Starting phenix.real_space_refine on Fri Jun 6 09:38:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbi_39902/06_2025/8zbi_39902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbi_39902/06_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_39902/06_2025/8zbi_39902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbi_39902/06_2025/8zbi_39902.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbi_39902/06_2025/8zbi_39902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbi_39902/06_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-5710/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: 4.59, per 1000 atoms: 0.60 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: 1.66 Conformation dependent library (CDL) restraints added in 1.0 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: 0.86 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: 2.06 Time building geometry restraints manager: 2.01 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: 0.710 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.980 Find NCS groups from input model: 0.070 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:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- 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 : 0.841 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: 1.0611 time to fit residues: 149.1445 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 : 0.741 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4817 r_free = 0.4817 target = 0.262706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.199296 restraints weight = 6861.114| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.12 r_work: 0.3955 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7834 Z= 0.174 Angle : 0.637 10.425 10636 Z= 0.335 Chirality : 0.045 0.165 1214 Planarity : 0.005 0.053 1333 Dihedral : 4.579 21.374 1065 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: -0.13 (0.28), residues: 958 helix: 1.94 (0.30), residues: 301 sheet: -0.73 (0.30), residues: 261 loop : -1.19 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 82 HIS 0.005 0.001 HIS C 54 PHE 0.018 0.002 PHE C 151 TYR 0.016 0.002 TYR C 105 ARG 0.003 0.000 ARG D 254 Details of bonding type rmsd hydrogen bonds : bond 0.04935 ( 344) hydrogen bonds : angle 5.42464 ( 975) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.60677 ( 6) covalent geometry : bond 0.00392 ( 7831) covalent geometry : angle 0.63713 (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 118 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: B 29 LYS cc_start: 0.7357 (tppp) cc_final: 0.6728 (tptp) REVERT: C 129 ARG cc_start: 0.7288 (tpt170) cc_final: 0.6870 (tpt170) REVERT: C 217 MET cc_start: 0.5021 (mmm) cc_final: 0.4407 (tmt) REVERT: C 243 THR cc_start: 0.7543 (p) cc_final: 0.7009 (m) REVERT: C 280 LYS cc_start: 0.8352 (tttp) cc_final: 0.8145 (tttt) REVERT: C 338 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7346 (mm) REVERT: D 260 VAL cc_start: 0.8135 (t) cc_final: 0.7889 (t) outliers start: 19 outliers final: 9 residues processed: 110 average time/residue: 1.2769 time to fit residues: 148.4646 Evaluate side-chains 101 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 281 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 8 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 40.0000 chunk 25 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4819 r_free = 0.4819 target = 0.263244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.199343 restraints weight = 6900.749| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.17 r_work: 0.3873 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7834 Z= 0.140 Angle : 0.570 8.983 10636 Z= 0.300 Chirality : 0.043 0.152 1214 Planarity : 0.004 0.046 1333 Dihedral : 4.480 21.942 1065 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.48 % Allowed : 9.71 % Favored : 86.81 % 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: -0.02 (0.28), residues: 958 helix: 2.00 (0.30), residues: 302 sheet: -0.59 (0.29), residues: 267 loop : -1.18 (0.33), residues: 389 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 0.028 0.001 PHE D 206 TYR 0.015 0.002 TYR F 228 ARG 0.003 0.000 ARG D 155 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 344) hydrogen bonds : angle 5.07548 ( 975) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.70570 ( 6) covalent geometry : bond 0.00313 ( 7831) covalent geometry : angle 0.57040 (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 132 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: B 29 LYS cc_start: 0.7276 (tppp) cc_final: 0.6687 (tptp) REVERT: C 129 ARG cc_start: 0.7315 (tpt170) cc_final: 0.6871 (tpt170) REVERT: C 217 MET cc_start: 0.4844 (mmm) cc_final: 0.4387 (tmt) REVERT: C 243 THR cc_start: 0.7481 (p) cc_final: 0.6909 (m) REVERT: C 338 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7270 (mm) REVERT: D 320 PHE cc_start: 0.5068 (m-10) cc_final: 0.4382 (m-80) outliers start: 29 outliers final: 12 residues processed: 118 average time/residue: 1.2090 time to fit residues: 151.1509 Evaluate side-chains 109 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 281 VAL 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: 0.0270 chunk 10 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.264866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.201493 restraints weight = 6950.329| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.19 r_work: 0.4050 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7834 Z= 0.119 Angle : 0.539 8.074 10636 Z= 0.285 Chirality : 0.042 0.141 1214 Planarity : 0.004 0.045 1333 Dihedral : 4.300 22.276 1065 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.64 % Allowed : 13.19 % Favored : 84.17 % 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 (0.28), residues: 958 helix: 2.15 (0.30), residues: 302 sheet: -0.37 (0.30), residues: 262 loop : -1.16 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS F 73 PHE 0.018 0.001 PHE D 206 TYR 0.013 0.001 TYR F 228 ARG 0.003 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 344) hydrogen bonds : angle 4.86741 ( 975) SS BOND : bond 0.00232 ( 3) SS BOND : angle 0.82615 ( 6) covalent geometry : bond 0.00259 ( 7831) covalent geometry : angle 0.53890 (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 123 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: B 29 LYS cc_start: 0.7385 (tppp) cc_final: 0.6840 (tptp) REVERT: C 129 ARG cc_start: 0.7312 (tpt170) cc_final: 0.6852 (tpt170) REVERT: C 217 MET cc_start: 0.4933 (mmm) cc_final: 0.4380 (tmt) REVERT: C 269 ILE cc_start: 0.5489 (OUTLIER) cc_final: 0.5267 (pt) REVERT: C 338 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7244 (mm) REVERT: D 188 MET cc_start: 0.5868 (ppp) cc_final: 0.4094 (mmm) REVERT: D 238 ARG cc_start: 0.5747 (mpt-90) cc_final: 0.5529 (mpt180) REVERT: D 320 PHE cc_start: 0.4931 (m-10) cc_final: 0.4106 (m-80) outliers start: 22 outliers final: 10 residues processed: 114 average time/residue: 1.1356 time to fit residues: 137.5227 Evaluate side-chains 109 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 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 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 281 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: 9.9990 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4684 r_free = 0.4684 target = 0.249734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.183508 restraints weight = 6836.176| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.13 r_work: 0.3960 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7834 Z= 0.207 Angle : 0.660 11.096 10636 Z= 0.345 Chirality : 0.045 0.171 1214 Planarity : 0.005 0.046 1333 Dihedral : 4.789 20.899 1065 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.64 % Allowed : 14.03 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.77 (0.30), residues: 303 sheet: -0.29 (0.30), residues: 266 loop : -1.24 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.024 0.002 PHE C 151 TYR 0.022 0.002 TYR F 97 ARG 0.003 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 344) hydrogen bonds : angle 5.07035 ( 975) SS BOND : bond 0.00370 ( 3) SS BOND : angle 0.95715 ( 6) covalent geometry : bond 0.00483 ( 7831) covalent geometry : angle 0.65954 (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 115 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.828 Fit side-chains REVERT: B 24 ARG cc_start: 0.6291 (mtm-85) cc_final: 0.5971 (mtp180) REVERT: B 29 LYS cc_start: 0.7332 (tppp) cc_final: 0.6799 (tptp) REVERT: B 345 LYS cc_start: 0.6257 (mptt) cc_final: 0.5492 (mtpt) REVERT: C 197 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6173 (mtp180) REVERT: C 217 MET cc_start: 0.4928 (mmm) cc_final: 0.4514 (tmt) REVERT: C 269 ILE cc_start: 0.5596 (OUTLIER) cc_final: 0.5390 (pt) REVERT: C 338 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7370 (mm) REVERT: D 188 MET cc_start: 0.5700 (ppp) cc_final: 0.3992 (mmm) outliers start: 22 outliers final: 13 residues processed: 107 average time/residue: 1.1523 time to fit residues: 131.1502 Evaluate side-chains 107 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 0.0000 chunk 56 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.4833 r_free = 0.4833 target = 0.265104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.202159 restraints weight = 6875.049| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.16 r_work: 0.3994 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7834 Z= 0.110 Angle : 0.527 8.214 10636 Z= 0.280 Chirality : 0.041 0.140 1214 Planarity : 0.004 0.047 1333 Dihedral : 4.285 22.030 1065 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.40 % Allowed : 15.47 % Favored : 82.13 % 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: 2.13 (0.30), residues: 304 sheet: -0.17 (0.30), residues: 270 loop : -1.07 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS D 192 PHE 0.015 0.001 PHE D 206 TYR 0.015 0.001 TYR F 97 ARG 0.002 0.000 ARG C 283 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 344) hydrogen bonds : angle 4.73489 ( 975) SS BOND : bond 0.00264 ( 3) SS BOND : angle 0.82569 ( 6) covalent geometry : bond 0.00234 ( 7831) covalent geometry : angle 0.52691 (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 122 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.753 Fit side-chains REVERT: B 29 LYS cc_start: 0.7180 (tppp) cc_final: 0.6665 (tptp) REVERT: B 345 LYS cc_start: 0.6116 (mptt) cc_final: 0.5382 (mtpt) REVERT: C 129 ARG cc_start: 0.7352 (tpt170) cc_final: 0.6665 (tpt170) REVERT: C 217 MET cc_start: 0.4859 (mmm) cc_final: 0.4423 (tmt) REVERT: C 269 ILE cc_start: 0.5576 (OUTLIER) cc_final: 0.5343 (pt) REVERT: C 338 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7173 (mm) REVERT: D 188 MET cc_start: 0.5310 (ppp) cc_final: 0.3399 (mtm) outliers start: 20 outliers final: 15 residues processed: 115 average time/residue: 1.1774 time to fit residues: 143.6889 Evaluate side-chains 109 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 MET 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 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 Chi-restraints excluded: chain D residue 320 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4816 r_free = 0.4816 target = 0.262854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.199338 restraints weight = 6788.450| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.13 r_work: 0.3964 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7834 Z= 0.140 Angle : 0.571 9.255 10636 Z= 0.299 Chirality : 0.042 0.148 1214 Planarity : 0.005 0.073 1333 Dihedral : 4.401 20.976 1065 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.64 % Allowed : 15.71 % Favored : 81.65 % 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: 0.30 (0.28), residues: 958 helix: 2.07 (0.30), residues: 304 sheet: -0.11 (0.30), residues: 273 loop : -1.10 (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 F 73 PHE 0.017 0.001 PHE C 151 TYR 0.018 0.002 TYR F 97 ARG 0.002 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 344) hydrogen bonds : angle 4.79893 ( 975) SS BOND : bond 0.00269 ( 3) SS BOND : angle 0.93711 ( 6) covalent geometry : bond 0.00316 ( 7831) covalent geometry : angle 0.57037 (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 112 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.834 Fit side-chains REVERT: B 29 LYS cc_start: 0.7176 (tppp) cc_final: 0.6665 (tptp) REVERT: B 345 LYS cc_start: 0.6164 (mptt) cc_final: 0.5400 (mtpt) REVERT: C 129 ARG cc_start: 0.7379 (tpt170) cc_final: 0.6637 (tpt170) REVERT: C 217 MET cc_start: 0.4858 (mmm) cc_final: 0.4426 (tmt) REVERT: C 338 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7293 (mm) REVERT: D 188 MET cc_start: 0.5315 (ppp) cc_final: 0.3309 (mpp) outliers start: 22 outliers final: 16 residues processed: 106 average time/residue: 1.0908 time to fit residues: 123.3134 Evaluate side-chains 106 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 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 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 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: 8.9990 chunk 55 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4814 r_free = 0.4814 target = 0.262645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.198238 restraints weight = 6905.202| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.18 r_work: 0.4023 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7834 Z= 0.141 Angle : 0.573 9.210 10636 Z= 0.302 Chirality : 0.042 0.150 1214 Planarity : 0.004 0.067 1333 Dihedral : 4.437 20.971 1065 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.52 % Allowed : 15.83 % Favored : 81.65 % 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: 2.07 (0.30), residues: 303 sheet: -0.08 (0.30), residues: 273 loop : -1.10 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS D 192 PHE 0.017 0.001 PHE C 151 TYR 0.018 0.002 TYR F 97 ARG 0.003 0.000 ARG D 238 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 344) hydrogen bonds : angle 4.79126 ( 975) SS BOND : bond 0.00294 ( 3) SS BOND : angle 0.88659 ( 6) covalent geometry : bond 0.00318 ( 7831) covalent geometry : angle 0.57244 (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 114 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.757 Fit side-chains REVERT: B 24 ARG cc_start: 0.6340 (mtm-85) cc_final: 0.6014 (mtp180) REVERT: B 29 LYS cc_start: 0.7328 (tppp) cc_final: 0.6810 (tptp) REVERT: C 129 ARG cc_start: 0.7360 (tpt170) cc_final: 0.6616 (tpt170) REVERT: C 197 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.6138 (mtp180) REVERT: C 217 MET cc_start: 0.4893 (mmm) cc_final: 0.4501 (tmt) REVERT: C 338 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7287 (mm) REVERT: D 188 MET cc_start: 0.5197 (ppp) cc_final: 0.3499 (mtm) outliers start: 21 outliers final: 14 residues processed: 109 average time/residue: 1.1053 time to fit residues: 128.2019 Evaluate side-chains 105 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 24 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4824 r_free = 0.4824 target = 0.264104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.200210 restraints weight = 6970.100| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.19 r_work: 0.3887 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7834 Z= 0.121 Angle : 0.546 7.779 10636 Z= 0.289 Chirality : 0.042 0.145 1214 Planarity : 0.004 0.059 1333 Dihedral : 4.302 20.293 1065 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.52 % Allowed : 15.83 % Favored : 81.65 % 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: 0.38 (0.28), residues: 958 helix: 2.14 (0.30), residues: 303 sheet: -0.01 (0.30), residues: 273 loop : -1.10 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS B 213 PHE 0.013 0.001 PHE C 151 TYR 0.016 0.001 TYR F 97 ARG 0.003 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 344) hydrogen bonds : angle 4.71299 ( 975) SS BOND : bond 0.00264 ( 3) SS BOND : angle 0.83070 ( 6) covalent geometry : bond 0.00265 ( 7831) covalent geometry : angle 0.54614 (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 116 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.726 Fit side-chains REVERT: B 29 LYS cc_start: 0.7169 (tppp) cc_final: 0.6691 (tptp) REVERT: B 345 LYS cc_start: 0.6162 (mptt) cc_final: 0.5390 (mtpt) REVERT: C 129 ARG cc_start: 0.7333 (tpt170) cc_final: 0.6616 (tpt170) REVERT: C 146 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6644 (tt) REVERT: C 197 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6105 (mtp180) REVERT: C 217 MET cc_start: 0.4776 (mmm) cc_final: 0.4352 (tmt) REVERT: C 234 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: C 338 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7233 (mm) REVERT: D 188 MET cc_start: 0.5107 (ppp) cc_final: 0.3336 (mpp) outliers start: 21 outliers final: 15 residues processed: 111 average time/residue: 1.0966 time to fit residues: 129.6368 Evaluate side-chains 107 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain C residue 197 ARG 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 55 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 101 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 44 optimal weight: 0.0010 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 0.0010 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- 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 = 0.4828 r_free = 0.4828 target = 0.264442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.201053 restraints weight = 6871.579| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.15 r_work: 0.3983 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7834 Z= 0.121 Angle : 0.552 8.061 10636 Z= 0.291 Chirality : 0.042 0.146 1214 Planarity : 0.004 0.057 1333 Dihedral : 4.281 20.072 1065 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.52 % Allowed : 16.67 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.28), residues: 958 helix: 2.11 (0.30), residues: 303 sheet: -0.04 (0.30), residues: 270 loop : -1.07 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS B 213 PHE 0.011 0.001 PHE C 199 TYR 0.014 0.001 TYR F 97 ARG 0.004 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 344) hydrogen bonds : angle 4.69604 ( 975) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.92052 ( 6) covalent geometry : bond 0.00268 ( 7831) covalent geometry : angle 0.55208 (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 115 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.770 Fit side-chains REVERT: B 29 LYS cc_start: 0.7173 (tppp) cc_final: 0.6715 (tptp) REVERT: B 345 LYS cc_start: 0.6105 (mptt) cc_final: 0.5357 (mtpt) REVERT: C 129 ARG cc_start: 0.7352 (tpt170) cc_final: 0.6646 (tpt170) REVERT: C 146 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6654 (tt) REVERT: C 197 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6065 (mtp180) REVERT: C 217 MET cc_start: 0.4819 (mmm) cc_final: 0.4386 (tmt) REVERT: C 234 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: C 338 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7264 (mm) REVERT: F 241 PHE cc_start: 0.7273 (m-80) cc_final: 0.7065 (m-80) REVERT: D 188 MET cc_start: 0.5056 (ppp) cc_final: 0.3235 (mpp) outliers start: 21 outliers final: 14 residues processed: 110 average time/residue: 1.0796 time to fit residues: 126.7412 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 : 0.845 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain C residue 197 ARG 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 55 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 101 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.4662 r_free = 0.4662 target = 0.247886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.180655 restraints weight = 6971.888| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.20 r_work: 0.3993 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7834 Z= 0.172 Angle : 0.619 9.965 10636 Z= 0.325 Chirality : 0.044 0.158 1214 Planarity : 0.005 0.059 1333 Dihedral : 4.575 20.969 1065 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.40 % Allowed : 16.67 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.28), residues: 958 helix: 1.90 (0.30), residues: 303 sheet: 0.06 (0.30), residues: 267 loop : -1.18 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 82 HIS 0.007 0.001 HIS B 195 PHE 0.021 0.001 PHE C 151 TYR 0.017 0.002 TYR C 264 ARG 0.005 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.04480 ( 344) hydrogen bonds : angle 4.85312 ( 975) SS BOND : bond 0.00335 ( 3) SS BOND : angle 0.96539 ( 6) covalent geometry : bond 0.00397 ( 7831) covalent geometry : angle 0.61858 (10630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7556.45 seconds wall clock time: 130 minutes 29.51 seconds (7829.51 seconds total)