: 0.6603 (pp30) REVERT: A 170 ARG cc_start: 0.6707 (tpp-160) cc_final: 0.5860 (tpt170) REVERT: A 172 TRP cc_start: 0.7246 (t60) cc_final: 0.6794 (t60) REVERT: A 176 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7550 (tm-30) REVERT: A 312 ILE cc_start: 0.8604 (mt) cc_final: 0.8326 (mt) REVERT: C 97 ASN cc_start: 0.8216 (t0) cc_final: 0.7791 (t0) REVERT: C 98 PHE cc_start: 0.8331 (t80) cc_final: 0.7870 (t80) REVERT: C 110 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7404 (mm-30) REVERT: C 224 ARG cc_start: 0.4517 (pmt170) cc_final: 0.4299 (ptm160) REVERT: C 238 MET cc_start: 0.8047 (mmp) cc_final: 0.7806 (mmp) REVERT: C 308 GLN cc_start: 0.7034 (pm20) cc_final: 0.6825 (pm20) REVERT: C 315 TYR cc_start: 0.7102 (m-10) cc_final: 0.6797 (m-10) REVERT: C 318 LYS cc_start: 0.7210 (mptt) cc_final: 0.6873 (mptt) REVERT: C 418 ARG cc_start: 0.6519 (ptm-80) cc_final: 0.6298 (ptt90) REVERT: D 53 GLN cc_start: 0.7817 (mp10) cc_final: 0.7578 (mp10) REVERT: D 66 LEU cc_start: 0.7581 (tt) cc_final: 0.7162 (tt) REVERT: D 71 GLU cc_start: 0.7426 (mp0) cc_final: 0.7115 (mp0) REVERT: D 81 GLN cc_start: 0.6462 (mp10) cc_final: 0.5735 (mp10) REVERT: D 136 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7728 (tm-30) REVERT: D 138 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7846 (mmmm) REVERT: D 149 GLN cc_start: 0.6883 (pp30) cc_final: 0.6602 (pp30) REVERT: D 170 ARG cc_start: 0.6706 (tpp-160) cc_final: 0.5857 (tpt170) REVERT: D 172 TRP cc_start: 0.7246 (t60) cc_final: 0.6749 (t60) REVERT: D 176 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7545 (tm-30) REVERT: D 312 ILE cc_start: 0.8600 (mt) cc_final: 0.8316 (mt) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.1321 time to fit residues: 77.1240 Evaluate side-chains 273 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS B 144 ASN B 408 ASN A 82 GLN ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS C 144 ASN C 408 ASN ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.146882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.100785 restraints weight = 27554.636| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.89 r_work: 0.3213 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13612 Z= 0.156 Angle : 0.646 8.249 18454 Z= 0.344 Chirality : 0.044 0.186 2116 Planarity : 0.005 0.047 2306 Dihedral : 4.039 18.088 1852 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.82 % Allowed : 11.24 % Favored : 86.94 % 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: 0.23 (0.21), residues: 1632 helix: 1.09 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.18 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 147 TYR 0.015 0.001 TYR D 188 PHE 0.019 0.002 PHE C 121 TRP 0.009 0.001 TRP D 172 HIS 0.004 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00335 (13612) covalent geometry : angle 0.64619 (18454) hydrogen bonds : bond 0.05365 ( 868) hydrogen bonds : angle 4.40149 ( 2532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 311 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7427 (mm110) cc_final: 0.6911 (mm-40) REVERT: B 97 ASN cc_start: 0.8283 (t0) cc_final: 0.7980 (t0) REVERT: B 98 PHE cc_start: 0.8356 (t80) cc_final: 0.8125 (t80) REVERT: B 110 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7683 (mm-30) REVERT: B 183 MET cc_start: 0.5468 (tpt) cc_final: 0.5215 (tpt) REVERT: B 224 ARG cc_start: 0.5061 (pmt170) cc_final: 0.4530 (ptm160) REVERT: B 318 LYS cc_start: 0.7355 (mptt) cc_final: 0.6997 (mptt) REVERT: B 346 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7973 (mm-30) REVERT: A 66 LEU cc_start: 0.7398 (tt) cc_final: 0.6919 (tt) REVERT: A 71 GLU cc_start: 0.7689 (mp0) cc_final: 0.7380 (mp0) REVERT: A 81 GLN cc_start: 0.6641 (mp10) cc_final: 0.6093 (mp10) REVERT: A 108 ARG cc_start: 0.6418 (mmt-90) cc_final: 0.5722 (mmt180) REVERT: A 138 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7795 (mmmm) REVERT: A 172 TRP cc_start: 0.6865 (t60) cc_final: 0.6579 (t60) REVERT: A 176 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 312 ILE cc_start: 0.8638 (mt) cc_final: 0.8432 (mt) REVERT: J 41 ILE cc_start: 0.8706 (mt) cc_final: 0.8381 (tt) REVERT: C 53 GLN cc_start: 0.7402 (mm110) cc_final: 0.6885 (mm-40) REVERT: C 97 ASN cc_start: 0.8269 (t0) cc_final: 0.7967 (t0) REVERT: C 98 PHE cc_start: 0.8359 (t80) cc_final: 0.8132 (t80) REVERT: C 110 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7687 (mm-30) REVERT: C 183 MET cc_start: 0.5467 (tpt) cc_final: 0.5207 (tpt) REVERT: C 224 ARG cc_start: 0.5050 (pmt170) cc_final: 0.4463 (ptm160) REVERT: C 318 LYS cc_start: 0.7345 (mptt) cc_final: 0.6985 (mptt) REVERT: D 66 LEU cc_start: 0.7400 (tt) cc_final: 0.6919 (tt) REVERT: D 71 GLU cc_start: 0.7680 (mp0) cc_final: 0.7369 (mp0) REVERT: D 81 GLN cc_start: 0.6618 (mp10) cc_final: 0.6090 (mp10) REVERT: D 108 ARG cc_start: 0.6356 (mmt-90) cc_final: 0.5649 (mmt180) REVERT: D 138 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7802 (mmmm) REVERT: D 172 TRP cc_start: 0.6873 (t60) cc_final: 0.6580 (t60) REVERT: D 176 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7664 (tm-30) REVERT: E 41 ILE cc_start: 0.8710 (mt) cc_final: 0.8381 (tt) outliers start: 26 outliers final: 13 residues processed: 325 average time/residue: 0.1127 time to fit residues: 53.4129 Evaluate side-chains 259 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 246 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 77 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 408 ASN C 144 ASN C 408 ASN D 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.145379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.100214 restraints weight = 27226.496| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.80 r_work: 0.3149 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13612 Z= 0.148 Angle : 0.624 8.456 18454 Z= 0.328 Chirality : 0.044 0.218 2116 Planarity : 0.005 0.048 2306 Dihedral : 4.055 17.046 1852 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.68 % Allowed : 15.22 % Favored : 83.10 % 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: 0.18 (0.21), residues: 1632 helix: 1.04 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.17 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 147 TYR 0.015 0.001 TYR D 188 PHE 0.021 0.002 PHE B 343 TRP 0.006 0.001 TRP D 172 HIS 0.003 0.001 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00326 (13612) covalent geometry : angle 0.62379 (18454) hydrogen bonds : bond 0.05003 ( 868) hydrogen bonds : angle 4.22209 ( 2532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ARG cc_start: 0.7709 (ppt170) cc_final: 0.7400 (ppt170) REVERT: B 53 GLN cc_start: 0.7569 (mm110) cc_final: 0.6933 (mm-40) REVERT: B 97 ASN cc_start: 0.8233 (t0) cc_final: 0.7555 (t0) REVERT: B 98 PHE cc_start: 0.8336 (t80) cc_final: 0.7872 (t80) REVERT: B 110 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 224 ARG cc_start: 0.5127 (pmt170) cc_final: 0.4446 (ptm160) REVERT: B 318 LYS cc_start: 0.7294 (mptt) cc_final: 0.6971 (mptt) REVERT: B 421 LYS cc_start: 0.8594 (tmmt) cc_final: 0.8328 (ptmt) REVERT: A 66 LEU cc_start: 0.7342 (tt) cc_final: 0.6781 (tt) REVERT: A 71 GLU cc_start: 0.7629 (mp0) cc_final: 0.7263 (mp0) REVERT: A 81 GLN cc_start: 0.6692 (mp10) cc_final: 0.6158 (mp10) REVERT: A 108 ARG cc_start: 0.6238 (mmt-90) cc_final: 0.5986 (mmt180) REVERT: A 138 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7795 (mmmm) REVERT: A 149 GLN cc_start: 0.6520 (pp30) cc_final: 0.6263 (pp30) REVERT: A 172 TRP cc_start: 0.6868 (t60) cc_final: 0.6518 (t60) REVERT: A 176 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7583 (tm-30) REVERT: J 41 ILE cc_start: 0.8672 (mt) cc_final: 0.8352 (tt) REVERT: C 51 ARG cc_start: 0.7722 (ppt170) cc_final: 0.7409 (ppt170) REVERT: C 53 GLN cc_start: 0.7569 (mm110) cc_final: 0.6931 (mm-40) REVERT: C 97 ASN cc_start: 0.8229 (t0) cc_final: 0.7546 (t0) REVERT: C 98 PHE cc_start: 0.8336 (t80) cc_final: 0.7871 (t80) REVERT: C 110 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7728 (mm-30) REVERT: C 224 ARG cc_start: 0.5119 (pmt170) cc_final: 0.4434 (ptm160) REVERT: C 318 LYS cc_start: 0.7277 (mptt) cc_final: 0.6952 (mptt) REVERT: C 421 LYS cc_start: 0.8594 (tmmt) cc_final: 0.8332 (ptmt) REVERT: D 66 LEU cc_start: 0.7328 (tt) cc_final: 0.6764 (tt) REVERT: D 71 GLU cc_start: 0.7626 (mp0) cc_final: 0.7260 (mp0) REVERT: D 81 GLN cc_start: 0.6550 (mp10) cc_final: 0.5987 (mp10) REVERT: D 82 GLN cc_start: 0.6587 (mm-40) cc_final: 0.6336 (mm110) REVERT: D 108 ARG cc_start: 0.6253 (mmt-90) cc_final: 0.6000 (mmt180) REVERT: D 138 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7790 (mmmm) REVERT: D 149 GLN cc_start: 0.6522 (pp30) cc_final: 0.6268 (pp30) REVERT: D 172 TRP cc_start: 0.6869 (t60) cc_final: 0.6520 (t60) REVERT: D 176 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7597 (tm-30) REVERT: E 41 ILE cc_start: 0.8674 (mt) cc_final: 0.8358 (tt) outliers start: 24 outliers final: 14 residues processed: 281 average time/residue: 0.1036 time to fit residues: 43.7047 Evaluate side-chains 254 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 240 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 HIS B 408 ASN A 414 HIS C 105 HIS C 408 ASN D 414 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.143037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094360 restraints weight = 27060.355| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.54 r_work: 0.3128 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13612 Z= 0.217 Angle : 0.674 9.125 18454 Z= 0.357 Chirality : 0.046 0.224 2116 Planarity : 0.005 0.054 2306 Dihedral : 4.217 17.625 1852 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.68 % Favored : 93.26 % Rotamer: Outliers : 3.07 % Allowed : 15.78 % Favored : 81.15 % 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: -0.04 (0.21), residues: 1632 helix: 0.86 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.21 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 147 TYR 0.022 0.002 TYR B 188 PHE 0.024 0.002 PHE D 194 TRP 0.008 0.001 TRP C 362 HIS 0.007 0.002 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00498 (13612) covalent geometry : angle 0.67382 (18454) hydrogen bonds : bond 0.05520 ( 868) hydrogen bonds : angle 4.40006 ( 2532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.477 Fit side-chains REVERT: B 51 ARG cc_start: 0.7691 (ppt170) cc_final: 0.7347 (ppt170) REVERT: B 53 GLN cc_start: 0.7574 (mm110) cc_final: 0.6875 (mm-40) REVERT: B 97 ASN cc_start: 0.8042 (t0) cc_final: 0.7537 (t0) REVERT: B 98 PHE cc_start: 0.8513 (t80) cc_final: 0.8003 (t80) REVERT: B 224 ARG cc_start: 0.5401 (pmt170) cc_final: 0.4614 (ptm160) REVERT: B 318 LYS cc_start: 0.7384 (mptt) cc_final: 0.7075 (mptt) REVERT: B 421 LYS cc_start: 0.8586 (tmmt) cc_final: 0.8291 (ptmt) REVERT: A 47 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8562 (m) REVERT: A 81 GLN cc_start: 0.6752 (mp10) cc_final: 0.6103 (mp10) REVERT: A 82 GLN cc_start: 0.6835 (mm-40) cc_final: 0.6441 (mm110) REVERT: A 108 ARG cc_start: 0.6305 (mmt-90) cc_final: 0.6052 (mmt180) REVERT: A 172 TRP cc_start: 0.6748 (t60) cc_final: 0.6370 (t60) REVERT: A 176 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7644 (tm-30) REVERT: J 41 ILE cc_start: 0.8708 (mt) cc_final: 0.8386 (tt) REVERT: C 51 ARG cc_start: 0.7680 (ppt170) cc_final: 0.7336 (ppt170) REVERT: C 53 GLN cc_start: 0.7570 (mm110) cc_final: 0.6868 (mm-40) REVERT: C 97 ASN cc_start: 0.8077 (t0) cc_final: 0.7573 (t0) REVERT: C 98 PHE cc_start: 0.8522 (t80) cc_final: 0.8027 (t80) REVERT: C 224 ARG cc_start: 0.5387 (pmt170) cc_final: 0.4603 (ptm160) REVERT: C 318 LYS cc_start: 0.7374 (mptt) cc_final: 0.7062 (mptt) REVERT: C 421 LYS cc_start: 0.8586 (tmmt) cc_final: 0.8290 (ptmt) REVERT: D 47 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8550 (m) REVERT: D 81 GLN cc_start: 0.6787 (mp10) cc_final: 0.6240 (mp10) REVERT: D 82 GLN cc_start: 0.6760 (mm-40) cc_final: 0.6445 (mm110) REVERT: D 108 ARG cc_start: 0.6297 (mmt-90) cc_final: 0.6047 (mmt180) REVERT: D 149 GLN cc_start: 0.6471 (pp30) cc_final: 0.6185 (pp30) REVERT: D 172 TRP cc_start: 0.6739 (t60) cc_final: 0.6365 (t60) REVERT: D 176 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7648 (tm-30) REVERT: E 41 ILE cc_start: 0.8707 (mt) cc_final: 0.8386 (tt) outliers start: 44 outliers final: 27 residues processed: 287 average time/residue: 0.1117 time to fit residues: 47.3676 Evaluate side-chains 254 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 99 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS D 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.143404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.097131 restraints weight = 27179.525| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.81 r_work: 0.3097 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13612 Z= 0.193 Angle : 0.658 9.696 18454 Z= 0.346 Chirality : 0.045 0.195 2116 Planarity : 0.005 0.054 2306 Dihedral : 4.239 21.312 1852 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.63 % Allowed : 17.46 % Favored : 78.91 % 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: -0.13 (0.20), residues: 1632 helix: 0.79 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.25 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 147 TYR 0.021 0.002 TYR C 188 PHE 0.021 0.002 PHE D 194 TRP 0.007 0.001 TRP C 362 HIS 0.005 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00447 (13612) covalent geometry : angle 0.65794 (18454) hydrogen bonds : bond 0.05290 ( 868) hydrogen bonds : angle 4.37433 ( 2532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7530 (mm110) cc_final: 0.6950 (mm-40) REVERT: B 97 ASN cc_start: 0.7988 (t0) cc_final: 0.7592 (t0) REVERT: B 98 PHE cc_start: 0.8474 (t80) cc_final: 0.7887 (t80) REVERT: B 175 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6355 (t80) REVERT: B 224 ARG cc_start: 0.5616 (pmt170) cc_final: 0.4693 (ptm160) REVERT: B 318 LYS cc_start: 0.7221 (mptt) cc_final: 0.6990 (mptt) REVERT: B 418 ARG cc_start: 0.6739 (ptm160) cc_final: 0.6203 (ttp80) REVERT: A 81 GLN cc_start: 0.6842 (mp10) cc_final: 0.6254 (mp10) REVERT: A 82 GLN cc_start: 0.6957 (mm-40) cc_final: 0.6574 (mm110) REVERT: A 149 GLN cc_start: 0.6372 (pp30) cc_final: 0.6160 (pm20) REVERT: A 176 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7643 (tm-30) REVERT: J 41 ILE cc_start: 0.8723 (mt) cc_final: 0.8425 (tt) REVERT: C 53 GLN cc_start: 0.7522 (mm110) cc_final: 0.6940 (mm-40) REVERT: C 97 ASN cc_start: 0.7991 (t0) cc_final: 0.7581 (t0) REVERT: C 98 PHE cc_start: 0.8485 (t80) cc_final: 0.7899 (t80) REVERT: C 175 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6361 (t80) REVERT: C 224 ARG cc_start: 0.5606 (pmt170) cc_final: 0.4682 (ptm160) REVERT: C 318 LYS cc_start: 0.7211 (mptt) cc_final: 0.6974 (mptt) REVERT: C 418 ARG cc_start: 0.6739 (ptm160) cc_final: 0.6204 (ttp80) REVERT: D 81 GLN cc_start: 0.6870 (mp10) cc_final: 0.6337 (mp10) REVERT: D 82 GLN cc_start: 0.6823 (mm-40) cc_final: 0.6520 (mm110) REVERT: D 149 GLN cc_start: 0.6460 (pp30) cc_final: 0.6239 (pm20) REVERT: D 176 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7638 (tm-30) REVERT: E 41 ILE cc_start: 0.8721 (mt) cc_final: 0.8422 (tt) outliers start: 52 outliers final: 36 residues processed: 286 average time/residue: 0.1138 time to fit residues: 47.5633 Evaluate side-chains 266 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 90 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS D 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.144549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.096543 restraints weight = 27056.052| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.52 r_work: 0.3170 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13612 Z= 0.162 Angle : 0.636 8.739 18454 Z= 0.334 Chirality : 0.044 0.205 2116 Planarity : 0.005 0.054 2306 Dihedral : 4.117 19.343 1852 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.70 % Allowed : 18.23 % Favored : 78.07 % 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: 0.02 (0.20), residues: 1632 helix: 0.91 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -2.14 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.019 0.002 TYR C 188 PHE 0.020 0.002 PHE C 343 TRP 0.012 0.001 TRP D 172 HIS 0.004 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00368 (13612) covalent geometry : angle 0.63565 (18454) hydrogen bonds : bond 0.04982 ( 868) hydrogen bonds : angle 4.28856 ( 2532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 263 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7442 (mm110) cc_final: 0.6847 (mm-40) REVERT: B 97 ASN cc_start: 0.7815 (t0) cc_final: 0.7496 (t0) REVERT: B 98 PHE cc_start: 0.8432 (t80) cc_final: 0.7788 (t80) REVERT: B 175 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6318 (t80) REVERT: B 224 ARG cc_start: 0.5542 (pmt170) cc_final: 0.4667 (ptm160) REVERT: B 318 LYS cc_start: 0.7345 (mptt) cc_final: 0.7098 (mptt) REVERT: B 418 ARG cc_start: 0.6725 (ptm160) cc_final: 0.6202 (ttp80) REVERT: A 81 GLN cc_start: 0.6857 (mp10) cc_final: 0.6344 (mp10) REVERT: A 176 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7616 (tm-30) REVERT: J 41 ILE cc_start: 0.8714 (mt) cc_final: 0.8392 (tt) REVERT: C 53 GLN cc_start: 0.7442 (mm110) cc_final: 0.6842 (mm-40) REVERT: C 97 ASN cc_start: 0.7818 (t0) cc_final: 0.7494 (t0) REVERT: C 98 PHE cc_start: 0.8427 (t80) cc_final: 0.7780 (t80) REVERT: C 175 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6331 (t80) REVERT: C 224 ARG cc_start: 0.5533 (pmt170) cc_final: 0.4654 (ptm160) REVERT: C 318 LYS cc_start: 0.7312 (mptt) cc_final: 0.7065 (mptt) REVERT: C 418 ARG cc_start: 0.6723 (ptm160) cc_final: 0.6142 (ttp80) REVERT: C 421 LYS cc_start: 0.8490 (tmmt) cc_final: 0.8214 (ptmt) REVERT: D 81 GLN cc_start: 0.6836 (mp10) cc_final: 0.6317 (mp10) REVERT: D 82 GLN cc_start: 0.6857 (mm-40) cc_final: 0.6542 (mm110) REVERT: D 149 GLN cc_start: 0.6485 (pp30) cc_final: 0.6275 (pm20) REVERT: D 176 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7609 (tm-30) REVERT: E 41 ILE cc_start: 0.8711 (mt) cc_final: 0.8391 (tt) outliers start: 53 outliers final: 39 residues processed: 304 average time/residue: 0.1117 time to fit residues: 50.1265 Evaluate side-chains 275 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 7 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 148 optimal weight: 0.0970 chunk 149 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 129 optimal weight: 0.2980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN A 82 GLN A 202 ASN A 414 HIS D 202 ASN D 414 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.146462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102717 restraints weight = 26814.599| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.74 r_work: 0.3191 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13612 Z= 0.133 Angle : 0.624 9.108 18454 Z= 0.325 Chirality : 0.043 0.226 2116 Planarity : 0.005 0.055 2306 Dihedral : 4.014 18.752 1852 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.21 % Allowed : 20.11 % Favored : 76.68 % 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: 0.17 (0.21), residues: 1632 helix: 1.03 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -2.12 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 147 TYR 0.016 0.001 TYR A 76 PHE 0.020 0.001 PHE C 343 TRP 0.009 0.001 TRP A 172 HIS 0.004 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00287 (13612) covalent geometry : angle 0.62418 (18454) hydrogen bonds : bond 0.04561 ( 868) hydrogen bonds : angle 4.17169 ( 2532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7401 (mm110) cc_final: 0.6764 (mm-40) REVERT: B 97 ASN cc_start: 0.7852 (t0) cc_final: 0.7588 (t0) REVERT: B 98 PHE cc_start: 0.8443 (t80) cc_final: 0.7893 (t80) REVERT: B 117 GLU cc_start: 0.7825 (mp0) cc_final: 0.7479 (mp0) REVERT: B 175 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6318 (t80) REVERT: B 224 ARG cc_start: 0.5562 (pmt170) cc_final: 0.4625 (ptm160) REVERT: B 248 LEU cc_start: 0.7271 (tt) cc_final: 0.7051 (tp) REVERT: B 318 LYS cc_start: 0.7385 (mptt) cc_final: 0.7150 (mptt) REVERT: B 392 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8171 (mt) REVERT: B 418 ARG cc_start: 0.6756 (ptm160) cc_final: 0.6334 (tmm160) REVERT: B 421 LYS cc_start: 0.8439 (tmmt) cc_final: 0.8138 (ptmt) REVERT: A 40 ASP cc_start: 0.2704 (m-30) cc_final: 0.2460 (m-30) REVERT: A 81 GLN cc_start: 0.6732 (mp10) cc_final: 0.6237 (mp10) REVERT: A 149 GLN cc_start: 0.6405 (OUTLIER) cc_final: 0.6132 (pm20) REVERT: A 176 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 233 ASP cc_start: 0.7739 (t0) cc_final: 0.7494 (t0) REVERT: J 41 ILE cc_start: 0.8710 (mt) cc_final: 0.8423 (tt) REVERT: C 53 GLN cc_start: 0.7398 (mm110) cc_final: 0.6757 (mm-40) REVERT: C 97 ASN cc_start: 0.7854 (t0) cc_final: 0.7575 (t0) REVERT: C 98 PHE cc_start: 0.8446 (t80) cc_final: 0.7894 (t80) REVERT: C 117 GLU cc_start: 0.7827 (mp0) cc_final: 0.7429 (mp0) REVERT: C 175 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6335 (t80) REVERT: C 224 ARG cc_start: 0.5549 (pmt170) cc_final: 0.4607 (ptm160) REVERT: C 248 LEU cc_start: 0.7254 (tt) cc_final: 0.7035 (tp) REVERT: C 318 LYS cc_start: 0.7348 (mptt) cc_final: 0.7115 (mptt) REVERT: C 392 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8247 (mt) REVERT: C 418 ARG cc_start: 0.6753 (ptm160) cc_final: 0.6330 (tmm160) REVERT: C 421 LYS cc_start: 0.8439 (tmmt) cc_final: 0.8136 (ptmt) REVERT: D 40 ASP cc_start: 0.2711 (m-30) cc_final: 0.2469 (m-30) REVERT: D 81 GLN cc_start: 0.6683 (mp10) cc_final: 0.6176 (mp10) REVERT: D 82 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6588 (mm110) REVERT: D 149 GLN cc_start: 0.6516 (pp30) cc_final: 0.6304 (pm20) REVERT: D 176 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7619 (tm-30) REVERT: E 41 ILE cc_start: 0.8706 (mt) cc_final: 0.8425 (tt) outliers start: 46 outliers final: 30 residues processed: 287 average time/residue: 0.1148 time to fit residues: 47.5795 Evaluate side-chains 267 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 105 HIS A 202 ASN A 414 HIS C 46 ASN C 202 ASN D 202 ASN D 414 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.144749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098102 restraints weight = 26670.508| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.74 r_work: 0.3126 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13612 Z= 0.181 Angle : 0.661 10.569 18454 Z= 0.343 Chirality : 0.045 0.307 2116 Planarity : 0.005 0.055 2306 Dihedral : 4.077 18.875 1852 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.70 % Allowed : 19.83 % Favored : 76.47 % 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: 0.14 (0.21), residues: 1632 helix: 0.99 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.12 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.018 0.002 TYR B 188 PHE 0.019 0.002 PHE C 343 TRP 0.012 0.001 TRP D 172 HIS 0.005 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00420 (13612) covalent geometry : angle 0.66060 (18454) hydrogen bonds : bond 0.05044 ( 868) hydrogen bonds : angle 4.24349 ( 2532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7105 (pp) REVERT: B 53 GLN cc_start: 0.7405 (mm110) cc_final: 0.6685 (mm-40) REVERT: B 98 PHE cc_start: 0.8531 (t80) cc_final: 0.8212 (t80) REVERT: B 175 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6310 (t80) REVERT: B 219 LEU cc_start: 0.4605 (OUTLIER) cc_final: 0.4372 (pp) REVERT: B 224 ARG cc_start: 0.5760 (pmt170) cc_final: 0.4712 (ptm160) REVERT: B 248 LEU cc_start: 0.7324 (tt) cc_final: 0.7085 (tp) REVERT: B 318 LYS cc_start: 0.7431 (mptt) cc_final: 0.7169 (mptt) REVERT: B 418 ARG cc_start: 0.6812 (ptm160) cc_final: 0.6218 (ttp80) REVERT: A 40 ASP cc_start: 0.2793 (m-30) cc_final: 0.2542 (m-30) REVERT: A 81 GLN cc_start: 0.6812 (mp10) cc_final: 0.6246 (mp10) REVERT: A 149 GLN cc_start: 0.6306 (pm20) cc_final: 0.6040 (pm20) REVERT: A 176 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7593 (tm-30) REVERT: J 41 ILE cc_start: 0.8721 (mt) cc_final: 0.8429 (tt) REVERT: C 42 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7097 (pp) REVERT: C 53 GLN cc_start: 0.7407 (mm110) cc_final: 0.6683 (mm-40) REVERT: C 98 PHE cc_start: 0.8539 (t80) cc_final: 0.8209 (t80) REVERT: C 175 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6300 (t80) REVERT: C 219 LEU cc_start: 0.4648 (OUTLIER) cc_final: 0.4436 (pp) REVERT: C 224 ARG cc_start: 0.5728 (pmt170) cc_final: 0.4695 (ptm160) REVERT: C 248 LEU cc_start: 0.7353 (tt) cc_final: 0.7122 (tp) REVERT: C 318 LYS cc_start: 0.7401 (mptt) cc_final: 0.7135 (mptt) REVERT: C 418 ARG cc_start: 0.6815 (ptm160) cc_final: 0.6161 (ttp80) REVERT: C 421 LYS cc_start: 0.8518 (tmmt) cc_final: 0.8249 (ptmt) REVERT: D 40 ASP cc_start: 0.2813 (m-30) cc_final: 0.2572 (m-30) REVERT: D 81 GLN cc_start: 0.6789 (mp10) cc_final: 0.6265 (mp10) REVERT: D 149 GLN cc_start: 0.6516 (pp30) cc_final: 0.6315 (pm20) REVERT: D 176 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7631 (tm-30) REVERT: E 41 ILE cc_start: 0.8718 (mt) cc_final: 0.8432 (tt) outliers start: 53 outliers final: 36 residues processed: 284 average time/residue: 0.1057 time to fit residues: 45.1644 Evaluate side-chains 274 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 118 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 112 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 414 HIS C 202 ASN D 82 GLN D 414 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.146471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.098693 restraints weight = 26906.325| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.51 r_work: 0.3196 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13612 Z= 0.140 Angle : 0.641 10.235 18454 Z= 0.330 Chirality : 0.043 0.171 2116 Planarity : 0.005 0.055 2306 Dihedral : 4.014 18.190 1852 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.79 % Allowed : 20.74 % Favored : 76.47 % 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: 0.24 (0.21), residues: 1632 helix: 1.06 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.07 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 147 TYR 0.018 0.001 TYR A 76 PHE 0.019 0.001 PHE C 343 TRP 0.011 0.001 TRP D 172 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00312 (13612) covalent geometry : angle 0.64139 (18454) hydrogen bonds : bond 0.04634 ( 868) hydrogen bonds : angle 4.17535 ( 2532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7254 (mm110) cc_final: 0.6615 (mm-40) REVERT: B 97 ASN cc_start: 0.8244 (t0) cc_final: 0.7478 (t0) REVERT: B 98 PHE cc_start: 0.8475 (t80) cc_final: 0.7917 (t80) REVERT: B 118 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7493 (tp30) REVERT: B 175 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6303 (t80) REVERT: B 219 LEU cc_start: 0.4657 (OUTLIER) cc_final: 0.4435 (pp) REVERT: B 224 ARG cc_start: 0.5733 (pmt170) cc_final: 0.4690 (ptm160) REVERT: B 248 LEU cc_start: 0.7291 (tt) cc_final: 0.7070 (tp) REVERT: B 318 LYS cc_start: 0.7413 (mptt) cc_final: 0.7159 (mptt) REVERT: B 392 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8286 (mt) REVERT: B 418 ARG cc_start: 0.6793 (ptm160) cc_final: 0.6476 (tmm160) REVERT: A 40 ASP cc_start: 0.2679 (m-30) cc_final: 0.2450 (m-30) REVERT: A 81 GLN cc_start: 0.6765 (mp10) cc_final: 0.6204 (mp10) REVERT: A 132 CYS cc_start: 0.4406 (p) cc_final: 0.3075 (t) REVERT: A 176 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7572 (tm-30) REVERT: J 41 ILE cc_start: 0.8710 (mt) cc_final: 0.8412 (tt) REVERT: C 53 GLN cc_start: 0.7248 (mm110) cc_final: 0.6625 (mm-40) REVERT: C 97 ASN cc_start: 0.8257 (t0) cc_final: 0.7489 (t0) REVERT: C 98 PHE cc_start: 0.8470 (t80) cc_final: 0.7904 (t80) REVERT: C 118 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7522 (tp30) REVERT: C 175 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6313 (t80) REVERT: C 219 LEU cc_start: 0.4597 (OUTLIER) cc_final: 0.4365 (pp) REVERT: C 224 ARG cc_start: 0.5702 (pmt170) cc_final: 0.4670 (ptm160) REVERT: C 248 LEU cc_start: 0.7318 (tt) cc_final: 0.7055 (tp) REVERT: C 318 LYS cc_start: 0.7383 (mptt) cc_final: 0.7128 (mptt) REVERT: C 392 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8206 (mt) REVERT: C 418 ARG cc_start: 0.6793 (ptm160) cc_final: 0.6387 (tmm160) REVERT: C 421 LYS cc_start: 0.8460 (tmmt) cc_final: 0.8165 (ptmt) REVERT: D 40 ASP cc_start: 0.2710 (m-30) cc_final: 0.2492 (m-30) REVERT: D 81 GLN cc_start: 0.6694 (mp10) cc_final: 0.6165 (mp10) REVERT: D 132 CYS cc_start: 0.4377 (p) cc_final: 0.3045 (t) REVERT: D 149 GLN cc_start: 0.6513 (pp30) cc_final: 0.6310 (pm20) REVERT: D 176 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7591 (tm-30) REVERT: E 41 ILE cc_start: 0.8709 (mt) cc_final: 0.8408 (tt) outliers start: 40 outliers final: 28 residues processed: 280 average time/residue: 0.1107 time to fit residues: 45.4846 Evaluate side-chains 260 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 112 optimal weight: 0.0070 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 414 HIS D 82 GLN D 414 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.146732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.102525 restraints weight = 26691.120| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.55 r_work: 0.3175 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13612 Z= 0.142 Angle : 0.663 9.893 18454 Z= 0.340 Chirality : 0.044 0.221 2116 Planarity : 0.005 0.093 2306 Dihedral : 4.018 17.890 1852 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.51 % Allowed : 21.16 % Favored : 76.33 % 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: 0.30 (0.21), residues: 1632 helix: 1.09 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -1.96 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 61 TYR 0.015 0.001 TYR C 188 PHE 0.019 0.002 PHE A 187 TRP 0.012 0.001 TRP D 172 HIS 0.004 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00313 (13612) covalent geometry : angle 0.66251 (18454) hydrogen bonds : bond 0.04597 ( 868) hydrogen bonds : angle 4.16282 ( 2532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7245 (mm110) cc_final: 0.6635 (mm-40) REVERT: B 97 ASN cc_start: 0.8169 (t0) cc_final: 0.7082 (t0) REVERT: B 98 PHE cc_start: 0.8480 (t80) cc_final: 0.7904 (t80) REVERT: B 118 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7500 (tp30) REVERT: B 175 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6328 (t80) REVERT: B 219 LEU cc_start: 0.4563 (OUTLIER) cc_final: 0.4320 (pp) REVERT: B 224 ARG cc_start: 0.5776 (pmt170) cc_final: 0.4745 (ptm160) REVERT: B 248 LEU cc_start: 0.7337 (tt) cc_final: 0.7096 (tp) REVERT: B 318 LYS cc_start: 0.7408 (mptt) cc_final: 0.7146 (mptt) REVERT: B 392 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8265 (mt) REVERT: B 418 ARG cc_start: 0.6795 (ptm160) cc_final: 0.6470 (tmm160) REVERT: A 40 ASP cc_start: 0.2908 (m-30) cc_final: 0.2658 (m-30) REVERT: A 81 GLN cc_start: 0.6627 (mp10) cc_final: 0.6106 (mp10) REVERT: A 132 CYS cc_start: 0.4292 (p) cc_final: 0.3034 (t) REVERT: A 176 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 312 ILE cc_start: 0.8644 (mt) cc_final: 0.8443 (mt) REVERT: J 41 ILE cc_start: 0.8698 (mt) cc_final: 0.8414 (tt) REVERT: C 42 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7067 (pp) REVERT: C 53 GLN cc_start: 0.7244 (mm110) cc_final: 0.6548 (mm-40) REVERT: C 97 ASN cc_start: 0.8183 (t0) cc_final: 0.7106 (t0) REVERT: C 98 PHE cc_start: 0.8482 (t80) cc_final: 0.7961 (t80) REVERT: C 100 ARG cc_start: 0.7151 (mtp-110) cc_final: 0.6845 (mtp180) REVERT: C 118 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7531 (tp30) REVERT: C 175 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6318 (t80) REVERT: C 219 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4536 (pp) REVERT: C 224 ARG cc_start: 0.5750 (pmt170) cc_final: 0.4728 (ptm160) REVERT: C 248 LEU cc_start: 0.7343 (tt) cc_final: 0.7102 (tp) REVERT: C 318 LYS cc_start: 0.7382 (mptt) cc_final: 0.7118 (mptt) REVERT: C 392 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8166 (mt) REVERT: C 418 ARG cc_start: 0.6776 (ptm160) cc_final: 0.6361 (tmm160) REVERT: C 421 LYS cc_start: 0.8453 (tmmt) cc_final: 0.8155 (ptmt) REVERT: D 40 ASP cc_start: 0.2923 (m-30) cc_final: 0.2688 (m-30) REVERT: D 81 GLN cc_start: 0.6676 (mp10) cc_final: 0.6158 (mp10) REVERT: D 132 CYS cc_start: 0.4256 (p) cc_final: 0.2999 (t) REVERT: D 149 GLN cc_start: 0.6508 (pp30) cc_final: 0.6305 (pm20) REVERT: D 176 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 238 MET cc_start: 0.7443 (mmt) cc_final: 0.7228 (mmt) REVERT: D 312 ILE cc_start: 0.8664 (mt) cc_final: 0.8460 (mt) REVERT: E 41 ILE cc_start: 0.8706 (mt) cc_final: 0.8421 (tt) outliers start: 36 outliers final: 28 residues processed: 261 average time/residue: 0.1079 time to fit residues: 41.6539 Evaluate side-chains 259 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 150 optimal weight: 0.0670 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN A 82 GLN A 414 HIS C 202 ASN D 82 GLN D 414 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.147593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.103370 restraints weight = 27117.937| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.66 r_work: 0.3200 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13612 Z= 0.136 Angle : 0.662 16.595 18454 Z= 0.334 Chirality : 0.043 0.176 2116 Planarity : 0.005 0.052 2306 Dihedral : 3.959 17.907 1852 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.72 % Allowed : 20.88 % Favored : 76.40 % 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 (0.21), residues: 1632 helix: 1.15 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.95 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 100 TYR 0.019 0.001 TYR A 76 PHE 0.017 0.001 PHE C 343 TRP 0.010 0.001 TRP D 172 HIS 0.004 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00299 (13612) covalent geometry : angle 0.66183 (18454) hydrogen bonds : bond 0.04434 ( 868) hydrogen bonds : angle 4.08998 ( 2532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3829.30 seconds wall clock time: 66 minutes 24.93 seconds (3984.93 seconds total)