Starting phenix.real_space_refine on Fri Jul 3 09:14:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9w_37383/07_2026/8w9w_37383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9w_37383/07_2026/8w9w_37383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w9w_37383/07_2026/8w9w_37383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9w_37383/07_2026/8w9w_37383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w9w_37383/07_2026/8w9w_37383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9w_37383/07_2026/8w9w_37383.map" } resolution = 3.74 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= 0.004 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 114 5.16 5 C 8972 2.51 5 N 2134 2.21 5 O 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13382 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "B" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "C" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "D" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'OPE': 1, 'UJO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'OPE': 1, 'UJO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'OPE': 1, 'UJO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'UJO': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'UJO': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'OPE': 1, 'UJO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.67, per 1000 atoms: 0.27 Number of scatterers: 13382 At special positions: 0 Unit cell: (144.1, 157.3, 80.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 4 15.00 O 2158 8.00 N 2134 7.00 C 8972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 293 " distance=2.06 Simple disulfide: pdb=" SG CYS E 261 " - pdb=" SG CYS E 293 " distance=2.05 Simple disulfide: pdb=" SG CYS F 261 " - pdb=" SG CYS F 293 " distance=2.04 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: 1.25 Conformation dependent library (CDL) restraints added in 602.9 milliseconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 58.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 148 through 174 removed outlier: 4.358A pdb=" N THR A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A 154 " --> pdb=" O TRP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 221 removed outlier: 3.793A pdb=" N GLU A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 250 removed outlier: 3.655A pdb=" N LEU A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.966A pdb=" N VAL A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 341 Processing helix chain 'A' and resid 345 through 369 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'B' and resid 151 through 175 removed outlier: 3.910A pdb=" N GLU B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 221 removed outlier: 3.779A pdb=" N GLU B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 250 removed outlier: 3.675A pdb=" N LEU B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 Processing helix chain 'B' and resid 299 through 315 removed outlier: 4.016A pdb=" N VAL B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 341 Processing helix chain 'B' and resid 345 through 370 Processing helix chain 'C' and resid 151 through 175 removed outlier: 3.796A pdb=" N GLU C 175 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 221 removed outlier: 4.040A pdb=" N GLU C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 250 removed outlier: 3.579A pdb=" N LEU C 228 " --> pdb=" O HIS C 224 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 281 Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.773A pdb=" N VAL C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 341 Processing helix chain 'C' and resid 345 through 370 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'D' and resid 151 through 174 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 200 through 221 removed outlier: 4.597A pdb=" N THR D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 250 removed outlier: 3.613A pdb=" N LEU D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 281 Processing helix chain 'D' and resid 299 through 315 removed outlier: 3.819A pdb=" N VAL D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 341 Processing helix chain 'D' and resid 345 through 370 Processing helix chain 'D' and resid 385 through 390 Processing helix chain 'E' and resid 151 through 174 Processing helix chain 'E' and resid 200 through 221 removed outlier: 4.313A pdb=" N THR E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 250 removed outlier: 3.524A pdb=" N LEU E 228 " --> pdb=" O HIS E 224 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER E 234 " --> pdb=" O ARG E 230 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 281 removed outlier: 4.303A pdb=" N LYS E 272 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N HIS E 274 " --> pdb=" O TRP E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 315 removed outlier: 3.890A pdb=" N VAL E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 341 Processing helix chain 'E' and resid 345 through 370 Processing helix chain 'E' and resid 385 through 390 Processing helix chain 'F' and resid 151 through 174 Processing helix chain 'F' and resid 199 through 221 removed outlier: 4.162A pdb=" N MET F 203 " --> pdb=" O TRP F 199 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU F 205 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 250 removed outlier: 3.550A pdb=" N LEU F 228 " --> pdb=" O HIS F 224 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 238 " --> pdb=" O SER F 234 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR F 250 " --> pdb=" O THR F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 281 Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.860A pdb=" N VAL F 303 " --> pdb=" O SER F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 341 Processing helix chain 'F' and resid 345 through 369 Processing helix chain 'F' and resid 370 through 375 removed outlier: 3.787A pdb=" N GLN F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 370 through 375' Processing helix chain 'F' and resid 385 through 390 679 hydrogen bonds defined for protein. 2037 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: 1.95 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2178 1.33 - 1.47: 5831 1.47 - 1.61: 5663 1.61 - 1.76: 12 1.76 - 1.90: 168 Bond restraints: 13852 Sorted by residual: bond pdb=" CG PRO D 403 " pdb=" CD PRO D 403 " ideal model delta sigma weight residual 1.503 1.253 0.250 3.40e-02 8.65e+02 5.43e+01 bond pdb=" CG PRO E 403 " pdb=" CD PRO E 403 " ideal model delta sigma weight residual 1.503 1.264 0.239 3.40e-02 8.65e+02 4.96e+01 bond pdb=" C12 UJO F 500 " pdb=" N14 UJO F 500 " ideal model delta sigma weight residual 1.338 1.454 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C12 UJO D 500 " pdb=" N14 UJO D 500 " ideal model delta sigma weight residual 1.338 1.453 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C12 UJO A 500 " pdb=" N14 UJO A 500 " ideal model delta sigma weight residual 1.338 1.453 -0.115 2.00e-02 2.50e+03 3.31e+01 ... (remaining 13847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 18578 3.89 - 7.78: 211 7.78 - 11.67: 28 11.67 - 15.56: 7 15.56 - 19.45: 4 Bond angle restraints: 18828 Sorted by residual: angle pdb=" CA PRO E 403 " pdb=" N PRO E 403 " pdb=" CD PRO E 403 " ideal model delta sigma weight residual 112.00 92.55 19.45 1.40e+00 5.10e-01 1.93e+02 angle pdb=" CA PRO D 403 " pdb=" N PRO D 403 " pdb=" CD PRO D 403 " ideal model delta sigma weight residual 112.00 92.59 19.41 1.40e+00 5.10e-01 1.92e+02 angle pdb=" CA PRO A 195 " pdb=" N PRO A 195 " pdb=" CD PRO A 195 " ideal model delta sigma weight residual 112.00 96.41 15.59 1.40e+00 5.10e-01 1.24e+02 angle pdb=" CA PRO B 195 " pdb=" N PRO B 195 " pdb=" CD PRO B 195 " ideal model delta sigma weight residual 112.00 96.49 15.51 1.40e+00 5.10e-01 1.23e+02 angle pdb=" N PRO D 403 " pdb=" CD PRO D 403 " pdb=" CG PRO D 403 " ideal model delta sigma weight residual 103.20 88.58 14.62 1.50e+00 4.44e-01 9.50e+01 ... (remaining 18823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.59: 7292 26.59 - 53.18: 598 53.18 - 79.76: 27 79.76 - 106.35: 3 106.35 - 132.94: 2 Dihedral angle restraints: 7922 sinusoidal: 3254 harmonic: 4668 Sorted by residual: dihedral pdb=" CA CYS E 293 " pdb=" C CYS E 293 " pdb=" N GLY E 294 " pdb=" CA GLY E 294 " ideal model delta harmonic sigma weight residual -180.00 -153.07 -26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA CYS D 293 " pdb=" C CYS D 293 " pdb=" N GLY D 294 " pdb=" CA GLY D 294 " ideal model delta harmonic sigma weight residual -180.00 -153.49 -26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA TRP D 270 " pdb=" C TRP D 270 " pdb=" N GLU D 271 " pdb=" CA GLU D 271 " ideal model delta harmonic sigma weight residual -180.00 -158.70 -21.30 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 7919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1938 0.094 - 0.189: 91 0.189 - 0.283: 9 0.283 - 0.377: 9 0.377 - 0.472: 5 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CB THR D 246 " pdb=" CA THR D 246 " pdb=" OG1 THR D 246 " pdb=" CG2 THR D 246 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CB ILE D 197 " pdb=" CA ILE D 197 " pdb=" CG1 ILE D 197 " pdb=" CG2 ILE D 197 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CA PRO C 317 " pdb=" N PRO C 317 " pdb=" C PRO C 317 " pdb=" CB PRO C 317 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 2049 not shown) Planarity restraints: 2262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 194 " 0.115 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO B 195 " -0.275 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 194 " -0.111 5.00e-02 4.00e+02 1.54e-01 3.78e+01 pdb=" N PRO A 195 " 0.265 5.00e-02 4.00e+02 pdb=" CA PRO A 195 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO A 195 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 382 " 0.086 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO F 383 " -0.216 5.00e-02 4.00e+02 pdb=" CA PRO F 383 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO F 383 " 0.066 5.00e-02 4.00e+02 ... (remaining 2259 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 113 2.56 - 3.15: 10696 3.15 - 3.73: 20237 3.73 - 4.32: 25427 4.32 - 4.90: 43737 Nonbonded interactions: 100210 Sorted by model distance: nonbonded pdb=" OG SER A 268 " pdb=" OE1 GLU A 271 " model vdw 1.975 3.040 nonbonded pdb=" OD2 ASP C 179 " pdb=" OG1 THR C 182 " model vdw 2.032 3.040 nonbonded pdb=" OG SER B 268 " pdb=" OE1 GLU B 271 " model vdw 2.059 3.040 nonbonded pdb=" N GLU B 271 " pdb=" OE1 GLU B 271 " model vdw 2.133 3.120 nonbonded pdb=" OD1 ASP D 188 " pdb=" N ILE D 189 " model vdw 2.175 3.120 ... (remaining 100205 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 144 through 500) selection = (chain 'B' and resid 144 through 500) selection = (chain 'C' and resid 144 through 500) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 144 through 500) } 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 group one per residue 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: 1.810 Set stop_for_unknowns flag: 0.010 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.330 Find NCS groups from input model: 0.220 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.007 0.250 13858 Z= 0.297 Angle : 1.008 19.445 18840 Z= 0.531 Chirality : 0.055 0.472 2052 Planarity : 0.009 0.159 2262 Dihedral : 16.836 132.941 4892 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.05 % Favored : 89.76 % Rotamer: Outliers : 1.11 % Allowed : 23.37 % Favored : 75.52 % Cbeta Deviations : 0.07 % 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 are not related in a simple way. whole: 0.01 (0.22), residues: 1572 helix: 1.57 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -2.65 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 230 TYR 0.038 0.002 TYR D 315 PHE 0.027 0.001 PHE E 201 TRP 0.027 0.001 TRP D 199 HIS 0.008 0.001 HIS F 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.30 (13852) covalent geometry : angle 0.99391 / 0.52 (18828) SS BOND : bond 0.01400 / 0.84 ( 6) SS BOND : angle 6.82791 / 5.05 ( 12) hydrogen bonds : bond 0.10744 / 7.47 ( 679) hydrogen bonds : angle 4.11336 / 2.87 ( 2037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 381 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7782 (mm-40) REVERT: B 190 PHE cc_start: 0.7242 (t80) cc_final: 0.6978 (t80) REVERT: B 228 LEU cc_start: 0.7830 (mt) cc_final: 0.7341 (mp) REVERT: B 264 LYS cc_start: 0.7926 (tptt) cc_final: 0.7465 (mttm) REVERT: C 151 LYS cc_start: 0.8450 (mttt) cc_final: 0.8216 (mtmt) REVERT: C 154 LEU cc_start: 0.8549 (mm) cc_final: 0.8223 (tp) REVERT: C 190 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6745 (t80) REVERT: C 241 LEU cc_start: 0.8371 (mm) cc_final: 0.7799 (tp) REVERT: D 180 MET cc_start: 0.7803 (tpp) cc_final: 0.7312 (ttt) REVERT: D 230 ARG cc_start: 0.7592 (ttm170) cc_final: 0.7333 (mpp80) REVERT: D 272 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7134 (mttt) REVERT: D 297 MET cc_start: 0.7458 (tmm) cc_final: 0.6429 (ttm) REVERT: E 180 MET cc_start: 0.6623 (ttp) cc_final: 0.6392 (ttm) REVERT: E 183 TYR cc_start: 0.5982 (m-80) cc_final: 0.5416 (m-80) REVERT: E 217 LEU cc_start: 0.9054 (mt) cc_final: 0.8831 (mt) REVERT: E 236 MET cc_start: 0.7444 (mmm) cc_final: 0.6923 (tpp) REVERT: E 274 HIS cc_start: 0.8064 (m-70) cc_final: 0.7835 (m170) REVERT: E 336 PHE cc_start: 0.8368 (t80) cc_final: 0.8124 (t80) REVERT: F 175 GLU cc_start: 0.8099 (pp20) cc_final: 0.7629 (tp30) REVERT: F 203 MET cc_start: 0.7621 (mmp) cc_final: 0.7389 (mmm) REVERT: F 241 LEU cc_start: 0.8539 (mm) cc_final: 0.8003 (tp) outliers start: 16 outliers final: 5 residues processed: 391 average time/residue: 0.0897 time to fit residues: 52.5746 Evaluate side-chains 305 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 299 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain E residue 320 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN C 391 ASN D 181 GLN D 301 HIS F 274 HIS F 373 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.211979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.152675 restraints weight = 17244.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137334 restraints weight = 19415.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139323 restraints weight = 15840.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139691 restraints weight = 12070.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139996 restraints weight = 12383.186| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13858 Z= 0.214 Angle : 0.713 9.876 18840 Z= 0.372 Chirality : 0.046 0.210 2052 Planarity : 0.005 0.081 2262 Dihedral : 10.090 141.270 1964 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.62 % Favored : 89.31 % Rotamer: Outliers : 5.95 % Allowed : 21.23 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -0.28 (0.21), residues: 1572 helix: 1.48 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -2.81 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 230 TYR 0.020 0.002 TYR D 315 PHE 0.022 0.002 PHE F 165 TRP 0.021 0.001 TRP D 199 HIS 0.007 0.001 HIS C 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.21 (13852) covalent geometry : angle 0.70904 / 0.37 (18828) SS BOND : bond 0.01038 / 0.61 ( 6) SS BOND : angle 3.01326 / 2.13 ( 12) hydrogen bonds : bond 0.06422 / 4.39 ( 679) hydrogen bonds : angle 3.70272 / 2.63 ( 2037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 322 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ILE cc_start: 0.8653 (tt) cc_final: 0.8363 (tt) REVERT: A 197 ILE cc_start: 0.9109 (mt) cc_final: 0.8780 (mt) REVERT: B 190 PHE cc_start: 0.7173 (t80) cc_final: 0.6969 (t80) REVERT: B 264 LYS cc_start: 0.7935 (tptt) cc_final: 0.7506 (mttp) REVERT: B 277 PHE cc_start: 0.8997 (t80) cc_final: 0.8795 (t80) REVERT: C 151 LYS cc_start: 0.8633 (mttt) cc_final: 0.8125 (mtmt) REVERT: C 154 LEU cc_start: 0.8595 (mm) cc_final: 0.8393 (tp) REVERT: C 190 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6872 (t80) REVERT: C 241 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.7869 (tp) REVERT: C 260 GLN cc_start: 0.8451 (mp10) cc_final: 0.8230 (mp10) REVERT: D 160 PHE cc_start: 0.7942 (m-80) cc_final: 0.7501 (m-80) REVERT: D 180 MET cc_start: 0.8280 (tpp) cc_final: 0.7901 (ttt) REVERT: D 197 ILE cc_start: 0.7952 (mt) cc_final: 0.7570 (tt) REVERT: D 201 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7417 (t80) REVERT: D 272 LYS cc_start: 0.7870 (mtmm) cc_final: 0.7302 (mttt) REVERT: D 274 HIS cc_start: 0.8323 (m-70) cc_final: 0.7989 (m-70) REVERT: D 297 MET cc_start: 0.8090 (tmm) cc_final: 0.7138 (ttp) REVERT: E 180 MET cc_start: 0.6559 (ttp) cc_final: 0.6268 (ttt) REVERT: E 183 TYR cc_start: 0.5942 (OUTLIER) cc_final: 0.5261 (m-80) REVERT: E 201 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7062 (t80) REVERT: E 205 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6842 (mm-30) REVERT: E 216 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8269 (mm) REVERT: E 274 HIS cc_start: 0.8047 (m-70) cc_final: 0.7840 (m-70) REVERT: E 285 MET cc_start: 0.8467 (mpp) cc_final: 0.8224 (mpp) REVERT: E 314 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8127 (tm-30) REVERT: F 175 GLU cc_start: 0.8531 (pp20) cc_final: 0.7848 (tp30) REVERT: F 176 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7909 (ttp80) REVERT: F 180 MET cc_start: 0.4520 (OUTLIER) cc_final: 0.4313 (mtm) REVERT: F 190 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6776 (t80) REVERT: F 203 MET cc_start: 0.7922 (mmp) cc_final: 0.7653 (mmm) REVERT: F 241 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.7994 (tp) outliers start: 86 outliers final: 46 residues processed: 372 average time/residue: 0.0989 time to fit residues: 56.4390 Evaluate side-chains 343 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 287 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 7 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 HIS A 321 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 HIS C 374 GLN E 342 HIS F 373 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.214094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143508 restraints weight = 17146.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143511 restraints weight = 12841.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144745 restraints weight = 11193.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.145941 restraints weight = 10261.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145981 restraints weight = 9784.226| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13858 Z= 0.150 Angle : 0.618 7.118 18840 Z= 0.326 Chirality : 0.042 0.176 2052 Planarity : 0.005 0.061 2262 Dihedral : 9.317 131.244 1957 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.05 % Favored : 89.89 % Rotamer: Outliers : 5.74 % Allowed : 22.06 % Favored : 72.20 % 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 are not related in a simple way. whole: -0.13 (0.22), residues: 1572 helix: 1.48 (0.17), residues: 954 sheet: None (None), residues: 0 loop : -2.78 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 275 TYR 0.014 0.001 TYR D 266 PHE 0.022 0.001 PHE E 336 TRP 0.009 0.001 TRP D 320 HIS 0.015 0.001 HIS F 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (13852) covalent geometry : angle 0.61600 / 0.33 (18828) SS BOND : bond 0.00634 / 0.29 ( 6) SS BOND : angle 1.90617 / 1.22 ( 12) hydrogen bonds : bond 0.05294 / 3.63 ( 679) hydrogen bonds : angle 3.48988 / 2.47 ( 2037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 297 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8444 (tt) REVERT: A 190 PHE cc_start: 0.7586 (t80) cc_final: 0.7364 (t80) REVERT: A 197 ILE cc_start: 0.9097 (mt) cc_final: 0.8795 (mt) REVERT: A 283 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: A 366 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7649 (mp) REVERT: C 151 LYS cc_start: 0.8456 (mttt) cc_final: 0.8010 (mtmt) REVERT: C 190 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6696 (t80) REVERT: C 241 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7825 (tp) REVERT: C 260 GLN cc_start: 0.8529 (mp10) cc_final: 0.8316 (mp10) REVERT: C 308 LEU cc_start: 0.7764 (mm) cc_final: 0.7229 (tt) REVERT: D 160 PHE cc_start: 0.8005 (m-80) cc_final: 0.7529 (m-80) REVERT: D 180 MET cc_start: 0.7934 (tpp) cc_final: 0.7642 (ttt) REVERT: D 201 PHE cc_start: 0.7308 (t80) cc_final: 0.7083 (t80) REVERT: D 272 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7429 (mttt) REVERT: D 285 MET cc_start: 0.7892 (mmt) cc_final: 0.7119 (mmm) REVERT: D 297 MET cc_start: 0.8037 (tmm) cc_final: 0.7142 (ttp) REVERT: D 387 PHE cc_start: 0.8341 (t80) cc_final: 0.5744 (m-80) REVERT: E 183 TYR cc_start: 0.6071 (OUTLIER) cc_final: 0.5323 (m-80) REVERT: E 201 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6663 (t80) REVERT: E 205 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6817 (mm-30) REVERT: E 209 MET cc_start: 0.8807 (mpp) cc_final: 0.8574 (mpp) REVERT: E 216 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8255 (mm) REVERT: E 314 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8036 (tm-30) REVERT: E 343 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7773 (mt-10) REVERT: F 151 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7527 (mtmt) REVERT: F 175 GLU cc_start: 0.8289 (pp20) cc_final: 0.7807 (tp30) REVERT: F 176 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7782 (ttp80) REVERT: F 190 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6545 (t80) REVERT: F 203 MET cc_start: 0.7964 (mmp) cc_final: 0.7709 (mmm) REVERT: F 241 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7991 (tp) REVERT: F 308 LEU cc_start: 0.7713 (mm) cc_final: 0.7363 (tp) outliers start: 83 outliers final: 57 residues processed: 352 average time/residue: 0.0938 time to fit residues: 51.6131 Evaluate side-chains 352 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 284 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 126 optimal weight: 0.4980 chunk 87 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN D 181 GLN D 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.214233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 135)---------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143995 restraints weight = 17187.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145233 restraints weight = 13862.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145186 restraints weight = 12279.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145493 restraints weight = 11513.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146011 restraints weight = 10699.459| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13858 Z= 0.136 Angle : 0.607 11.203 18840 Z= 0.317 Chirality : 0.042 0.169 2052 Planarity : 0.004 0.053 2262 Dihedral : 8.661 124.681 1957 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.05 % Favored : 89.89 % Rotamer: Outliers : 5.67 % Allowed : 23.17 % Favored : 71.16 % 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 are not related in a simple way. whole: 0.11 (0.22), residues: 1572 helix: 2.03 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.78 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 176 TYR 0.016 0.001 TYR C 362 PHE 0.019 0.001 PHE C 388 TRP 0.009 0.001 TRP D 320 HIS 0.004 0.001 HIS D 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (13852) covalent geometry : angle 0.60648 / 0.32 (18828) SS BOND : bond 0.00379 / 0.21 ( 6) SS BOND : angle 1.48922 / 0.96 ( 12) hydrogen bonds : bond 0.04871 / 3.35 ( 679) hydrogen bonds : angle 3.39670 / 2.40 ( 2037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 285 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.7547 (t80) cc_final: 0.7285 (t80) REVERT: A 197 ILE cc_start: 0.9094 (mt) cc_final: 0.8794 (mt) REVERT: A 366 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7449 (mp) REVERT: C 151 LYS cc_start: 0.8512 (mttt) cc_final: 0.8158 (mtmt) REVERT: C 190 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6610 (t80) REVERT: C 236 MET cc_start: 0.7673 (mmm) cc_final: 0.7024 (mmm) REVERT: C 241 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7824 (tp) REVERT: C 260 GLN cc_start: 0.8621 (mp10) cc_final: 0.8348 (mp10) REVERT: C 308 LEU cc_start: 0.7796 (mm) cc_final: 0.7269 (tt) REVERT: D 160 PHE cc_start: 0.8015 (m-80) cc_final: 0.7567 (m-80) REVERT: D 180 MET cc_start: 0.8052 (tpp) cc_final: 0.7155 (tmm) REVERT: D 201 PHE cc_start: 0.7223 (t80) cc_final: 0.6736 (t80) REVERT: D 216 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7883 (mm) REVERT: D 271 GLU cc_start: 0.7842 (mp0) cc_final: 0.7635 (mp0) REVERT: D 272 LYS cc_start: 0.7503 (mtmm) cc_final: 0.7052 (mttt) REVERT: D 285 MET cc_start: 0.7765 (mmt) cc_final: 0.7497 (mmm) REVERT: D 296 TYR cc_start: 0.8360 (m-10) cc_final: 0.7141 (m-10) REVERT: D 297 MET cc_start: 0.8110 (tmm) cc_final: 0.7169 (ttp) REVERT: D 387 PHE cc_start: 0.8283 (t80) cc_final: 0.5825 (m-80) REVERT: E 149 TYR cc_start: 0.8184 (m-80) cc_final: 0.7850 (m-80) REVERT: E 180 MET cc_start: 0.6328 (ttt) cc_final: 0.6118 (ttt) REVERT: E 183 TYR cc_start: 0.6104 (OUTLIER) cc_final: 0.5294 (m-80) REVERT: E 209 MET cc_start: 0.8808 (mpp) cc_final: 0.8571 (mpp) REVERT: E 216 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8290 (mm) REVERT: E 285 MET cc_start: 0.8136 (mpp) cc_final: 0.7792 (mpp) REVERT: E 314 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7955 (tm-30) REVERT: E 343 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7792 (mt-10) REVERT: F 175 GLU cc_start: 0.8352 (pp20) cc_final: 0.7757 (tp30) REVERT: F 236 MET cc_start: 0.7623 (mmm) cc_final: 0.7083 (mmm) REVERT: F 241 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8086 (tp) REVERT: F 308 LEU cc_start: 0.7689 (mm) cc_final: 0.7382 (tp) REVERT: F 355 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8298 (tp) outliers start: 82 outliers final: 58 residues processed: 337 average time/residue: 0.0939 time to fit residues: 49.6689 Evaluate side-chains 341 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 275 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 7 optimal weight: 0.4980 chunk 120 optimal weight: 0.6980 chunk 89 optimal weight: 0.0370 chunk 3 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.216056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149319 restraints weight = 17125.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.151070 restraints weight = 12960.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150526 restraints weight = 10804.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150596 restraints weight = 10866.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150689 restraints weight = 10032.340| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13858 Z= 0.121 Angle : 0.587 9.136 18840 Z= 0.307 Chirality : 0.041 0.202 2052 Planarity : 0.004 0.049 2262 Dihedral : 7.913 119.611 1954 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.29 % Favored : 90.65 % Rotamer: Outliers : 5.19 % Allowed : 24.14 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: 0.29 (0.22), residues: 1572 helix: 2.23 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.78 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 230 TYR 0.023 0.001 TYR C 362 PHE 0.032 0.001 PHE C 388 TRP 0.010 0.001 TRP C 280 HIS 0.004 0.001 HIS D 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13852) covalent geometry : angle 0.58299 / 0.31 (18828) SS BOND : bond 0.00404 / 0.23 ( 6) SS BOND : angle 2.77895 / 1.83 ( 12) hydrogen bonds : bond 0.04270 / 2.93 ( 679) hydrogen bonds : angle 3.28813 / 2.32 ( 2037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 279 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.7360 (t80) cc_final: 0.7111 (t80) REVERT: A 321 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8402 (p0) REVERT: A 366 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7417 (mp) REVERT: B 264 LYS cc_start: 0.7290 (mptt) cc_final: 0.6888 (mmtt) REVERT: C 151 LYS cc_start: 0.8308 (mttt) cc_final: 0.8034 (mtmt) REVERT: C 190 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6552 (t80) REVERT: C 241 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7736 (tp) REVERT: C 260 GLN cc_start: 0.8269 (mp10) cc_final: 0.7990 (pp30) REVERT: C 272 LYS cc_start: 0.8232 (mttm) cc_final: 0.7980 (mmtt) REVERT: C 308 LEU cc_start: 0.7725 (mm) cc_final: 0.7227 (tt) REVERT: D 160 PHE cc_start: 0.8016 (m-80) cc_final: 0.7548 (m-80) REVERT: D 180 MET cc_start: 0.7788 (tpp) cc_final: 0.7133 (tmm) REVERT: D 201 PHE cc_start: 0.7019 (t80) cc_final: 0.6675 (t80) REVERT: D 216 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7941 (mm) REVERT: D 271 GLU cc_start: 0.7712 (mp0) cc_final: 0.7499 (mp0) REVERT: D 272 LYS cc_start: 0.7495 (mtmm) cc_final: 0.7183 (mttt) REVERT: D 285 MET cc_start: 0.7945 (mmt) cc_final: 0.7652 (mmm) REVERT: D 296 TYR cc_start: 0.8437 (m-10) cc_final: 0.7259 (m-10) REVERT: D 297 MET cc_start: 0.8071 (tmm) cc_final: 0.7149 (ttp) REVERT: D 387 PHE cc_start: 0.8185 (t80) cc_final: 0.5879 (m-80) REVERT: E 149 TYR cc_start: 0.8060 (m-80) cc_final: 0.7809 (m-80) REVERT: E 183 TYR cc_start: 0.5963 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: E 205 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7289 (mt-10) REVERT: E 258 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.7128 (m90) REVERT: E 314 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7951 (tm-30) REVERT: E 343 GLU cc_start: 0.7664 (mt-10) cc_final: 0.6917 (mt-10) REVERT: F 175 GLU cc_start: 0.8311 (pp20) cc_final: 0.7836 (tp30) REVERT: F 190 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6638 (t80) REVERT: F 241 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8065 (tp) REVERT: F 308 LEU cc_start: 0.7633 (mm) cc_final: 0.7383 (tp) outliers start: 75 outliers final: 52 residues processed: 327 average time/residue: 0.0942 time to fit residues: 48.2749 Evaluate side-chains 339 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 278 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 364 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 143 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.214509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 121)---------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157311 restraints weight = 17167.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142550 restraints weight = 20488.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143890 restraints weight = 17043.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144371 restraints weight = 12740.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144794 restraints weight = 11700.435| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13858 Z= 0.132 Angle : 0.595 8.964 18840 Z= 0.310 Chirality : 0.042 0.204 2052 Planarity : 0.004 0.047 2262 Dihedral : 7.669 118.679 1954 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.29 % Favored : 90.65 % Rotamer: Outliers : 5.81 % Allowed : 23.58 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: 0.27 (0.22), residues: 1572 helix: 2.22 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.80 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 176 TYR 0.023 0.001 TYR C 362 PHE 0.024 0.001 PHE D 336 TRP 0.014 0.001 TRP D 320 HIS 0.002 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13852) covalent geometry : angle 0.59279 / 0.31 (18828) SS BOND : bond 0.00320 / 0.16 ( 6) SS BOND : angle 2.03509 / 1.37 ( 12) hydrogen bonds : bond 0.04541 / 3.12 ( 679) hydrogen bonds : angle 3.32878 / 2.34 ( 2037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 288 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.7369 (t80) cc_final: 0.7137 (t80) REVERT: A 366 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7428 (mp) REVERT: C 151 LYS cc_start: 0.8403 (mttt) cc_final: 0.8090 (mtmt) REVERT: C 190 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6547 (t80) REVERT: C 241 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7727 (tp) REVERT: C 272 LYS cc_start: 0.8311 (mttm) cc_final: 0.8007 (mmtt) REVERT: C 308 LEU cc_start: 0.7801 (mm) cc_final: 0.7272 (tt) REVERT: D 160 PHE cc_start: 0.8052 (m-80) cc_final: 0.7565 (m-80) REVERT: D 180 MET cc_start: 0.8177 (tpp) cc_final: 0.7281 (tmm) REVERT: D 201 PHE cc_start: 0.7304 (t80) cc_final: 0.6636 (t80) REVERT: D 216 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8020 (mm) REVERT: D 285 MET cc_start: 0.8109 (mmt) cc_final: 0.7542 (mmm) REVERT: D 296 TYR cc_start: 0.8576 (m-10) cc_final: 0.7395 (m-10) REVERT: D 297 MET cc_start: 0.7980 (tmm) cc_final: 0.7153 (ttp) REVERT: D 387 PHE cc_start: 0.8131 (t80) cc_final: 0.5768 (m-80) REVERT: E 183 TYR cc_start: 0.5780 (OUTLIER) cc_final: 0.5024 (m-80) REVERT: E 314 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7923 (tm-30) REVERT: E 343 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7100 (mt-10) REVERT: F 175 GLU cc_start: 0.8439 (pp20) cc_final: 0.7938 (tp30) REVERT: F 190 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6615 (t80) REVERT: F 241 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8037 (tp) REVERT: F 308 LEU cc_start: 0.7706 (mm) cc_final: 0.7434 (tp) REVERT: F 355 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8212 (tp) outliers start: 84 outliers final: 64 residues processed: 344 average time/residue: 0.0922 time to fit residues: 49.8044 Evaluate side-chains 336 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 264 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 29 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 153 optimal weight: 0.0980 chunk 146 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** C 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 HIS ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.214205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 142)---------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146121 restraints weight = 17177.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147602 restraints weight = 13657.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147389 restraints weight = 11148.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147511 restraints weight = 11093.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147594 restraints weight = 10537.612| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13858 Z= 0.133 Angle : 0.608 11.426 18840 Z= 0.316 Chirality : 0.042 0.215 2052 Planarity : 0.004 0.047 2262 Dihedral : 7.528 117.249 1954 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.67 % Favored : 90.27 % Rotamer: Outliers : 6.36 % Allowed : 23.72 % Favored : 69.92 % 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 are not related in a simple way. whole: 0.31 (0.22), residues: 1572 helix: 2.22 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 243 TYR 0.023 0.001 TYR C 362 PHE 0.020 0.001 PHE E 337 TRP 0.014 0.001 TRP F 199 HIS 0.010 0.001 HIS C 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (13852) covalent geometry : angle 0.60632 / 0.32 (18828) SS BOND : bond 0.00310 / 0.17 ( 6) SS BOND : angle 1.95426 / 1.27 ( 12) hydrogen bonds : bond 0.04526 / 3.10 ( 679) hydrogen bonds : angle 3.35905 / 2.36 ( 2037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 275 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.7359 (t80) cc_final: 0.7110 (t80) REVERT: A 283 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7701 (m-10) REVERT: A 366 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7434 (mp) REVERT: C 151 LYS cc_start: 0.8325 (mttt) cc_final: 0.8012 (mtmt) REVERT: C 180 MET cc_start: 0.4463 (pmm) cc_final: 0.3752 (pmm) REVERT: C 190 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6540 (t80) REVERT: C 241 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7731 (tp) REVERT: C 272 LYS cc_start: 0.8230 (mttm) cc_final: 0.7932 (mmtt) REVERT: C 308 LEU cc_start: 0.7785 (mm) cc_final: 0.7273 (tt) REVERT: D 180 MET cc_start: 0.7772 (tpp) cc_final: 0.7230 (tmm) REVERT: D 197 ILE cc_start: 0.7609 (mm) cc_final: 0.7321 (tt) REVERT: D 201 PHE cc_start: 0.7020 (t80) cc_final: 0.6517 (t80) REVERT: D 216 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7976 (mm) REVERT: D 285 MET cc_start: 0.8129 (mmt) cc_final: 0.7575 (mmm) REVERT: D 296 TYR cc_start: 0.8467 (m-10) cc_final: 0.7381 (m-10) REVERT: D 297 MET cc_start: 0.8020 (tmm) cc_final: 0.7350 (ttp) REVERT: D 387 PHE cc_start: 0.8099 (t80) cc_final: 0.5799 (m-80) REVERT: E 183 TYR cc_start: 0.5777 (OUTLIER) cc_final: 0.4978 (m-80) REVERT: E 314 GLU cc_start: 0.8213 (tm-30) cc_final: 0.8005 (tm-30) REVERT: F 175 GLU cc_start: 0.8292 (pp20) cc_final: 0.7839 (tp30) REVERT: F 190 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6612 (t80) REVERT: F 236 MET cc_start: 0.7680 (mmm) cc_final: 0.7067 (mmm) REVERT: F 241 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7978 (tp) REVERT: F 308 LEU cc_start: 0.7723 (mm) cc_final: 0.7448 (tp) REVERT: F 355 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8140 (tp) outliers start: 92 outliers final: 73 residues processed: 339 average time/residue: 0.0923 time to fit residues: 48.9486 Evaluate side-chains 347 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 265 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.213469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 151)---------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145017 restraints weight = 16997.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145471 restraints weight = 13149.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145354 restraints weight = 11334.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145404 restraints weight = 10671.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145521 restraints weight = 10571.885| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13858 Z= 0.137 Angle : 0.621 11.875 18840 Z= 0.322 Chirality : 0.042 0.201 2052 Planarity : 0.004 0.045 2262 Dihedral : 7.421 116.345 1954 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 6.02 % Allowed : 24.20 % Favored : 69.78 % 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 are not related in a simple way. whole: 0.32 (0.22), residues: 1572 helix: 2.22 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.71 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 243 TYR 0.024 0.001 TYR C 362 PHE 0.025 0.001 PHE D 336 TRP 0.015 0.001 TRP F 199 HIS 0.006 0.001 HIS F 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13852) covalent geometry : angle 0.61913 / 0.32 (18828) SS BOND : bond 0.00340 / 0.18 ( 6) SS BOND : angle 1.74803 / 1.11 ( 12) hydrogen bonds : bond 0.04625 / 3.18 ( 679) hydrogen bonds : angle 3.37751 / 2.37 ( 2037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 272 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.7380 (t80) cc_final: 0.7156 (t80) REVERT: A 283 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7796 (m-10) REVERT: A 366 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7448 (mp) REVERT: C 151 LYS cc_start: 0.8371 (mttt) cc_final: 0.8009 (mtmt) REVERT: C 180 MET cc_start: 0.4458 (pmm) cc_final: 0.3739 (pmm) REVERT: C 190 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6529 (t80) REVERT: C 205 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6824 (mt-10) REVERT: C 241 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7742 (tp) REVERT: C 272 LYS cc_start: 0.8338 (mttm) cc_final: 0.8009 (mmtt) REVERT: C 308 LEU cc_start: 0.7792 (mm) cc_final: 0.7272 (tt) REVERT: D 180 MET cc_start: 0.7933 (tpp) cc_final: 0.7272 (tmm) REVERT: D 197 ILE cc_start: 0.7531 (mm) cc_final: 0.7235 (tt) REVERT: D 201 PHE cc_start: 0.7109 (t80) cc_final: 0.6603 (t80) REVERT: D 216 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8017 (mm) REVERT: D 285 MET cc_start: 0.8180 (mmt) cc_final: 0.7586 (mmm) REVERT: D 296 TYR cc_start: 0.8493 (m-10) cc_final: 0.7298 (m-10) REVERT: D 297 MET cc_start: 0.8037 (tmm) cc_final: 0.7388 (ttp) REVERT: D 387 PHE cc_start: 0.8105 (t80) cc_final: 0.5818 (m-80) REVERT: E 183 TYR cc_start: 0.5923 (OUTLIER) cc_final: 0.5164 (m-80) REVERT: E 296 TYR cc_start: 0.8294 (m-80) cc_final: 0.7424 (m-80) REVERT: E 314 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7965 (tm-30) REVERT: F 173 VAL cc_start: 0.8774 (t) cc_final: 0.8433 (p) REVERT: F 175 GLU cc_start: 0.8353 (pp20) cc_final: 0.7798 (tp30) REVERT: F 190 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6602 (t80) REVERT: F 236 MET cc_start: 0.7617 (mmm) cc_final: 0.7003 (mmm) REVERT: F 241 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.7945 (tp) REVERT: F 308 LEU cc_start: 0.7747 (mm) cc_final: 0.7453 (tp) REVERT: F 355 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8150 (tp) REVERT: F 380 ILE cc_start: 0.8214 (mm) cc_final: 0.7941 (mm) outliers start: 87 outliers final: 72 residues processed: 337 average time/residue: 0.0935 time to fit residues: 49.5438 Evaluate side-chains 347 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 266 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 22 optimal weight: 0.0040 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.215335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 128)---------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159645 restraints weight = 17265.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 97)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142590 restraints weight = 21010.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144366 restraints weight = 17978.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146921 restraints weight = 13188.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147339 restraints weight = 10668.634| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13858 Z= 0.121 Angle : 0.617 12.728 18840 Z= 0.320 Chirality : 0.042 0.263 2052 Planarity : 0.004 0.044 2262 Dihedral : 7.237 114.068 1954 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.70 % Allowed : 25.24 % Favored : 70.06 % 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 are not related in a simple way. whole: 0.45 (0.22), residues: 1572 helix: 2.33 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.66 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 176 TYR 0.023 0.001 TYR C 362 PHE 0.015 0.001 PHE E 337 TRP 0.026 0.001 TRP E 199 HIS 0.010 0.001 HIS F 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13852) covalent geometry : angle 0.61616 / 0.32 (18828) SS BOND : bond 0.00310 / 0.16 ( 6) SS BOND : angle 1.62062 / 1.03 ( 12) hydrogen bonds : bond 0.04122 / 2.84 ( 679) hydrogen bonds : angle 3.35708 / 2.34 ( 2037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.7303 (t80) cc_final: 0.7069 (t80) REVERT: A 366 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7454 (mp) REVERT: C 151 LYS cc_start: 0.8346 (mttt) cc_final: 0.7964 (mtmt) REVERT: C 180 MET cc_start: 0.4608 (OUTLIER) cc_final: 0.3932 (pmm) REVERT: C 241 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7760 (tp) REVERT: C 272 LYS cc_start: 0.8377 (mttm) cc_final: 0.8100 (mmtt) REVERT: C 308 LEU cc_start: 0.7737 (mm) cc_final: 0.7255 (tt) REVERT: D 180 MET cc_start: 0.7919 (tpp) cc_final: 0.7236 (tmm) REVERT: D 197 ILE cc_start: 0.7468 (mm) cc_final: 0.7180 (tt) REVERT: D 201 PHE cc_start: 0.7138 (t80) cc_final: 0.6586 (t80) REVERT: D 216 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8023 (mm) REVERT: D 285 MET cc_start: 0.8220 (mmt) cc_final: 0.7694 (mmm) REVERT: D 296 TYR cc_start: 0.8502 (m-10) cc_final: 0.7362 (m-10) REVERT: D 297 MET cc_start: 0.7990 (tmm) cc_final: 0.7335 (ttp) REVERT: D 387 PHE cc_start: 0.7998 (t80) cc_final: 0.5723 (m-80) REVERT: E 148 GLU cc_start: 0.8411 (tp30) cc_final: 0.8174 (tp30) REVERT: E 183 TYR cc_start: 0.5605 (OUTLIER) cc_final: 0.4848 (m-80) REVERT: E 199 TRP cc_start: 0.7687 (p90) cc_final: 0.7299 (p90) REVERT: E 296 TYR cc_start: 0.8274 (m-80) cc_final: 0.7459 (m-80) REVERT: F 173 VAL cc_start: 0.8747 (t) cc_final: 0.8450 (p) REVERT: F 175 GLU cc_start: 0.8292 (pp20) cc_final: 0.7789 (tp30) REVERT: F 236 MET cc_start: 0.7637 (mmm) cc_final: 0.6984 (mmm) REVERT: F 241 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7788 (tp) REVERT: F 308 LEU cc_start: 0.7696 (mm) cc_final: 0.7223 (tt) REVERT: F 355 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8066 (tp) REVERT: F 380 ILE cc_start: 0.8197 (mm) cc_final: 0.7923 (mm) outliers start: 68 outliers final: 57 residues processed: 320 average time/residue: 0.0924 time to fit residues: 46.6661 Evaluate side-chains 332 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 268 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 364 HIS Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 364 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 75 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 HIS A 291 HIS ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.211478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159552 restraints weight = 17166.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 82)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140376 restraints weight = 17193.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142077 restraints weight = 16740.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142619 restraints weight = 12352.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142688 restraints weight = 11170.057| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13858 Z= 0.164 Angle : 0.680 15.363 18840 Z= 0.346 Chirality : 0.043 0.262 2052 Planarity : 0.004 0.044 2262 Dihedral : 7.328 116.140 1952 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.03 % Favored : 90.90 % Rotamer: Outliers : 5.33 % Allowed : 24.69 % Favored : 69.99 % 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 are not related in a simple way. whole: 0.27 (0.22), residues: 1572 helix: 2.13 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.66 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 176 TYR 0.025 0.001 TYR C 362 PHE 0.027 0.001 PHE D 336 TRP 0.031 0.001 TRP E 199 HIS 0.010 0.001 HIS E 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (13852) covalent geometry : angle 0.67909 / 0.35 (18828) SS BOND : bond 0.00319 / 0.17 ( 6) SS BOND : angle 1.52735 / 0.97 ( 12) hydrogen bonds : bond 0.05045 / 3.47 ( 679) hydrogen bonds : angle 3.49797 / 2.44 ( 2037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 269 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.7271 (t80) cc_final: 0.7043 (t80) REVERT: A 197 ILE cc_start: 0.9090 (mt) cc_final: 0.8791 (mt) REVERT: A 283 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.8020 (m-10) REVERT: A 366 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7499 (mp) REVERT: A 399 GLU cc_start: 0.8341 (pm20) cc_final: 0.8111 (pm20) REVERT: C 151 LYS cc_start: 0.8313 (mttt) cc_final: 0.7927 (mtmt) REVERT: C 180 MET cc_start: 0.4359 (OUTLIER) cc_final: 0.3671 (pmm) REVERT: C 241 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7789 (tp) REVERT: C 308 LEU cc_start: 0.7825 (mm) cc_final: 0.7320 (tt) REVERT: D 180 MET cc_start: 0.7740 (tpp) cc_final: 0.7216 (tmm) REVERT: D 197 ILE cc_start: 0.7413 (mm) cc_final: 0.7142 (tt) REVERT: D 201 PHE cc_start: 0.6990 (t80) cc_final: 0.6495 (t80) REVERT: D 216 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7955 (mm) REVERT: D 285 MET cc_start: 0.8230 (mmt) cc_final: 0.7717 (mmm) REVERT: D 296 TYR cc_start: 0.8493 (m-10) cc_final: 0.7278 (m-10) REVERT: D 297 MET cc_start: 0.8029 (tmm) cc_final: 0.7356 (ttp) REVERT: D 387 PHE cc_start: 0.8118 (t80) cc_final: 0.5820 (m-80) REVERT: E 183 TYR cc_start: 0.5916 (OUTLIER) cc_final: 0.5098 (m-80) REVERT: E 314 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7986 (tm-30) REVERT: F 175 GLU cc_start: 0.8252 (pp20) cc_final: 0.7666 (tp30) REVERT: F 180 MET cc_start: 0.4914 (mtt) cc_final: 0.4482 (mpp) REVERT: F 236 MET cc_start: 0.7661 (mmm) cc_final: 0.7129 (mmm) REVERT: F 241 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7874 (tp) REVERT: F 308 LEU cc_start: 0.7788 (mm) cc_final: 0.7289 (tt) REVERT: F 355 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8206 (tp) REVERT: F 380 ILE cc_start: 0.8250 (mm) cc_final: 0.7977 (mm) REVERT: F 389 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7739 (mm-30) outliers start: 77 outliers final: 64 residues processed: 330 average time/residue: 0.0946 time to fit residues: 49.1033 Evaluate side-chains 335 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 263 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 364 HIS Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 121 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 147 optimal weight: 0.0040 chunk 86 optimal weight: 0.0870 chunk 29 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 HIS ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.214417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158024 restraints weight = 17238.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144888 restraints weight = 19595.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148026 restraints weight = 16001.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147943 restraints weight = 12336.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148341 restraints weight = 11405.003| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13858 Z= 0.129 Angle : 0.678 14.828 18840 Z= 0.341 Chirality : 0.043 0.259 2052 Planarity : 0.004 0.045 2262 Dihedral : 7.143 113.481 1952 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.36 % Allowed : 25.66 % Favored : 69.99 % 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 are not related in a simple way. whole: 0.42 (0.22), residues: 1572 helix: 2.28 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.63 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 176 TYR 0.023 0.001 TYR C 362 PHE 0.028 0.001 PHE D 336 TRP 0.023 0.001 TRP E 199 HIS 0.008 0.001 HIS E 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13852) covalent geometry : angle 0.67683 / 0.34 (18828) SS BOND : bond 0.00315 / 0.17 ( 6) SS BOND : angle 1.42113 / 0.90 ( 12) hydrogen bonds : bond 0.04310 / 2.95 ( 679) hydrogen bonds : angle 3.45162 / 2.39 ( 2037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2883.39 seconds wall clock time: 50 minutes 26.09 seconds (3026.09 seconds total)