Starting phenix.real_space_refine on Sun May 11 05:17:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbi_39902/05_2025/8zbi_39902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbi_39902/05_2025/8zbi_39902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zbi_39902/05_2025/8zbi_39902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbi_39902/05_2025/8zbi_39902.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbi_39902/05_2025/8zbi_39902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbi_39902/05_2025/8zbi_39902.cif" } resolution = 2.79 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 4905 2.51 5 N 1305 2.21 5 O 1391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7657 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 920 Classifications: {'peptide': 112} Link IDs: {'TRANS': 111} Chain breaks: 5 Chain: "C" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2392 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 306} Chain: "E" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 4, 'TRANS': 31} Chain: "F" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "D" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2188 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 4.88, per 1000 atoms: 0.64 Number of scatterers: 7657 At special positions: 0 Unit cell: (89.888, 101.76, 120.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1391 8.00 N 1305 7.00 C 4905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 197 " - pdb=" SG CYS F 267 " distance=2.03 Simple disulfide: pdb=" SG CYS D 116 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS S 3 " - pdb=" SG CYS S 14 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 16 sheets defined 33.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'B' and resid 6 through 30 removed outlier: 3.585A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.683A pdb=" N TRP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'F' and resid 66 through 70 removed outlier: 3.531A pdb=" N SER F 69 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.837A pdb=" N THR F 129 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 72 removed outlier: 3.970A pdb=" N ILE D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Proline residue: D 48 - end of helix Processing helix chain 'D' and resid 78 through 107 Proline residue: D 98 - end of helix removed outlier: 3.989A pdb=" N ALA D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 107 " --> pdb=" O GLN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 147 removed outlier: 3.647A pdb=" N MET D 120 " --> pdb=" O CYS D 116 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 175 Processing helix chain 'D' and resid 175 through 181 Processing helix chain 'D' and resid 198 through 217 Processing helix chain 'D' and resid 217 through 239 Processing helix chain 'D' and resid 248 through 254 removed outlier: 4.145A pdb=" N ARG D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 283 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 290 No H-bonds generated for 'chain 'D' and resid 288 through 290' Processing helix chain 'D' and resid 291 through 314 removed outlier: 4.254A pdb=" N TYR D 295 " --> pdb=" O PHE D 291 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE D 296 " --> pdb=" O PHE D 292 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 297 " --> pdb=" O GLY D 293 " (cutoff:3.500A) Proline residue: D 302 - end of helix Proline residue: D 310 - end of helix Processing helix chain 'D' and resid 317 through 325 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 38 Processing sheet with id=AA2, first strand: chain 'B' and resid 221 through 223 removed outlier: 6.479A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.564A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.854A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.570A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.832A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.587A pdb=" N VAL C 200 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.831A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 277 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 285 " --> pdb=" O TRP C 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AB2, first strand: chain 'F' and resid 41 through 45 removed outlier: 3.977A pdb=" N SER F 59 " --> pdb=" O SER F 45 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 48 through 50 removed outlier: 5.990A pdb=" N GLY F 48 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N MET F 72 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR F 88 " --> pdb=" O MET F 72 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP F 74 " --> pdb=" O VAL F 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 178 through 179 removed outlier: 3.517A pdb=" N THR F 179 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG F 198 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL F 193 " --> pdb=" O ILE F 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 185 through 186 removed outlier: 6.404A pdb=" N VAL F 185 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 227 through 228 Processing sheet with id=AB7, first strand: chain 'D' and resid 182 through 183 removed outlier: 3.532A pdb=" N HIS D 192 " --> pdb=" O GLY D 183 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2438 1.34 - 1.46: 1906 1.46 - 1.58: 3407 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 7831 Sorted by residual: bond pdb=" N THR C 29 " pdb=" CA THR C 29 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N ARG E 27 " pdb=" CA ARG E 27 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N ALA D 41 " pdb=" CA ALA D 41 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N LEU B 5 " pdb=" CA LEU B 5 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N CYS S 3 " pdb=" CA CYS S 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 ... (remaining 7826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 10221 1.14 - 2.27: 336 2.27 - 3.41: 44 3.41 - 4.55: 23 4.55 - 5.68: 6 Bond angle restraints: 10630 Sorted by residual: angle pdb=" C ARG F 229 " pdb=" N MET F 230 " pdb=" CA MET F 230 " ideal model delta sigma weight residual 121.54 125.96 -4.42 1.91e+00 2.74e-01 5.36e+00 angle pdb=" N GLY F 247 " pdb=" CA GLY F 247 " pdb=" C GLY F 247 " ideal model delta sigma weight residual 111.36 114.06 -2.70 1.17e+00 7.31e-01 5.31e+00 angle pdb=" N PHE D 315 " pdb=" CA PHE D 315 " pdb=" C PHE D 315 " ideal model delta sigma weight residual 113.18 110.48 2.70 1.33e+00 5.65e-01 4.13e+00 angle pdb=" C SER F 246 " pdb=" N GLY F 247 " pdb=" CA GLY F 247 " ideal model delta sigma weight residual 119.92 121.81 -1.89 9.60e-01 1.09e+00 3.89e+00 angle pdb=" C ASP F 111 " pdb=" N ASP F 112 " pdb=" CA ASP F 112 " ideal model delta sigma weight residual 119.78 122.12 -2.34 1.24e+00 6.50e-01 3.57e+00 ... (remaining 10625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.10: 4014 11.10 - 22.21: 419 22.21 - 33.31: 118 33.31 - 44.42: 36 44.42 - 55.52: 7 Dihedral angle restraints: 4594 sinusoidal: 1757 harmonic: 2837 Sorted by residual: dihedral pdb=" CA ARG F 229 " pdb=" C ARG F 229 " pdb=" N MET F 230 " pdb=" CA MET F 230 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TYR F 139 " pdb=" C TYR F 139 " pdb=" N TYR F 140 " pdb=" CA TYR F 140 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 4591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 703 0.027 - 0.054: 323 0.054 - 0.082: 106 0.082 - 0.109: 48 0.109 - 0.136: 34 Chirality restraints: 1214 Sorted by residual: chirality pdb=" CA VAL F 237 " pdb=" N VAL F 237 " pdb=" C VAL F 237 " pdb=" CB VAL F 237 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA TYR F 273 " pdb=" N TYR F 273 " pdb=" C TYR F 273 " pdb=" CB TYR F 273 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL E 54 " pdb=" N VAL E 54 " pdb=" C VAL E 54 " pdb=" CB VAL E 54 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1211 not shown) Planarity restraints: 1333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 213 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LEU D 213 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU D 213 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY D 214 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO C 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 48 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO E 49 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 49 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 49 " -0.022 5.00e-02 4.00e+02 ... (remaining 1330 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 110 2.65 - 3.22: 7017 3.22 - 3.78: 11163 3.78 - 4.34: 16079 4.34 - 4.90: 27198 Nonbonded interactions: 61567 Sorted by model distance: nonbonded pdb=" OH TYR B 320 " pdb=" OD2 ASP B 341 " model vdw 2.092 3.040 nonbonded pdb=" NE ARG C 137 " pdb=" O ILE C 171 " model vdw 2.136 3.120 nonbonded pdb=" O THR C 86 " pdb=" OG1 THR C 87 " model vdw 2.175 3.040 nonbonded pdb=" O ASP B 350 " pdb=" NH2 ARG D 319 " model vdw 2.176 3.120 nonbonded pdb=" O SER C 189 " pdb=" OG SER C 201 " model vdw 2.185 3.040 ... (remaining 61562 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7834 Z= 0.142 Angle : 0.522 5.684 10636 Z= 0.282 Chirality : 0.041 0.136 1214 Planarity : 0.004 0.039 1333 Dihedral : 10.589 55.523 2755 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.29 (0.28), residues: 958 helix: 1.95 (0.31), residues: 299 sheet: -1.01 (0.30), residues: 287 loop : -1.23 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 8 HIS 0.003 0.001 HIS D 72 PHE 0.015 0.001 PHE C 151 TYR 0.012 0.001 TYR B 320 ARG 0.004 0.000 ARG D 254 Details of bonding type rmsd hydrogen bonds : bond 0.19224 ( 344) hydrogen bonds : angle 7.34650 ( 975) SS BOND : bond 0.00202 ( 3) SS BOND : angle 0.67789 ( 6) covalent geometry : bond 0.00310 ( 7831) covalent geometry : angle 0.52202 (10630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.802 Fit side-chains REVERT: C 129 ARG cc_start: 0.7231 (tpt170) cc_final: 0.6855 (tpt170) REVERT: C 217 MET cc_start: 0.4805 (mmm) cc_final: 0.4387 (tmt) REVERT: C 243 THR cc_start: 0.7371 (p) cc_final: 0.6883 (m) REVERT: D 115 MET cc_start: 0.5269 (ptm) cc_final: 0.4912 (ptt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 1.0645 time to fit residues: 149.5616 Evaluate side-chains 94 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 62 HIS C 239 ASN C 340 ASN E 59 ASN F 270 HIS ** D 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.263589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.205067 restraints weight = 6862.437| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.16 r_work: 0.3865 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7834 Z= 0.156 Angle : 0.614 9.731 10636 Z= 0.321 Chirality : 0.044 0.161 1214 Planarity : 0.005 0.053 1333 Dihedral : 4.514 20.896 1065 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.28 % Allowed : 8.51 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.28), residues: 958 helix: 2.01 (0.30), residues: 301 sheet: -0.71 (0.30), residues: 261 loop : -1.17 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS C 54 PHE 0.016 0.001 PHE C 151 TYR 0.016 0.002 TYR D 318 ARG 0.003 0.000 ARG D 319 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 344) hydrogen bonds : angle 5.35901 ( 975) SS BOND : bond 0.00263 ( 3) SS BOND : angle 0.59017 ( 6) covalent geometry : bond 0.00349 ( 7831) covalent geometry : angle 0.61382 (10630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: B 29 LYS cc_start: 0.7350 (tppp) cc_final: 0.6723 (tptp) REVERT: C 129 ARG cc_start: 0.7306 (tpt170) cc_final: 0.6898 (tpt170) REVERT: C 217 MET cc_start: 0.4962 (mmm) cc_final: 0.4336 (tmt) REVERT: C 243 THR cc_start: 0.7621 (p) cc_final: 0.7074 (m) REVERT: C 280 LYS cc_start: 0.8286 (tttp) cc_final: 0.8073 (tttt) REVERT: C 338 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7268 (mm) REVERT: D 260 VAL cc_start: 0.8106 (t) cc_final: 0.7870 (t) REVERT: D 267 VAL cc_start: 0.7059 (OUTLIER) cc_final: 0.6844 (p) outliers start: 19 outliers final: 8 residues processed: 111 average time/residue: 1.2575 time to fit residues: 147.7918 Evaluate side-chains 102 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain D residue 267 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 8 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.0170 chunk 85 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.262242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.198122 restraints weight = 6900.605| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.16 r_work: 0.3852 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7834 Z= 0.160 Angle : 0.594 9.200 10636 Z= 0.313 Chirality : 0.043 0.160 1214 Planarity : 0.005 0.047 1333 Dihedral : 4.584 21.565 1065 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.48 % Allowed : 9.95 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.28), residues: 958 helix: 1.94 (0.30), residues: 302 sheet: -0.55 (0.30), residues: 261 loop : -1.21 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.020 0.001 PHE D 206 TYR 0.018 0.002 TYR C 105 ARG 0.003 0.000 ARG D 155 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 344) hydrogen bonds : angle 5.12824 ( 975) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.74336 ( 6) covalent geometry : bond 0.00362 ( 7831) covalent geometry : angle 0.59434 (10630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: B 29 LYS cc_start: 0.7263 (tppp) cc_final: 0.6675 (tptp) REVERT: C 129 ARG cc_start: 0.7336 (tpt170) cc_final: 0.6877 (tpt170) REVERT: C 217 MET cc_start: 0.4872 (mmm) cc_final: 0.4400 (tmt) REVERT: C 234 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: C 243 THR cc_start: 0.7452 (p) cc_final: 0.6950 (m) REVERT: C 269 ILE cc_start: 0.5542 (OUTLIER) cc_final: 0.5325 (pt) REVERT: C 338 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7295 (mm) REVERT: D 188 MET cc_start: 0.5810 (ppp) cc_final: 0.4097 (mmm) REVERT: D 319 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.6184 (ttt180) REVERT: D 320 PHE cc_start: 0.5084 (m-10) cc_final: 0.4388 (m-80) outliers start: 29 outliers final: 12 residues processed: 116 average time/residue: 1.1770 time to fit residues: 144.6321 Evaluate side-chains 111 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain D residue 319 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.259671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.200721 restraints weight = 6965.562| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.38 r_work: 0.3957 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7834 Z= 0.147 Angle : 0.576 9.552 10636 Z= 0.303 Chirality : 0.043 0.154 1214 Planarity : 0.004 0.047 1333 Dihedral : 4.500 21.862 1065 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.88 % Allowed : 13.19 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.28), residues: 958 helix: 1.99 (0.30), residues: 303 sheet: -0.41 (0.30), residues: 261 loop : -1.21 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 PHE 0.016 0.001 PHE C 151 TYR 0.016 0.002 TYR F 97 ARG 0.002 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 344) hydrogen bonds : angle 4.98579 ( 975) SS BOND : bond 0.00286 ( 3) SS BOND : angle 0.89413 ( 6) covalent geometry : bond 0.00331 ( 7831) covalent geometry : angle 0.57567 (10630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: B 29 LYS cc_start: 0.7209 (tppp) cc_final: 0.6680 (tptp) REVERT: C 129 ARG cc_start: 0.7322 (tpt170) cc_final: 0.6855 (tpt170) REVERT: C 217 MET cc_start: 0.4877 (mmm) cc_final: 0.4443 (tmt) REVERT: C 234 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: C 243 THR cc_start: 0.7476 (p) cc_final: 0.6917 (m) REVERT: C 338 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7321 (mm) REVERT: D 188 MET cc_start: 0.5556 (ppp) cc_final: 0.4006 (mmm) REVERT: D 320 PHE cc_start: 0.4877 (m-10) cc_final: 0.3587 (t80) outliers start: 24 outliers final: 10 residues processed: 114 average time/residue: 1.1709 time to fit residues: 141.6961 Evaluate side-chains 105 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 12 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.245709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179899 restraints weight = 6866.201| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.45 r_work: 0.3769 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7834 Z= 0.222 Angle : 0.676 11.291 10636 Z= 0.355 Chirality : 0.046 0.177 1214 Planarity : 0.005 0.048 1333 Dihedral : 4.927 20.874 1065 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.12 % Allowed : 14.15 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.27), residues: 958 helix: 1.64 (0.30), residues: 303 sheet: -0.40 (0.30), residues: 262 loop : -1.28 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.025 0.002 PHE C 151 TYR 0.021 0.002 TYR F 97 ARG 0.004 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.05240 ( 344) hydrogen bonds : angle 5.16634 ( 975) SS BOND : bond 0.00352 ( 3) SS BOND : angle 1.01971 ( 6) covalent geometry : bond 0.00519 ( 7831) covalent geometry : angle 0.67603 (10630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.776 Fit side-chains REVERT: B 29 LYS cc_start: 0.7095 (tppp) cc_final: 0.6563 (tptp) REVERT: C 197 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.6092 (mtp180) REVERT: C 217 MET cc_start: 0.4700 (mmm) cc_final: 0.4264 (tmt) REVERT: C 243 THR cc_start: 0.7362 (p) cc_final: 0.6943 (m) REVERT: C 338 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7305 (mm) REVERT: F 178 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.5438 (mtt) REVERT: D 188 MET cc_start: 0.5373 (ppp) cc_final: 0.3476 (mtm) outliers start: 26 outliers final: 16 residues processed: 109 average time/residue: 1.1414 time to fit residues: 131.9586 Evaluate side-chains 111 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain D residue 320 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN E 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.262589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.199239 restraints weight = 6854.982| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.14 r_work: 0.3966 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7834 Z= 0.128 Angle : 0.556 8.541 10636 Z= 0.295 Chirality : 0.042 0.152 1214 Planarity : 0.004 0.048 1333 Dihedral : 4.479 21.567 1065 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.52 % Allowed : 15.59 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.28), residues: 958 helix: 1.99 (0.30), residues: 304 sheet: -0.27 (0.30), residues: 273 loop : -1.15 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS B 195 PHE 0.013 0.001 PHE C 151 TYR 0.016 0.001 TYR F 97 ARG 0.004 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 344) hydrogen bonds : angle 4.86948 ( 975) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.84815 ( 6) covalent geometry : bond 0.00282 ( 7831) covalent geometry : angle 0.55618 (10630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.781 Fit side-chains REVERT: B 29 LYS cc_start: 0.7179 (tppp) cc_final: 0.6661 (tptp) REVERT: B 345 LYS cc_start: 0.6252 (mptt) cc_final: 0.5493 (mtpt) REVERT: C 129 ARG cc_start: 0.7370 (tpt170) cc_final: 0.6645 (tpt170) REVERT: C 146 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6664 (tt) REVERT: C 197 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.6159 (mtp180) REVERT: C 217 MET cc_start: 0.4857 (mmm) cc_final: 0.4451 (tmt) REVERT: C 269 ILE cc_start: 0.5624 (OUTLIER) cc_final: 0.5399 (pt) REVERT: C 338 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7209 (mm) REVERT: F 178 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.5832 (mtt) REVERT: D 188 MET cc_start: 0.5337 (ppp) cc_final: 0.3492 (mtm) outliers start: 21 outliers final: 13 residues processed: 115 average time/residue: 1.1249 time to fit residues: 137.2502 Evaluate side-chains 108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 281 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 72 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 36 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 92 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN C 239 ASN E 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.264640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.201982 restraints weight = 6812.892| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.14 r_work: 0.3992 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7834 Z= 0.112 Angle : 0.528 7.039 10636 Z= 0.280 Chirality : 0.041 0.141 1214 Planarity : 0.004 0.047 1333 Dihedral : 4.260 19.988 1065 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.40 % Allowed : 16.43 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.28), residues: 958 helix: 2.18 (0.30), residues: 303 sheet: -0.11 (0.30), residues: 273 loop : -1.12 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS D 192 PHE 0.011 0.001 PHE C 151 TYR 0.014 0.001 TYR F 97 ARG 0.004 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 344) hydrogen bonds : angle 4.70205 ( 975) SS BOND : bond 0.00258 ( 3) SS BOND : angle 0.85299 ( 6) covalent geometry : bond 0.00243 ( 7831) covalent geometry : angle 0.52824 (10630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.873 Fit side-chains REVERT: B 29 LYS cc_start: 0.7108 (tppp) cc_final: 0.6629 (tptp) REVERT: B 345 LYS cc_start: 0.6055 (mptt) cc_final: 0.5348 (mtpt) REVERT: C 129 ARG cc_start: 0.7333 (tpt170) cc_final: 0.6593 (tpt170) REVERT: C 197 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6069 (mtp180) REVERT: C 217 MET cc_start: 0.4768 (mmm) cc_final: 0.4282 (tmt) REVERT: C 338 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7291 (mm) REVERT: F 178 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.5761 (mtt) REVERT: D 188 MET cc_start: 0.5219 (ppp) cc_final: 0.3254 (mtm) outliers start: 20 outliers final: 13 residues processed: 115 average time/residue: 1.1310 time to fit residues: 138.2023 Evaluate side-chains 113 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 320 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN C 239 ASN E 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.246445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.178962 restraints weight = 6992.083| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.21 r_work: 0.3979 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7834 Z= 0.186 Angle : 0.631 10.530 10636 Z= 0.331 Chirality : 0.044 0.161 1214 Planarity : 0.005 0.078 1333 Dihedral : 4.648 21.325 1065 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.88 % Allowed : 15.59 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.28), residues: 958 helix: 1.83 (0.30), residues: 304 sheet: -0.13 (0.30), residues: 268 loop : -1.21 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.004 0.001 HIS B 195 PHE 0.023 0.001 PHE C 151 TYR 0.018 0.002 TYR F 97 ARG 0.006 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 344) hydrogen bonds : angle 4.91759 ( 975) SS BOND : bond 0.00336 ( 3) SS BOND : angle 1.01500 ( 6) covalent geometry : bond 0.00432 ( 7831) covalent geometry : angle 0.63093 (10630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.836 Fit side-chains REVERT: B 29 LYS cc_start: 0.7261 (tppp) cc_final: 0.6752 (tptp) REVERT: B 345 LYS cc_start: 0.6165 (mptt) cc_final: 0.5381 (mtpt) REVERT: C 129 ARG cc_start: 0.7327 (tpt170) cc_final: 0.6578 (tpt170) REVERT: C 197 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6108 (mtp180) REVERT: C 217 MET cc_start: 0.4835 (mmm) cc_final: 0.4433 (tmt) REVERT: C 234 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: C 338 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7299 (mm) REVERT: F 178 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.5724 (mtt) REVERT: D 188 MET cc_start: 0.5303 (ppp) cc_final: 0.3320 (mtm) outliers start: 24 outliers final: 14 residues processed: 108 average time/residue: 1.2022 time to fit residues: 137.5804 Evaluate side-chains 109 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 44 optimal weight: 0.0870 chunk 84 optimal weight: 1.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN C 239 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.247496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.181501 restraints weight = 7087.701| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.15 r_work: 0.3827 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7834 Z= 0.160 Angle : 0.604 10.204 10636 Z= 0.318 Chirality : 0.043 0.158 1214 Planarity : 0.005 0.073 1333 Dihedral : 4.612 21.062 1065 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.88 % Allowed : 16.43 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.28), residues: 958 helix: 1.79 (0.30), residues: 304 sheet: -0.04 (0.30), residues: 267 loop : -1.24 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS B 195 PHE 0.019 0.001 PHE C 151 TYR 0.019 0.002 TYR F 97 ARG 0.005 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 344) hydrogen bonds : angle 4.89258 ( 975) SS BOND : bond 0.00305 ( 3) SS BOND : angle 0.98224 ( 6) covalent geometry : bond 0.00366 ( 7831) covalent geometry : angle 0.60365 (10630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.900 Fit side-chains REVERT: B 345 LYS cc_start: 0.5902 (mptt) cc_final: 0.5164 (mtpt) REVERT: C 129 ARG cc_start: 0.7347 (tpt170) cc_final: 0.6541 (tpt170) REVERT: C 146 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6603 (tt) REVERT: C 197 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.6047 (mtp180) REVERT: C 217 MET cc_start: 0.4690 (mmm) cc_final: 0.4266 (tmt) REVERT: C 234 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: C 338 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7236 (mm) REVERT: F 178 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.5846 (mtt) REVERT: D 188 MET cc_start: 0.5263 (ppp) cc_final: 0.3287 (mtm) outliers start: 24 outliers final: 15 residues processed: 105 average time/residue: 1.0976 time to fit residues: 122.9258 Evaluate side-chains 109 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain D residue 281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN C 239 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.245440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.178302 restraints weight = 6964.565| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.17 r_work: 0.3806 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7834 Z= 0.197 Angle : 0.658 10.993 10636 Z= 0.346 Chirality : 0.045 0.173 1214 Planarity : 0.005 0.071 1333 Dihedral : 4.822 21.183 1065 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.76 % Allowed : 16.55 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.27), residues: 958 helix: 1.63 (0.30), residues: 304 sheet: -0.10 (0.31), residues: 262 loop : -1.28 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.004 0.001 HIS B 195 PHE 0.023 0.002 PHE C 151 TYR 0.021 0.002 TYR C 264 ARG 0.003 0.000 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 344) hydrogen bonds : angle 5.01214 ( 975) SS BOND : bond 0.00390 ( 3) SS BOND : angle 1.07808 ( 6) covalent geometry : bond 0.00456 ( 7831) covalent geometry : angle 0.65796 (10630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.860 Fit side-chains REVERT: C 129 ARG cc_start: 0.7305 (tpt170) cc_final: 0.6528 (tpt170) REVERT: C 146 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6625 (tt) REVERT: C 197 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.6061 (mtp180) REVERT: C 217 MET cc_start: 0.4716 (mmm) cc_final: 0.4288 (tmt) REVERT: C 338 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7285 (mm) REVERT: F 178 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6071 (mtt) REVERT: D 188 MET cc_start: 0.5355 (ppp) cc_final: 0.3478 (mtm) outliers start: 23 outliers final: 16 residues processed: 103 average time/residue: 1.1510 time to fit residues: 126.2405 Evaluate side-chains 107 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain D residue 281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.0010 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN C 239 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.263242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.200013 restraints weight = 6881.739| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.15 r_work: 0.3894 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7834 Z= 0.119 Angle : 0.554 7.435 10636 Z= 0.295 Chirality : 0.042 0.146 1214 Planarity : 0.004 0.067 1333 Dihedral : 4.386 19.986 1065 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.40 % Allowed : 17.39 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.28), residues: 958 helix: 1.99 (0.30), residues: 303 sheet: -0.01 (0.31), residues: 271 loop : -1.07 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS B 195 PHE 0.012 0.001 PHE C 199 TYR 0.015 0.001 TYR F 97 ARG 0.004 0.000 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 344) hydrogen bonds : angle 4.75207 ( 975) SS BOND : bond 0.00327 ( 3) SS BOND : angle 0.94745 ( 6) covalent geometry : bond 0.00256 ( 7831) covalent geometry : angle 0.55358 (10630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7229.83 seconds wall clock time: 124 minutes 34.46 seconds (7474.46 seconds total)