Starting phenix.real_space_refine on Wed Sep 17 09:12:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbi_39902/09_2025/8zbi_39902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbi_39902/09_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_39902/09_2025/8zbi_39902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbi_39902/09_2025/8zbi_39902.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbi_39902/09_2025/8zbi_39902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbi_39902/09_2025/8zbi_39902.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.79, per 1000 atoms: 0.23 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: 0.67 Conformation dependent library (CDL) restraints added in 331.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.28 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: 1.13 Time building geometry restraints manager: 0.84 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: 1.070 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- 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 : 2.89 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (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 ARG 0.004 0.000 ARG D 254 TYR 0.012 0.001 TYR B 320 PHE 0.015 0.001 PHE C 151 TRP 0.007 0.001 TRP S 8 HIS 0.003 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7831) covalent geometry : angle 0.52202 (10630) SS BOND : bond 0.00202 ( 3) SS BOND : angle 0.67789 ( 6) hydrogen bonds : bond 0.19224 ( 344) hydrogen bonds : angle 7.34650 ( 975) *********************** 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 : 0.290 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: 0.4911 (ptt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.5339 time to fit residues: 74.7076 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 : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 305 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.259900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.196100 restraints weight = 6851.902| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.30 r_work: 0.3997 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7834 Z= 0.209 Angle : 0.685 12.588 10636 Z= 0.358 Chirality : 0.046 0.173 1214 Planarity : 0.005 0.053 1333 Dihedral : 4.776 21.115 1065 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.40 % Allowed : 9.11 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.27), residues: 958 helix: 1.76 (0.30), residues: 301 sheet: -0.79 (0.30), residues: 261 loop : -1.24 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 254 TYR 0.021 0.002 TYR C 105 PHE 0.022 0.002 PHE C 151 TRP 0.014 0.002 TRP C 82 HIS 0.006 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 7831) covalent geometry : angle 0.68497 (10630) SS BOND : bond 0.00355 ( 3) SS BOND : angle 0.71331 ( 6) hydrogen bonds : bond 0.05274 ( 344) hydrogen bonds : angle 5.49066 ( 975) *********************** 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: 20 poor density : 99 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: B 29 LYS cc_start: 0.7422 (tppp) cc_final: 0.6784 (tptp) REVERT: C 129 ARG cc_start: 0.7332 (tpt170) cc_final: 0.6889 (tpt170) REVERT: C 217 MET cc_start: 0.4957 (mmm) cc_final: 0.4506 (tmt) REVERT: C 243 THR cc_start: 0.7493 (p) cc_final: 0.7011 (m) REVERT: C 280 LYS cc_start: 0.8367 (tttp) cc_final: 0.8147 (tttt) REVERT: C 338 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7393 (mm) REVERT: D 117 ARG cc_start: 0.5852 (ttt90) cc_final: 0.5569 (ttt180) REVERT: D 260 VAL cc_start: 0.8056 (t) cc_final: 0.7806 (t) outliers start: 20 outliers final: 10 residues processed: 110 average time/residue: 0.6511 time to fit residues: 75.5889 Evaluate side-chains 101 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.262673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.199167 restraints weight = 6901.792| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.15 r_work: 0.3864 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1759 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= 0.141 Angle : 0.577 8.871 10636 Z= 0.304 Chirality : 0.043 0.153 1214 Planarity : 0.004 0.048 1333 Dihedral : 4.531 21.892 1065 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.12 % Allowed : 10.91 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.28), residues: 958 helix: 1.94 (0.30), residues: 302 sheet: -0.60 (0.30), residues: 261 loop : -1.22 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 155 TYR 0.014 0.001 TYR F 97 PHE 0.014 0.001 PHE C 151 TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7831) covalent geometry : angle 0.57667 (10630) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.70810 ( 6) hydrogen bonds : bond 0.04540 ( 344) hydrogen bonds : angle 5.11986 ( 975) *********************** 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 125 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: B 29 LYS cc_start: 0.7224 (tppp) cc_final: 0.6636 (tptp) REVERT: C 129 ARG cc_start: 0.7293 (tpt170) cc_final: 0.6827 (tpt170) REVERT: C 217 MET cc_start: 0.4789 (mmm) cc_final: 0.4279 (tmt) REVERT: C 243 THR cc_start: 0.7470 (p) cc_final: 0.6918 (m) REVERT: C 269 ILE cc_start: 0.5548 (OUTLIER) cc_final: 0.5333 (pt) REVERT: C 338 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7270 (mm) REVERT: D 260 VAL cc_start: 0.8030 (t) cc_final: 0.7775 (t) outliers start: 26 outliers final: 11 residues processed: 115 average time/residue: 0.5830 time to fit residues: 70.8140 Evaluate side-chains 107 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 281 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4835 r_free = 0.4835 target = 0.265388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.202598 restraints weight = 6968.063| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.15 r_work: 0.3996 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: 0.7119 moved from start: 0.2062 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= 0.113 Angle : 0.530 8.005 10636 Z= 0.280 Chirality : 0.041 0.139 1214 Planarity : 0.004 0.046 1333 Dihedral : 4.260 21.851 1065 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.16 % Allowed : 13.79 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.28), residues: 958 helix: 2.17 (0.30), residues: 302 sheet: -0.38 (0.30), residues: 269 loop : -1.09 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.014 0.001 TYR F 97 PHE 0.011 0.001 PHE C 151 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7831) covalent geometry : angle 0.52999 (10630) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.76595 ( 6) hydrogen bonds : bond 0.03903 ( 344) hydrogen bonds : angle 4.84905 ( 975) *********************** 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 119 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.303 Fit side-chains REVERT: B 29 LYS cc_start: 0.7234 (tppp) cc_final: 0.6694 (tptp) REVERT: B 345 LYS cc_start: 0.6174 (mptt) cc_final: 0.5464 (mtpt) REVERT: C 129 ARG cc_start: 0.7309 (tpt170) cc_final: 0.6835 (tpt170) REVERT: C 217 MET cc_start: 0.4923 (mmm) cc_final: 0.4342 (tmt) REVERT: C 338 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7293 (mm) REVERT: D 188 MET cc_start: 0.5805 (ppp) cc_final: 0.4085 (mmt) REVERT: D 238 ARG cc_start: 0.5755 (mpt-90) cc_final: 0.5543 (mpt180) outliers start: 18 outliers final: 9 residues processed: 110 average time/residue: 0.5572 time to fit residues: 64.9210 Evaluate side-chains 108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 28 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.4744 r_free = 0.4744 target = 0.256452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.190116 restraints weight = 6834.660| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.19 r_work: 0.3960 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2121 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= 0.182 Angle : 0.631 10.470 10636 Z= 0.329 Chirality : 0.044 0.163 1214 Planarity : 0.005 0.046 1333 Dihedral : 4.662 21.202 1065 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.52 % Allowed : 14.39 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.28), residues: 958 helix: 1.88 (0.30), residues: 303 sheet: -0.31 (0.30), residues: 267 loop : -1.21 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 283 TYR 0.021 0.002 TYR F 97 PHE 0.022 0.002 PHE C 151 TRP 0.012 0.002 TRP C 82 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 7831) covalent geometry : angle 0.63041 (10630) SS BOND : bond 0.00319 ( 3) SS BOND : angle 0.91607 ( 6) hydrogen bonds : bond 0.04730 ( 344) hydrogen bonds : angle 5.01515 ( 975) *********************** 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 118 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.314 Fit side-chains REVERT: B 24 ARG cc_start: 0.6249 (mtm-85) cc_final: 0.5920 (mtp180) REVERT: B 29 LYS cc_start: 0.7294 (tppp) cc_final: 0.6747 (tptp) REVERT: B 345 LYS cc_start: 0.6166 (mptt) cc_final: 0.5416 (mtpt) REVERT: C 217 MET cc_start: 0.4871 (mmm) cc_final: 0.4442 (tmt) REVERT: C 338 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7299 (mm) REVERT: D 188 MET cc_start: 0.5578 (ppp) cc_final: 0.3985 (mmm) outliers start: 21 outliers final: 15 residues processed: 111 average time/residue: 0.5710 time to fit residues: 67.2858 Evaluate side-chains 108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 78 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 0.0270 chunk 64 optimal weight: 0.0270 chunk 31 optimal weight: 0.5980 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.4837 r_free = 0.4837 target = 0.265722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.202702 restraints weight = 6899.333| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.18 r_work: 0.4002 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2292 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= 0.105 Angle : 0.518 6.928 10636 Z= 0.275 Chirality : 0.041 0.137 1214 Planarity : 0.004 0.046 1333 Dihedral : 4.235 21.083 1065 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.16 % Allowed : 15.59 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.28), residues: 958 helix: 2.16 (0.30), residues: 304 sheet: -0.15 (0.30), residues: 269 loop : -1.05 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 283 TYR 0.017 0.001 TYR F 97 PHE 0.013 0.001 PHE C 335 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7831) covalent geometry : angle 0.51787 (10630) SS BOND : bond 0.00234 ( 3) SS BOND : angle 0.79256 ( 6) hydrogen bonds : bond 0.03744 ( 344) hydrogen bonds : angle 4.72223 ( 975) *********************** 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 121 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.302 Fit side-chains REVERT: B 29 LYS cc_start: 0.7239 (tppp) cc_final: 0.6694 (tptp) REVERT: B 345 LYS cc_start: 0.6112 (mptt) cc_final: 0.5391 (mtpt) REVERT: C 129 ARG cc_start: 0.7341 (tpt170) cc_final: 0.6604 (tpt170) REVERT: C 217 MET cc_start: 0.4853 (mmm) cc_final: 0.4440 (tmt) REVERT: C 269 ILE cc_start: 0.5472 (OUTLIER) cc_final: 0.5260 (pt) REVERT: C 338 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7234 (mm) REVERT: D 117 ARG cc_start: 0.5682 (ttt90) cc_final: 0.5406 (tpt170) REVERT: D 188 MET cc_start: 0.5286 (ppp) cc_final: 0.3422 (mtm) outliers start: 18 outliers final: 14 residues processed: 116 average time/residue: 0.6101 time to fit residues: 75.0373 Evaluate side-chains 110 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 27 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4817 r_free = 0.4817 target = 0.262917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.198476 restraints weight = 6876.457| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.17 r_work: 0.3961 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2292 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= 0.137 Angle : 0.566 9.079 10636 Z= 0.296 Chirality : 0.042 0.149 1214 Planarity : 0.004 0.074 1333 Dihedral : 4.348 20.887 1065 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.64 % Allowed : 16.31 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.28), residues: 958 helix: 2.08 (0.30), residues: 304 sheet: -0.05 (0.30), residues: 266 loop : -1.13 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 150 TYR 0.018 0.002 TYR F 97 PHE 0.015 0.001 PHE C 151 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7831) covalent geometry : angle 0.56587 (10630) SS BOND : bond 0.00248 ( 3) SS BOND : angle 0.86149 ( 6) hydrogen bonds : bond 0.04087 ( 344) hydrogen bonds : angle 4.79134 ( 975) *********************** 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 117 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.286 Fit side-chains REVERT: B 24 ARG cc_start: 0.6191 (mtm-85) cc_final: 0.5887 (mtp180) REVERT: B 29 LYS cc_start: 0.7177 (tppp) cc_final: 0.6669 (tptp) REVERT: B 345 LYS cc_start: 0.6221 (mptt) cc_final: 0.5462 (mtpt) REVERT: C 129 ARG cc_start: 0.7390 (tpt170) cc_final: 0.6637 (tpt170) REVERT: C 217 MET cc_start: 0.4849 (mmm) cc_final: 0.4412 (tmt) REVERT: C 338 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7291 (mm) REVERT: D 117 ARG cc_start: 0.5652 (ttt90) cc_final: 0.5418 (ttt90) REVERT: D 188 MET cc_start: 0.5295 (ppp) cc_final: 0.3334 (mpp) outliers start: 22 outliers final: 16 residues processed: 110 average time/residue: 0.5969 time to fit residues: 69.4949 Evaluate side-chains 107 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 135 VAL 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.0050 chunk 25 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN C 293 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 = 0.4839 r_free = 0.4839 target = 0.266178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.203087 restraints weight = 6939.986| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.18 r_work: 0.4093 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2495 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= 0.105 Angle : 0.516 6.769 10636 Z= 0.273 Chirality : 0.041 0.132 1214 Planarity : 0.004 0.063 1333 Dihedral : 4.116 20.106 1065 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.40 % Allowed : 15.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.28), residues: 958 helix: 2.25 (0.30), residues: 303 sheet: -0.00 (0.31), residues: 263 loop : -1.07 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.016 0.001 TYR F 97 PHE 0.010 0.001 PHE C 335 TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 7831) covalent geometry : angle 0.51612 (10630) SS BOND : bond 0.00196 ( 3) SS BOND : angle 0.81594 ( 6) hydrogen bonds : bond 0.03564 ( 344) hydrogen bonds : angle 4.62933 ( 975) *********************** 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 120 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.298 Fit side-chains REVERT: B 29 LYS cc_start: 0.7291 (tppp) cc_final: 0.6802 (tptp) REVERT: B 345 LYS cc_start: 0.6210 (mptt) cc_final: 0.5462 (mtpt) REVERT: C 129 ARG cc_start: 0.7330 (tpt170) cc_final: 0.6608 (tpt170) REVERT: C 217 MET cc_start: 0.4859 (mmm) cc_final: 0.4438 (tmt) REVERT: C 338 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7184 (mm) REVERT: D 188 MET cc_start: 0.5177 (ppp) cc_final: 0.3507 (mtm) outliers start: 20 outliers final: 12 residues processed: 115 average time/residue: 0.5372 time to fit residues: 65.8039 Evaluate side-chains 110 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 44 GLU Chi-restraints excluded: chain F residue 55 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 0.0170 chunk 83 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- 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 = 0.4824 r_free = 0.4824 target = 0.263978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.199742 restraints weight = 6869.615| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.16 r_work: 0.3878 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 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= 0.129 Angle : 0.555 8.461 10636 Z= 0.292 Chirality : 0.042 0.143 1214 Planarity : 0.004 0.060 1333 Dihedral : 4.269 20.117 1065 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.16 % Allowed : 16.43 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.28), residues: 958 helix: 2.12 (0.30), residues: 303 sheet: 0.11 (0.31), residues: 261 loop : -1.10 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 150 TYR 0.013 0.001 TYR F 97 PHE 0.015 0.001 PHE C 151 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7831) covalent geometry : angle 0.55508 (10630) SS BOND : bond 0.00244 ( 3) SS BOND : angle 0.82286 ( 6) hydrogen bonds : bond 0.03896 ( 344) hydrogen bonds : angle 4.70266 ( 975) *********************** 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 111 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.296 Fit side-chains REVERT: B 29 LYS cc_start: 0.7191 (tppp) cc_final: 0.6710 (tptp) REVERT: B 37 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7882 (tp) REVERT: B 345 LYS cc_start: 0.6177 (mptt) cc_final: 0.5427 (mtpt) REVERT: C 129 ARG cc_start: 0.7363 (tpt170) cc_final: 0.6654 (tpt170) REVERT: C 146 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6672 (tt) REVERT: C 217 MET cc_start: 0.4717 (mmm) cc_final: 0.4234 (tmt) REVERT: C 338 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7240 (mm) REVERT: D 188 MET cc_start: 0.5125 (ppp) cc_final: 0.3320 (mpp) outliers start: 18 outliers final: 15 residues processed: 108 average time/residue: 0.5212 time to fit residues: 60.0883 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 : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU 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 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 44 GLU Chi-restraints excluded: chain F residue 55 SER 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 86 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.0040 chunk 77 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 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 = 0.4843 r_free = 0.4843 target = 0.266454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.202783 restraints weight = 6874.774| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.18 r_work: 0.4000 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7834 Z= 0.109 Angle : 0.527 7.013 10636 Z= 0.278 Chirality : 0.041 0.145 1214 Planarity : 0.004 0.058 1333 Dihedral : 4.132 19.755 1065 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.28 % Allowed : 16.31 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.28), residues: 958 helix: 2.19 (0.30), residues: 303 sheet: 0.09 (0.31), residues: 264 loop : -1.01 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 141 TYR 0.014 0.001 TYR F 97 PHE 0.012 0.001 PHE C 335 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7831) covalent geometry : angle 0.52692 (10630) SS BOND : bond 0.00278 ( 3) SS BOND : angle 0.77159 ( 6) hydrogen bonds : bond 0.03583 ( 344) hydrogen bonds : angle 4.61126 ( 975) ********************** 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: 19 poor density : 96 time to evaluate : 0.228 Fit side-chains REVERT: B 29 LYS cc_start: 0.7107 (tppp) cc_final: 0.6648 (tptp) REVERT: B 345 LYS cc_start: 0.6137 (mptt) cc_final: 0.5386 (mtpt) REVERT: C 129 ARG cc_start: 0.7319 (tpt170) cc_final: 0.6611 (tpt170) REVERT: C 217 MET cc_start: 0.4812 (mmm) cc_final: 0.4222 (tmt) REVERT: C 338 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7225 (mm) REVERT: D 188 MET cc_start: 0.4960 (ppp) cc_final: 0.3345 (mtm) REVERT: D 320 PHE cc_start: 0.4932 (m-80) cc_final: 0.4662 (m-80) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 0.5364 time to fit residues: 63.3208 Evaluate side-chains 105 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 58 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 63 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- 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 = 0.4668 r_free = 0.4668 target = 0.248758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.184507 restraints weight = 6955.903| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.37 r_work: 0.3978 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2508 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= 0.161 Angle : 0.605 9.727 10636 Z= 0.318 Chirality : 0.043 0.154 1214 Planarity : 0.004 0.059 1333 Dihedral : 4.469 20.915 1065 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.92 % Allowed : 16.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.28), residues: 958 helix: 1.97 (0.30), residues: 303 sheet: 0.13 (0.30), residues: 267 loop : -1.09 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 150 TYR 0.016 0.002 TYR F 141 PHE 0.020 0.001 PHE C 151 TRP 0.010 0.001 TRP C 82 HIS 0.006 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7831) covalent geometry : angle 0.60479 (10630) SS BOND : bond 0.00334 ( 3) SS BOND : angle 0.99573 ( 6) hydrogen bonds : bond 0.04293 ( 344) hydrogen bonds : angle 4.79944 ( 975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3662.84 seconds wall clock time: 63 minutes 5.07 seconds (3785.07 seconds total)