Starting phenix.real_space_refine on Tue Jul 29 10:28:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j80_36055/07_2025/8j80_36055.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j80_36055/07_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_36055/07_2025/8j80_36055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j80_36055/07_2025/8j80_36055.map" model { file = "/net/cci-nas-00/data/ceres_data/8j80_36055/07_2025/8j80_36055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j80_36055/07_2025/8j80_36055.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.77, per 1000 atoms: 0.61 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: 2.53 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.45 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: 3.86 Time building geometry restraints manager: 3.07 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.420 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.002 TRP F 159 HIS 0.007 0.001 HIS A 240 PHE 0.024 0.002 PHE D 36 TYR 0.024 0.002 TYR C 91 ARG 0.018 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.13077 ( 615) hydrogen bonds : angle 6.40935 ( 1809) metal coordination : bond 0.24874 ( 2) SS BOND : bond 0.00465 ( 8) SS BOND : angle 1.02485 ( 16) covalent geometry : bond 0.00465 (11443) covalent geometry : angle 0.72836 (15579) *********************** 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 : 1.225 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: 1.1063 time to fit residues: 227.8309 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 : 1.157 ------------------------------------------------------------------------------- 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 119 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 110 optimal weight: 30.0000 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 40.0000 chunk 128 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.4653 r_free = 0.4653 target = 0.248893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.232376 restraints weight = 10984.641| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 0.75 r_work: 0.4386 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.4351 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11453 Z= 0.195 Angle : 0.622 8.553 15595 Z= 0.325 Chirality : 0.046 0.276 1783 Planarity : 0.005 0.050 1973 Dihedral : 6.238 93.508 1566 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.82 % Allowed : 23.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1428 helix: 1.44 (0.25), residues: 420 sheet: 0.86 (0.23), residues: 479 loop : -0.22 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 52 HIS 0.006 0.001 HIS A 240 PHE 0.019 0.002 PHE A 359 TYR 0.017 0.002 TYR F 94 ARG 0.012 0.001 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 615) hydrogen bonds : angle 4.82561 ( 1809) metal coordination : bond 0.00265 ( 2) SS BOND : bond 0.00374 ( 8) SS BOND : angle 0.93414 ( 16) covalent geometry : bond 0.00443 (11443) covalent geometry : angle 0.62195 (15579) *********************** 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 200 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 140 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 376 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6207 (tpt) REVERT: D 32 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6653 (m-10) outliers start: 60 outliers final: 21 residues processed: 178 average time/residue: 1.2538 time to fit residues: 241.3549 Evaluate side-chains 157 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 E residue 53 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain B residue 44 LEU 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 331 SER Chi-restraints excluded: chain B residue 338 LEU 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 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 23 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 140 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN 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 = 0.4702 r_free = 0.4702 target = 0.252345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.216991 restraints weight = 11417.328| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 1.40 r_work: 0.4163 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4127 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11453 Z= 0.191 Angle : 0.602 7.486 15595 Z= 0.315 Chirality : 0.045 0.270 1783 Planarity : 0.005 0.051 1973 Dihedral : 5.540 59.745 1557 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.10 % Allowed : 23.61 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.22), residues: 1428 helix: 1.57 (0.25), residues: 421 sheet: 0.92 (0.23), residues: 476 loop : -0.15 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 52 HIS 0.011 0.001 HIS B 137 PHE 0.018 0.002 PHE A 359 TYR 0.017 0.002 TYR F 94 ARG 0.005 0.001 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 615) hydrogen bonds : angle 4.60668 ( 1809) metal coordination : bond 0.00623 ( 2) SS BOND : bond 0.00379 ( 8) SS BOND : angle 0.85153 ( 16) covalent geometry : bond 0.00435 (11443) covalent geometry : angle 0.60157 (15579) *********************** 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 183 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: E 5 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6822 (mp10) REVERT: B 322 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: B 376 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6599 (tpt) REVERT: D 32 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.6782 (m-10) outliers start: 51 outliers final: 21 residues processed: 166 average time/residue: 1.2816 time to fit residues: 229.4220 Evaluate side-chains 157 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 68 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 141 LEU 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 B residue 376 MET Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain D residue 32 TYR 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 123 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 85 optimal weight: 40.0000 chunk 93 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 40.0000 chunk 31 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 overall best weight: 1.6582 ------------------------------------------------------------------------------- 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 111 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 = 0.4714 r_free = 0.4714 target = 0.253514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.225132 restraints weight = 11341.201| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 1.33 r_work: 0.4203 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4165 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11453 Z= 0.133 Angle : 0.560 8.974 15595 Z= 0.289 Chirality : 0.043 0.253 1783 Planarity : 0.004 0.053 1973 Dihedral : 5.375 58.638 1557 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.61 % Allowed : 24.10 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.22), residues: 1428 helix: 1.87 (0.25), residues: 421 sheet: 1.08 (0.23), residues: 481 loop : -0.14 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 52 HIS 0.007 0.001 HIS B 137 PHE 0.016 0.001 PHE E 80 TYR 0.013 0.001 TYR F 94 ARG 0.008 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 615) hydrogen bonds : angle 4.36532 ( 1809) metal coordination : bond 0.00432 ( 2) SS BOND : bond 0.00324 ( 8) SS BOND : angle 0.68001 ( 16) covalent geometry : bond 0.00296 (11443) covalent geometry : angle 0.55970 (15579) *********************** 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 175 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: E 18 LEU cc_start: 0.8108 (tp) cc_final: 0.7594 (tp) REVERT: B 288 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: B 322 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7581 (mt0) REVERT: D 32 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6591 (m-10) outliers start: 45 outliers final: 21 residues processed: 158 average time/residue: 1.2627 time to fit residues: 215.2304 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 : 1.243 ------------------------------------------------------------------------------- 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 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 53 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 110 GLN 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 322 GLN 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 77 GLN Chi-restraints excluded: chain F residue 155 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 115 optimal weight: 40.0000 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 E 110 GLN E 201 ASN B 164 HIS B 259 GLN F 3 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 = 0.4700 r_free = 0.4700 target = 0.252219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.217349 restraints weight = 11352.601| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 1.60 r_work: 0.4162 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 2.095 11453 Z= 0.686 Angle : 0.604 7.312 15595 Z= 0.316 Chirality : 0.045 0.217 1783 Planarity : 0.005 0.066 1973 Dihedral : 5.563 59.892 1557 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.42 % Allowed : 23.86 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1428 helix: 1.74 (0.25), residues: 421 sheet: 1.08 (0.23), residues: 479 loop : -0.15 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 52 HIS 0.005 0.001 HIS B 137 PHE 0.020 0.002 PHE A 359 TYR 0.019 0.002 TYR F 94 ARG 0.005 0.001 ARG C 16 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 615) hydrogen bonds : angle 4.41743 ( 1809) metal coordination : bond 1.48117 ( 2) SS BOND : bond 0.00436 ( 8) SS BOND : angle 0.96331 ( 16) covalent geometry : bond 0.00487 (11443) covalent geometry : angle 0.60353 (15579) *********************** 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 185 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 1.147 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 55 TYR cc_start: 0.3835 (OUTLIER) cc_final: 0.3624 (t80) REVERT: E 18 LEU cc_start: 0.8180 (tp) cc_final: 0.7697 (tp) REVERT: B 322 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: D 32 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6880 (m-10) outliers start: 55 outliers final: 26 residues processed: 165 average time/residue: 1.1898 time to fit residues: 212.7302 Evaluate side-chains 159 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 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 68 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain B residue 42 LEU 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 285 LEU 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 F residue 174 VAL Chi-restraints excluded: chain D residue 11 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 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 120 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 128 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 5 GLN E 83 ASN E 110 GLN E 201 ASN B 164 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.253396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.219693 restraints weight = 11534.958| |-----------------------------------------------------------------------------| r_work (start): 0.4418 rms_B_bonded: 1.58 r_work: 0.4176 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.660 11453 Z= 0.534 Angle : 0.559 8.061 15595 Z= 0.288 Chirality : 0.043 0.199 1783 Planarity : 0.004 0.054 1973 Dihedral : 5.357 58.825 1557 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.94 % Allowed : 24.58 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.22), residues: 1428 helix: 1.96 (0.25), residues: 420 sheet: 1.21 (0.23), residues: 481 loop : -0.10 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 52 HIS 0.004 0.001 HIS B 164 PHE 0.017 0.001 PHE C 213 TYR 0.014 0.001 TYR F 94 ARG 0.008 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 615) hydrogen bonds : angle 4.28701 ( 1809) metal coordination : bond 1.17414 ( 2) SS BOND : bond 0.00338 ( 8) SS BOND : angle 0.69669 ( 16) covalent geometry : bond 0.00291 (11443) covalent geometry : angle 0.55862 (15579) *********************** 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 184 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.3819 (OUTLIER) cc_final: 0.3614 (t80) REVERT: E 18 LEU cc_start: 0.8204 (tp) cc_final: 0.7783 (tp) REVERT: E 70 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.8239 (p) REVERT: D 32 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6563 (m-10) REVERT: D 97 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7740 (tp30) outliers start: 49 outliers final: 22 residues processed: 163 average time/residue: 1.2244 time to fit residues: 215.8043 Evaluate side-chains 158 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 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 68 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain B residue 42 LEU 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 331 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 155 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 130 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 68 optimal weight: 40.0000 chunk 98 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 161 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 = 0.4701 r_free = 0.4701 target = 0.252437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.218357 restraints weight = 11512.860| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 1.57 r_work: 0.4158 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4119 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11453 Z= 0.209 Angle : 0.612 9.936 15595 Z= 0.316 Chirality : 0.045 0.186 1783 Planarity : 0.005 0.064 1973 Dihedral : 5.494 58.905 1557 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.86 % Allowed : 24.90 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.22), residues: 1428 helix: 1.73 (0.25), residues: 420 sheet: 1.21 (0.23), residues: 479 loop : -0.09 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 52 HIS 0.005 0.001 HIS B 325 PHE 0.021 0.002 PHE A 359 TYR 0.018 0.002 TYR F 94 ARG 0.009 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 615) hydrogen bonds : angle 4.38070 ( 1809) metal coordination : bond 0.00142 ( 2) SS BOND : bond 0.00448 ( 8) SS BOND : angle 0.99487 ( 16) covalent geometry : bond 0.00480 (11443) covalent geometry : angle 0.61164 (15579) *********************** 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 181 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.3955 (OUTLIER) cc_final: 0.3733 (t80) REVERT: E 5 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: B 322 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: D 32 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6781 (m-10) outliers start: 48 outliers final: 31 residues processed: 162 average time/residue: 1.4410 time to fit residues: 252.0810 Evaluate side-chains 162 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 331 SER 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 68 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ARG 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 B residue 338 LEU 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 F residue 155 VAL Chi-restraints excluded: chain D residue 11 LEU 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 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 70 optimal weight: 50.0000 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 40.0000 chunk 57 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 140 optimal weight: 30.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 5 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.253551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.221194 restraints weight = 11487.992| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 1.46 r_work: 0.4201 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4166 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.754 11453 Z= 0.561 Angle : 0.569 10.427 15595 Z= 0.288 Chirality : 0.043 0.177 1783 Planarity : 0.004 0.053 1973 Dihedral : 5.014 58.548 1555 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.49 % Allowed : 26.43 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1428 helix: 2.00 (0.25), residues: 420 sheet: 1.26 (0.23), residues: 479 loop : -0.04 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 52 HIS 0.003 0.001 HIS B 137 PHE 0.016 0.001 PHE E 80 TYR 0.012 0.001 TYR F 94 ARG 0.010 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 615) hydrogen bonds : angle 4.21490 ( 1809) metal coordination : bond 1.24061 ( 2) SS BOND : bond 0.00310 ( 8) SS BOND : angle 0.65134 ( 16) covalent geometry : bond 0.00273 (11443) covalent geometry : angle 0.56919 (15579) *********************** 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 165 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 LEU cc_start: 0.8169 (tp) cc_final: 0.7536 (tp) REVERT: B 322 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: D 32 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6451 (m-10) REVERT: D 97 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7453 (tp30) outliers start: 31 outliers final: 21 residues processed: 154 average time/residue: 1.3652 time to fit residues: 226.7186 Evaluate side-chains 154 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 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 5 GLN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ARG 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 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 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 67 optimal weight: 50.0000 chunk 130 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 91 optimal weight: 0.0270 chunk 54 optimal weight: 0.4980 chunk 62 optimal weight: 9.9990 chunk 124 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- 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 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 = 0.4712 r_free = 0.4712 target = 0.253629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.216717 restraints weight = 11526.735| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 1.60 r_work: 0.4186 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4146 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.597 11453 Z= 0.513 Angle : 0.563 10.608 15595 Z= 0.285 Chirality : 0.043 0.173 1783 Planarity : 0.004 0.052 1973 Dihedral : 4.882 58.454 1554 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.97 % Allowed : 26.10 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1428 helix: 2.07 (0.25), residues: 420 sheet: 1.28 (0.23), residues: 480 loop : -0.04 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 52 HIS 0.003 0.001 HIS B 325 PHE 0.016 0.001 PHE E 80 TYR 0.012 0.001 TYR F 94 ARG 0.011 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 615) hydrogen bonds : angle 4.15285 ( 1809) metal coordination : bond 1.12950 ( 2) SS BOND : bond 0.00335 ( 8) SS BOND : angle 0.70511 ( 16) covalent geometry : bond 0.00275 (11443) covalent geometry : angle 0.56308 (15579) *********************** 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 169 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 1.304 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: 0.8081 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: D 32 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.6425 (m-10) REVERT: D 97 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7455 (tp30) outliers start: 37 outliers final: 27 residues processed: 158 average time/residue: 1.3456 time to fit residues: 229.3959 Evaluate side-chains 159 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 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 70 SER Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ARG 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 B residue 338 LEU 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 155 VAL 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 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 54 optimal weight: 0.4980 chunk 62 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 71 optimal weight: 60.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 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 = 0.4711 r_free = 0.4711 target = 0.253509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.221143 restraints weight = 11510.375| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 1.55 r_work: 0.4189 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.593 11453 Z= 0.513 Angle : 0.586 13.078 15595 Z= 0.292 Chirality : 0.043 0.173 1783 Planarity : 0.004 0.052 1973 Dihedral : 4.870 58.457 1554 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.41 % Allowed : 27.15 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1428 helix: 2.06 (0.25), residues: 420 sheet: 1.35 (0.23), residues: 482 loop : -0.08 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 159 HIS 0.003 0.001 HIS B 325 PHE 0.016 0.001 PHE E 80 TYR 0.016 0.001 TYR E 94 ARG 0.012 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 615) hydrogen bonds : angle 4.14998 ( 1809) metal coordination : bond 1.12640 ( 2) SS BOND : bond 0.00329 ( 8) SS BOND : angle 0.71338 ( 16) covalent geometry : bond 0.00291 (11443) covalent geometry : angle 0.58614 (15579) ********************** 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 164 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.304 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 18 LEU cc_start: 0.8180 (tp) cc_final: 0.7550 (tp) REVERT: E 70 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8205 (p) REVERT: B 322 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7724 (mt0) REVERT: D 32 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6451 (m-10) REVERT: D 97 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7711 (tp30) outliers start: 30 outliers final: 25 residues processed: 156 average time/residue: 1.2284 time to fit residues: 207.0832 Evaluate side-chains 161 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 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 70 SER Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ARG 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 B residue 338 LEU 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 155 VAL 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 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 121 optimal weight: 20.0000 chunk 115 optimal weight: 50.0000 chunk 124 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 67 optimal weight: 50.0000 chunk 78 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 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 = 0.4698 r_free = 0.4698 target = 0.252477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.224065 restraints weight = 11274.281| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 1.22 r_work: 0.4202 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.4165 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.606 11453 Z= 0.520 Angle : 0.588 11.028 15595 Z= 0.295 Chirality : 0.043 0.170 1783 Planarity : 0.004 0.052 1973 Dihedral : 4.889 58.524 1554 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.41 % Allowed : 27.23 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1428 helix: 2.01 (0.25), residues: 420 sheet: 1.39 (0.23), residues: 479 loop : -0.09 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 159 HIS 0.003 0.001 HIS B 325 PHE 0.016 0.001 PHE E 80 TYR 0.014 0.001 TYR F 94 ARG 0.012 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 615) hydrogen bonds : angle 4.15362 ( 1809) metal coordination : bond 1.13534 ( 2) SS BOND : bond 0.00341 ( 8) SS BOND : angle 0.75332 ( 16) covalent geometry : bond 0.00319 (11443) covalent geometry : angle 0.58732 (15579) =============================================================================== Job complete usr+sys time: 9097.32 seconds wall clock time: 159 minutes 2.97 seconds (9542.97 seconds total)