Starting phenix.real_space_refine on Sat Aug 23 09:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j80_36055/08_2025/8j80_36055.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j80_36055/08_2025/8j80_36055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j80_36055/08_2025/8j80_36055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j80_36055/08_2025/8j80_36055.map" model { file = "/net/cci-nas-00/data/ceres_data/8j80_36055/08_2025/8j80_36055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j80_36055/08_2025/8j80_36055.cif" } resolution = 2.68 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 ------------------------------------------------------------------------------- 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= 0.013 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 48 5.16 5 C 7149 2.51 5 N 1862 2.21 5 O 2112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11172 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2281 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "B" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2262 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain breaks: 1 Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.80, per 1000 atoms: 0.25 Number of scatterers: 11172 At special positions: 0 Unit cell: (89.832, 112.684, 159.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 48 16.00 O 2112 8.00 N 1862 7.00 C 7149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 533.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 70 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 164 " 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2698 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 26 sheets defined 33.2% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 3.842A pdb=" N PHE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 58 Processing helix chain 'A' and resid 60 through 89 removed outlier: 3.599A pdb=" N LEU A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N SER A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 129 removed outlier: 3.967A pdb=" N VAL A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 159 Processing helix chain 'A' and resid 160 through 163 removed outlier: 3.684A pdb=" N GLY A 163 " --> pdb=" O LYS A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 230 through 260 removed outlier: 3.774A pdb=" N LEU A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 294 removed outlier: 3.668A pdb=" N ILE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.419A pdb=" N ASN A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 347 through 363 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.831A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 186 through 193 removed outlier: 3.829A pdb=" N HIS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.638A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'B' and resid 24 through 32 removed outlier: 3.755A pdb=" N SER B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 59 removed outlier: 3.534A pdb=" N LEU B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 89 removed outlier: 3.655A pdb=" N ILE B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 132 removed outlier: 3.525A pdb=" N THR B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 158 Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 241 through 260 removed outlier: 5.095A pdb=" N GLY B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 294 removed outlier: 3.910A pdb=" N ILE B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.558A pdb=" N ASN B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.555A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.518A pdb=" N ASP D 86 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 87' Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.920A pdb=" N HIS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 330 removed outlier: 5.698A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.559A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.559A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.841A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.458A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.612A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 125 through 129 removed outlier: 5.880A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 129 removed outlier: 5.880A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'B' and resid 318 through 330 removed outlier: 5.669A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.530A pdb=" N VAL F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.929A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 129 removed outlier: 6.219A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 125 through 129 removed outlier: 6.219A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.530A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 14 removed outlier: 3.712A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AC7, first strand: chain 'D' and resid 118 through 122 removed outlier: 5.790A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 157 through 159 removed outlier: 4.577A pdb=" N TRP D 152 " --> pdb=" O ARG D 159 " (cutoff:3.500A) 663 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3523 1.34 - 1.46: 2537 1.46 - 1.58: 5313 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 11443 Sorted by residual: bond pdb=" N HIS B 138 " pdb=" CA HIS B 138 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.19e-02 7.06e+03 7.56e+00 bond pdb=" CA PRO A 133 " pdb=" C PRO A 133 " ideal model delta sigma weight residual 1.517 1.541 -0.024 9.30e-03 1.16e+04 6.80e+00 bond pdb=" N ASP A 135 " pdb=" CA ASP A 135 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.34e+00 bond pdb=" N MET E 140 " pdb=" CA MET E 140 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.17e+00 bond pdb=" N VAL A 136 " pdb=" CA VAL A 136 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.25e-02 6.40e+03 6.17e+00 ... (remaining 11438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 15274 2.20 - 4.40: 246 4.40 - 6.61: 48 6.61 - 8.81: 7 8.81 - 11.01: 4 Bond angle restraints: 15579 Sorted by residual: angle pdb=" N PRO A 133 " pdb=" CA PRO A 133 " pdb=" C PRO A 133 " ideal model delta sigma weight residual 110.70 115.54 -4.84 1.22e+00 6.72e-01 1.57e+01 angle pdb=" CA PRO A 133 " pdb=" C PRO A 133 " pdb=" N PRO A 134 " ideal model delta sigma weight residual 117.93 122.38 -4.45 1.20e+00 6.94e-01 1.38e+01 angle pdb=" CA ASP B 267 " pdb=" CB ASP B 267 " pdb=" CG ASP B 267 " ideal model delta sigma weight residual 112.60 116.03 -3.43 1.00e+00 1.00e+00 1.18e+01 angle pdb=" CA MET C 179 " pdb=" CB MET C 179 " pdb=" CG MET C 179 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.00e+01 angle pdb=" CA LEU C 129 " pdb=" CB LEU C 129 " pdb=" CG LEU C 129 " ideal model delta sigma weight residual 116.30 127.31 -11.01 3.50e+00 8.16e-02 9.89e+00 ... (remaining 15574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5869 17.99 - 35.99: 659 35.99 - 53.98: 167 53.98 - 71.98: 48 71.98 - 89.97: 13 Dihedral angle restraints: 6756 sinusoidal: 2570 harmonic: 4186 Sorted by residual: dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 200 " pdb=" CB CYS E 200 " ideal model delta sinusoidal sigma weight residual 93.00 49.18 43.82 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 198 " pdb=" CB CYS D 198 " ideal model delta sinusoidal sigma weight residual -86.00 -124.02 38.02 1 1.00e+01 1.00e-02 2.04e+01 dihedral pdb=" CA TYR E 94 " pdb=" C TYR E 94 " pdb=" N CYS E 95 " pdb=" CA CYS E 95 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 6753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1328 0.049 - 0.099: 345 0.099 - 0.148: 97 0.148 - 0.197: 9 0.197 - 0.246: 4 Chirality restraints: 1783 Sorted by residual: chirality pdb=" CA ASP B 267 " pdb=" N ASP B 267 " pdb=" C ASP B 267 " pdb=" CB ASP B 267 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL F 188 " pdb=" CA VAL F 188 " pdb=" CG1 VAL F 188 " pdb=" CG2 VAL F 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA VAL A 136 " pdb=" N VAL A 136 " pdb=" C VAL A 136 " pdb=" CB VAL A 136 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1780 not shown) Planarity restraints: 1973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 140 " 0.435 9.50e-02 1.11e+02 1.95e-01 2.34e+01 pdb=" NE ARG B 140 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG B 140 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 140 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 140 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 287 " -0.264 9.50e-02 1.11e+02 1.18e-01 8.61e+00 pdb=" NE ARG A 287 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 287 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 287 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 287 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 188 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO F 189 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " -0.032 5.00e-02 4.00e+02 ... (remaining 1970 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 76 2.57 - 3.15: 8703 3.15 - 3.74: 18060 3.74 - 4.32: 25536 4.32 - 4.90: 41560 Nonbonded interactions: 93935 Sorted by model distance: nonbonded pdb=" OD2 ASP B 74 " pdb="ZN ZN B 401 " model vdw 1.989 2.230 nonbonded pdb=" OD2 ASP B 244 " pdb="ZN ZN B 401 " model vdw 2.027 2.230 nonbonded pdb=" OD1 ASP B 74 " pdb="ZN ZN B 401 " model vdw 2.074 2.230 nonbonded pdb=" OD1 ASP A 74 " pdb=" NE2 HIS A 240 " model vdw 2.256 3.120 nonbonded pdb=" O VAL A 318 " pdb=" NH1 ARG E 56 " model vdw 2.257 3.120 ... (remaining 93930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 163 or resid 233 through 376)) selection = (chain 'B' and (resid 22 through 163 or resid 233 through 376)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.890 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 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 : 0.006 0.250 11453 Z= 0.247 Angle : 0.729 11.009 15595 Z= 0.387 Chirality : 0.048 0.246 1783 Planarity : 0.007 0.195 1973 Dihedral : 17.007 89.971 4034 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.05 % Allowed : 25.06 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.22), residues: 1428 helix: 0.84 (0.26), residues: 417 sheet: 0.68 (0.23), residues: 479 loop : -0.32 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 18 TYR 0.024 0.002 TYR C 91 PHE 0.024 0.002 PHE D 36 TRP 0.025 0.002 TRP F 159 HIS 0.007 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00465 (11443) covalent geometry : angle 0.72836 (15579) SS BOND : bond 0.00465 ( 8) SS BOND : angle 1.02485 ( 16) hydrogen bonds : bond 0.13077 ( 615) hydrogen bonds : angle 6.40935 ( 1809) metal coordination : bond 0.24874 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6983 (tmm-80) REVERT: A 287 ARG cc_start: 0.7360 (ttp-170) cc_final: 0.6152 (mmp-170) REVERT: A 322 GLN cc_start: 0.7785 (pt0) cc_final: 0.7083 (pm20) REVERT: C 10 SER cc_start: 0.8380 (t) cc_final: 0.8078 (m) REVERT: C 11 LEU cc_start: 0.7358 (tt) cc_final: 0.6943 (pt) REVERT: C 58 LEU cc_start: 0.8537 (mt) cc_final: 0.8270 (mm) REVERT: C 72 ARG cc_start: 0.6186 (ttm-80) cc_final: 0.5133 (mtp85) REVERT: C 97 GLU cc_start: 0.7623 (tt0) cc_final: 0.6391 (tm-30) REVERT: E 5 GLN cc_start: 0.7150 (mt0) cc_final: 0.6491 (mp10) REVERT: E 94 TYR cc_start: 0.7492 (m-80) cc_final: 0.7281 (m-80) REVERT: B 48 PHE cc_start: 0.7940 (t80) cc_final: 0.7740 (t80) REVERT: B 89 LYS cc_start: 0.7483 (mttp) cc_final: 0.7268 (mttp) REVERT: B 287 ARG cc_start: 0.6777 (ttm110) cc_final: 0.5405 (mmt180) REVERT: B 288 GLU cc_start: 0.7031 (tt0) cc_final: 0.6595 (tm-30) REVERT: B 303 ASN cc_start: 0.7708 (m-40) cc_final: 0.7470 (m110) REVERT: B 307 GLN cc_start: 0.6282 (tm-30) cc_final: 0.6013 (tp-100) REVERT: B 310 GLN cc_start: 0.7587 (tt0) cc_final: 0.6559 (mm110) REVERT: F 3 GLN cc_start: 0.7321 (tt0) cc_final: 0.6322 (tm-30) REVERT: F 46 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6213 (mt-10) REVERT: D 72 ARG cc_start: 0.6486 (mtm-85) cc_final: 0.5911 (mtp85) REVERT: D 203 LYS cc_start: 0.8815 (tmmm) cc_final: 0.8348 (tmmt) outliers start: 38 outliers final: 14 residues processed: 189 average time/residue: 0.5598 time to fit residues: 114.7178 Evaluate side-chains 143 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 161 HIS A 232 GLN A 303 ASN A 310 GLN A 325 HIS A 356 HIS C 57 ASN C 141 ASN E 73 ASN E 83 ASN E 160 ASN E 204 HIS B 137 HIS B 260 ASN B 356 HIS F 73 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.250639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.234590 restraints weight = 11064.510| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 0.76 r_work: 0.4409 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.4370 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11453 Z= 0.132 Angle : 0.579 8.645 15595 Z= 0.299 Chirality : 0.044 0.276 1783 Planarity : 0.004 0.051 1973 Dihedral : 5.955 92.711 1566 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.86 % Allowed : 24.10 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.22), residues: 1428 helix: 1.68 (0.26), residues: 419 sheet: 0.99 (0.23), residues: 477 loop : -0.22 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 159 TYR 0.013 0.001 TYR F 94 PHE 0.017 0.001 PHE E 80 TRP 0.012 0.001 TRP B 327 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00285 (11443) covalent geometry : angle 0.57909 (15579) SS BOND : bond 0.00297 ( 8) SS BOND : angle 0.70324 ( 16) hydrogen bonds : bond 0.04086 ( 615) hydrogen bonds : angle 4.73195 ( 1809) metal coordination : bond 0.00588 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: F 5 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6925 (pm20) outliers start: 48 outliers final: 14 residues processed: 171 average time/residue: 0.6716 time to fit residues: 123.2541 Evaluate side-chains 148 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 100 optimal weight: 8.9990 chunk 71 optimal weight: 50.0000 chunk 6 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN D 128 GLN D 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.254348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.219623 restraints weight = 11569.492| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 1.49 r_work: 0.4199 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4163 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11453 Z= 0.127 Angle : 0.557 7.582 15595 Z= 0.288 Chirality : 0.043 0.273 1783 Planarity : 0.004 0.051 1973 Dihedral : 5.210 58.967 1556 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.61 % Allowed : 23.94 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.22), residues: 1428 helix: 1.86 (0.25), residues: 421 sheet: 1.08 (0.23), residues: 477 loop : -0.09 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 231 TYR 0.012 0.001 TYR F 94 PHE 0.016 0.001 PHE E 80 TRP 0.011 0.001 TRP B 327 HIS 0.013 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00278 (11443) covalent geometry : angle 0.55729 (15579) SS BOND : bond 0.00293 ( 8) SS BOND : angle 0.61168 ( 16) hydrogen bonds : bond 0.03786 ( 615) hydrogen bonds : angle 4.45812 ( 1809) metal coordination : bond 0.00482 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 0.444 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: E 5 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6706 (mp10) REVERT: B 288 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: D 32 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.6447 (m-80) outliers start: 45 outliers final: 21 residues processed: 166 average time/residue: 0.6797 time to fit residues: 121.0414 Evaluate side-chains 154 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 112 optimal weight: 0.0970 chunk 110 optimal weight: 30.0000 chunk 47 optimal weight: 50.0000 chunk 63 optimal weight: 0.0870 chunk 61 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 overall best weight: 3.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN E 110 GLN B 164 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 325 HIS ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.252215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.217596 restraints weight = 11463.609| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 1.59 r_work: 0.4169 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 2.084 11453 Z= 0.688 Angle : 0.628 8.868 15595 Z= 0.327 Chirality : 0.046 0.256 1783 Planarity : 0.005 0.072 1973 Dihedral : 5.536 59.234 1556 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.69 % Allowed : 24.10 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.22), residues: 1428 helix: 1.70 (0.25), residues: 421 sheet: 1.04 (0.23), residues: 479 loop : -0.16 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 231 TYR 0.017 0.002 TYR E 94 PHE 0.021 0.002 PHE A 359 TRP 0.018 0.002 TRP F 52 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00522 (11443) covalent geometry : angle 0.62759 (15579) SS BOND : bond 0.00443 ( 8) SS BOND : angle 1.00646 ( 16) hydrogen bonds : bond 0.04436 ( 615) hydrogen bonds : angle 4.51529 ( 1809) metal coordination : bond 1.47350 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: E 5 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6838 (mp10) REVERT: E 18 LEU cc_start: 0.8152 (tp) cc_final: 0.7633 (tp) REVERT: B 288 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: B 322 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: B 376 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6563 (tpt) REVERT: D 32 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.6983 (m-10) outliers start: 46 outliers final: 20 residues processed: 159 average time/residue: 0.6806 time to fit residues: 116.2129 Evaluate side-chains 153 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 52 optimal weight: 4.9990 chunk 63 optimal weight: 50.0000 chunk 101 optimal weight: 0.3980 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 83 ASN E 201 ASN B 111 ASN B 164 HIS B 259 GLN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** 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 = 0.4711 r_free = 0.4711 target = 0.253326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.219077 restraints weight = 11410.006| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 1.60 r_work: 0.4171 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4131 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.817 11453 Z= 0.588 Angle : 0.577 7.614 15595 Z= 0.298 Chirality : 0.044 0.222 1783 Planarity : 0.004 0.052 1973 Dihedral : 5.391 57.724 1556 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.86 % Allowed : 24.34 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.22), residues: 1428 helix: 1.83 (0.25), residues: 421 sheet: 1.11 (0.23), residues: 476 loop : -0.08 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 36 TYR 0.016 0.002 TYR E 94 PHE 0.017 0.002 PHE C 36 TRP 0.013 0.002 TRP F 52 HIS 0.005 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00363 (11443) covalent geometry : angle 0.57672 (15579) SS BOND : bond 0.00367 ( 8) SS BOND : angle 0.80523 ( 16) hydrogen bonds : bond 0.03979 ( 615) hydrogen bonds : angle 4.35903 ( 1809) metal coordination : bond 1.28477 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.3794 (OUTLIER) cc_final: 0.3588 (t80) REVERT: A 302 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: E 5 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6872 (mp10) REVERT: E 18 LEU cc_start: 0.8216 (tp) cc_final: 0.7759 (tp) REVERT: B 288 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: D 32 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.6826 (m-10) outliers start: 48 outliers final: 23 residues processed: 159 average time/residue: 0.6951 time to fit residues: 118.6175 Evaluate side-chains 154 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 102 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 40.0000 chunk 11 optimal weight: 50.0000 chunk 79 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 66 optimal weight: 0.3980 chunk 31 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN E 110 GLN E 201 ASN B 325 HIS ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.254774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.217445 restraints weight = 11558.010| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 1.62 r_work: 0.4195 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4152 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11453 Z= 0.105 Angle : 0.543 8.865 15595 Z= 0.276 Chirality : 0.042 0.199 1783 Planarity : 0.004 0.055 1973 Dihedral : 5.190 58.509 1556 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.97 % Allowed : 24.90 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.22), residues: 1428 helix: 2.13 (0.25), residues: 419 sheet: 1.23 (0.23), residues: 479 loop : -0.02 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 36 TYR 0.011 0.001 TYR E 94 PHE 0.016 0.001 PHE E 80 TRP 0.015 0.001 TRP C 152 HIS 0.004 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00225 (11443) covalent geometry : angle 0.54273 (15579) SS BOND : bond 0.00293 ( 8) SS BOND : angle 0.60006 ( 16) hydrogen bonds : bond 0.03436 ( 615) hydrogen bonds : angle 4.17569 ( 1809) metal coordination : bond 0.00060 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6772 (mp10) REVERT: B 288 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: D 32 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6582 (m-10) outliers start: 37 outliers final: 19 residues processed: 156 average time/residue: 0.6232 time to fit residues: 104.4249 Evaluate side-chains 154 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 131 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 135 optimal weight: 0.1980 chunk 62 optimal weight: 0.1980 chunk 121 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN E 110 GLN E 201 ASN B 164 HIS B 307 GLN F 83 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.253819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.221758 restraints weight = 11457.897| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 1.51 r_work: 0.4194 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.844 11453 Z= 0.591 Angle : 0.575 10.091 15595 Z= 0.291 Chirality : 0.043 0.202 1783 Planarity : 0.004 0.053 1973 Dihedral : 5.165 58.332 1555 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.81 % Allowed : 25.62 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.22), residues: 1428 helix: 2.06 (0.25), residues: 419 sheet: 1.29 (0.23), residues: 476 loop : -0.05 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 36 TYR 0.014 0.001 TYR E 94 PHE 0.023 0.002 PHE B 48 TRP 0.011 0.001 TRP F 52 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00316 (11443) covalent geometry : angle 0.57431 (15579) SS BOND : bond 0.00308 ( 8) SS BOND : angle 0.74099 ( 16) hydrogen bonds : bond 0.03667 ( 615) hydrogen bonds : angle 4.20360 ( 1809) metal coordination : bond 1.30356 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.3696 (OUTLIER) cc_final: 0.2929 (t80) REVERT: A 302 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: E 5 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6764 (mp10) REVERT: B 288 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: B 322 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: D 32 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6642 (m-10) outliers start: 35 outliers final: 19 residues processed: 154 average time/residue: 0.5969 time to fit residues: 98.2711 Evaluate side-chains 154 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 96 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 139 optimal weight: 40.0000 chunk 42 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN B 161 HIS B 325 HIS F 83 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.251359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.216779 restraints weight = 11427.506| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 1.57 r_work: 0.4145 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4104 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 11453 Z= 0.323 Angle : 0.707 11.584 15595 Z= 0.367 Chirality : 0.049 0.183 1783 Planarity : 0.006 0.109 1973 Dihedral : 5.514 58.147 1555 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.37 % Allowed : 25.46 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.22), residues: 1428 helix: 1.50 (0.25), residues: 420 sheet: 1.06 (0.23), residues: 479 loop : -0.15 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 36 TYR 0.023 0.003 TYR F 94 PHE 0.029 0.003 PHE A 359 TRP 0.024 0.003 TRP F 52 HIS 0.008 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00752 (11443) covalent geometry : angle 0.70603 (15579) SS BOND : bond 0.00591 ( 8) SS BOND : angle 1.31848 ( 16) hydrogen bonds : bond 0.04901 ( 615) hydrogen bonds : angle 4.56080 ( 1809) metal coordination : bond 0.00568 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.7310 (mmp-170) cc_final: 0.6818 (mmp80) REVERT: B 288 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: B 322 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: D 32 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.7086 (m-10) outliers start: 42 outliers final: 23 residues processed: 159 average time/residue: 0.6342 time to fit residues: 108.0212 Evaluate side-chains 153 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 83 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 131 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN B 164 HIS F 83 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.251792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.214867 restraints weight = 11317.437| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 1.64 r_work: 0.4154 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.755 11453 Z= 0.605 Angle : 0.666 10.386 15595 Z= 0.342 Chirality : 0.047 0.174 1783 Planarity : 0.005 0.081 1973 Dihedral : 5.215 57.819 1553 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.89 % Allowed : 26.10 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.22), residues: 1428 helix: 1.50 (0.25), residues: 420 sheet: 1.13 (0.23), residues: 477 loop : -0.19 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 36 TYR 0.019 0.002 TYR E 94 PHE 0.025 0.002 PHE A 359 TRP 0.020 0.002 TRP F 52 HIS 0.006 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00600 (11443) covalent geometry : angle 0.66498 (15579) SS BOND : bond 0.00481 ( 8) SS BOND : angle 1.08690 ( 16) hydrogen bonds : bond 0.04523 ( 615) hydrogen bonds : angle 4.50312 ( 1809) metal coordination : bond 1.24108 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 ASP cc_start: 0.6997 (p0) cc_final: 0.6792 (p0) REVERT: B 322 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: D 32 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.6940 (m-10) outliers start: 36 outliers final: 26 residues processed: 155 average time/residue: 0.6277 time to fit residues: 104.3416 Evaluate side-chains 158 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 43 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN E 110 GLN B 164 HIS B 307 GLN F 83 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.253038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.217519 restraints weight = 11516.103| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 1.63 r_work: 0.4169 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4130 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.681 11453 Z= 0.544 Angle : 0.604 12.686 15595 Z= 0.304 Chirality : 0.043 0.173 1783 Planarity : 0.004 0.052 1973 Dihedral : 4.998 57.573 1553 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.09 % Allowed : 27.23 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.22), residues: 1428 helix: 1.82 (0.25), residues: 422 sheet: 1.23 (0.23), residues: 478 loop : -0.10 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 36 TYR 0.014 0.001 TYR E 94 PHE 0.016 0.002 PHE C 36 TRP 0.013 0.001 TRP F 52 HIS 0.004 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00333 (11443) covalent geometry : angle 0.60405 (15579) SS BOND : bond 0.00331 ( 8) SS BOND : angle 0.74663 ( 16) hydrogen bonds : bond 0.03857 ( 615) hydrogen bonds : angle 4.30090 ( 1809) metal coordination : bond 1.18832 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 322 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: D 32 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6691 (m-10) REVERT: D 97 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7405 (tp30) outliers start: 26 outliers final: 22 residues processed: 151 average time/residue: 0.6646 time to fit residues: 107.4119 Evaluate side-chains 152 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 94 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 123 optimal weight: 9.9990 chunk 41 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 126 optimal weight: 0.0980 chunk 6 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 45 optimal weight: 30.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN E 83 ASN E 110 GLN B 164 HIS B 307 GLN F 83 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** 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 = 0.4707 r_free = 0.4707 target = 0.252954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.217072 restraints weight = 11546.031| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 1.60 r_work: 0.4170 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4132 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.632 11453 Z= 0.532 Angle : 0.894 59.199 15595 Z= 0.498 Chirality : 0.044 0.436 1783 Planarity : 0.004 0.052 1973 Dihedral : 4.999 57.569 1553 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.17 % Allowed : 27.23 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.22), residues: 1428 helix: 1.85 (0.25), residues: 422 sheet: 1.24 (0.23), residues: 478 loop : -0.15 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 36 TYR 0.013 0.001 TYR E 94 PHE 0.016 0.001 PHE C 36 TRP 0.015 0.001 TRP E 159 HIS 0.004 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00334 (11443) covalent geometry : angle 0.89460 (15579) SS BOND : bond 0.00310 ( 8) SS BOND : angle 0.74522 ( 16) hydrogen bonds : bond 0.03807 ( 615) hydrogen bonds : angle 4.29996 ( 1809) metal coordination : bond 1.15436 ( 2) =============================================================================== Job complete usr+sys time: 4246.72 seconds wall clock time: 73 minutes 11.95 seconds (4391.95 seconds total)