Starting phenix.real_space_refine on Wed Feb 4 09:58:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mh9_48268/02_2026/9mh9_48268.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mh9_48268/02_2026/9mh9_48268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mh9_48268/02_2026/9mh9_48268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mh9_48268/02_2026/9mh9_48268.map" model { file = "/net/cci-nas-00/data/ceres_data/9mh9_48268/02_2026/9mh9_48268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mh9_48268/02_2026/9mh9_48268.cif" } resolution = 3.68 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= 0.009 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 6357 2.51 5 N 1590 2.21 5 O 1764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9762 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2539 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 316} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 6, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2380 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 10, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'TRP:plan': 1, 'GLU:plan': 8, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 120 Chain: "C" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2383 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 4, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 97 Chain: "D" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2460 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 76 Time building chain proxies: 1.91, per 1000 atoms: 0.20 Number of scatterers: 9762 At special positions: 0 Unit cell: (94.072, 95.141, 133.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1764 8.00 N 1590 7.00 C 6357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 431.0 milliseconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 20 sheets defined 39.5% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 69 through 86 removed outlier: 4.222A pdb=" N ARG A 73 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 120 removed outlier: 4.721A pdb=" N PHE A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 Processing helix chain 'A' and resid 166 through 197 Processing helix chain 'A' and resid 289 through 293 removed outlier: 3.875A pdb=" N GLU A 293 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 303 removed outlier: 4.094A pdb=" N LYS A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 356 Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'B' and resid 76 through 121 removed outlier: 3.521A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 98 " --> pdb=" O ASN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 140 through 153 Processing helix chain 'B' and resid 166 through 197 removed outlier: 3.593A pdb=" N GLN B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 removed outlier: 3.985A pdb=" N GLU B 293 " --> pdb=" O PRO B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 4.001A pdb=" N LYS B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 356 Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'C' and resid 78 through 86 Processing helix chain 'C' and resid 92 through 120 Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 140 through 153 Processing helix chain 'C' and resid 166 through 196 Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.220A pdb=" N GLU C 293 " --> pdb=" O PRO C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 removed outlier: 4.214A pdb=" N LYS C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 356 Processing helix chain 'C' and resid 368 through 381 Processing helix chain 'D' and resid 75 through 86 removed outlier: 4.033A pdb=" N LEU D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 121 removed outlier: 4.024A pdb=" N PHE D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 139 through 153 removed outlier: 4.081A pdb=" N PHE D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 153 " --> pdb=" O ILE D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 196 Processing helix chain 'D' and resid 289 through 294 removed outlier: 4.186A pdb=" N GLU D 293 " --> pdb=" O PRO D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 303 removed outlier: 4.334A pdb=" N LYS D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 356 Processing helix chain 'D' and resid 368 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 201 removed outlier: 3.779A pdb=" N GLU A 305 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N MET A 313 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLU A 236 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA A 241 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP A 261 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 243 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN A 259 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS A 245 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU A 257 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 247 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 207 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 207 removed outlier: 6.660A pdb=" N ALA A 211 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 345 Processing sheet with id=AA5, first strand: chain 'B' and resid 206 through 207 removed outlier: 3.705A pdb=" N GLY B 227 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 206 through 207 removed outlier: 3.705A pdb=" N GLY B 227 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 211 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 254 through 261 removed outlier: 4.811A pdb=" N LYS B 247 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 254 through 261 removed outlier: 4.811A pdb=" N LYS B 247 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 336 through 338 Processing sheet with id=AB1, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AB2, first strand: chain 'C' and resid 279 through 284 removed outlier: 6.543A pdb=" N ALA C 211 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 254 through 261 removed outlier: 5.078A pdb=" N LYS C 247 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU C 236 " --> pdb=" O MET C 313 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 336 through 338 Processing sheet with id=AB5, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AB6, first strand: chain 'D' and resid 199 through 200 removed outlier: 6.251A pdb=" N LYS D 200 " --> pdb=" O GLN D 322 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ARG D 324 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU D 236 " --> pdb=" O MET D 313 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA D 241 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS D 247 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 199 through 200 removed outlier: 6.251A pdb=" N LYS D 200 " --> pdb=" O GLN D 322 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ARG D 324 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU D 236 " --> pdb=" O MET D 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 205 through 207 Processing sheet with id=AB9, first strand: chain 'D' and resid 205 through 207 removed outlier: 6.740A pdb=" N ALA D 211 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 336 through 338 Processing sheet with id=AC2, first strand: chain 'D' and resid 342 through 344 536 hydrogen bonds defined for protein. 1515 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: 1.41 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2171 1.33 - 1.45: 2235 1.45 - 1.57: 5504 1.57 - 1.69: 0 1.69 - 1.82: 81 Bond restraints: 9991 Sorted by residual: bond pdb=" CA VAL A 99 " pdb=" CB VAL A 99 " ideal model delta sigma weight residual 1.540 1.480 0.060 1.25e-02 6.40e+03 2.33e+01 bond pdb=" CA VAL A 99 " pdb=" C VAL A 99 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.27e-02 6.20e+03 1.69e+01 bond pdb=" N VAL A 99 " pdb=" CA VAL A 99 " ideal model delta sigma weight residual 1.461 1.413 0.047 1.19e-02 7.06e+03 1.58e+01 bond pdb=" N VAL A 101 " pdb=" CA VAL A 101 " ideal model delta sigma weight residual 1.461 1.422 0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" CA TRP A 91 " pdb=" C TRP A 91 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 1.00e+01 ... (remaining 9986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 13171 1.49 - 2.98: 343 2.98 - 4.47: 85 4.47 - 5.96: 11 5.96 - 7.44: 3 Bond angle restraints: 13613 Sorted by residual: angle pdb=" C VAL A 99 " pdb=" CA VAL A 99 " pdb=" CB VAL A 99 " ideal model delta sigma weight residual 112.14 106.20 5.94 1.35e+00 5.49e-01 1.94e+01 angle pdb=" N VAL A 101 " pdb=" CA VAL A 101 " pdb=" C VAL A 101 " ideal model delta sigma weight residual 110.62 105.87 4.75 1.14e+00 7.69e-01 1.74e+01 angle pdb=" N VAL A 99 " pdb=" CA VAL A 99 " pdb=" C VAL A 99 " ideal model delta sigma weight residual 110.62 106.50 4.12 1.02e+00 9.61e-01 1.63e+01 angle pdb=" N VAL B 235 " pdb=" CA VAL B 235 " pdb=" C VAL B 235 " ideal model delta sigma weight residual 113.71 109.92 3.79 9.50e-01 1.11e+00 1.59e+01 angle pdb=" C LEU A 96 " pdb=" N ILE A 97 " pdb=" CA ILE A 97 " ideal model delta sigma weight residual 120.60 115.73 4.87 1.29e+00 6.01e-01 1.43e+01 ... (remaining 13608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.98: 5054 13.98 - 27.95: 558 27.95 - 41.93: 160 41.93 - 55.90: 43 55.90 - 69.88: 10 Dihedral angle restraints: 5825 sinusoidal: 2098 harmonic: 3727 Sorted by residual: dihedral pdb=" CA LEU A 86 " pdb=" C LEU A 86 " pdb=" N VAL A 87 " pdb=" CA VAL A 87 " ideal model delta harmonic sigma weight residual -180.00 -150.29 -29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ASN A 139 " pdb=" C ASN A 139 " pdb=" N GLY A 140 " pdb=" CA GLY A 140 " ideal model delta harmonic sigma weight residual -180.00 -154.04 -25.96 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ASN D 139 " pdb=" C ASN D 139 " pdb=" N GLY D 140 " pdb=" CA GLY D 140 " ideal model delta harmonic sigma weight residual -180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 5822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1366 0.059 - 0.119: 209 0.119 - 0.178: 25 0.178 - 0.237: 1 0.237 - 0.296: 1 Chirality restraints: 1602 Sorted by residual: chirality pdb=" CA THR A 103 " pdb=" N THR A 103 " pdb=" C THR A 103 " pdb=" CB THR A 103 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB ILE D 112 " pdb=" CA ILE D 112 " pdb=" CG1 ILE D 112 " pdb=" CG2 ILE D 112 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA ILE D 55 " pdb=" N ILE D 55 " pdb=" C ILE D 55 " pdb=" CB ILE D 55 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1599 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 98 " -0.016 2.00e-02 2.50e+03 1.45e-02 3.70e+00 pdb=" CG PHE D 98 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE D 98 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 98 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 98 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE D 98 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 60 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.48e+00 pdb=" C ARG D 60 " -0.027 2.00e-02 2.50e+03 pdb=" O ARG D 60 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS D 61 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 197 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.06e+00 pdb=" N PRO C 198 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 198 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 198 " -0.020 5.00e-02 4.00e+02 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1139 2.74 - 3.28: 10334 3.28 - 3.82: 15838 3.82 - 4.36: 17996 4.36 - 4.90: 31516 Nonbonded interactions: 76823 Sorted by model distance: nonbonded pdb=" N GLN D 288 " pdb=" OE1 GLN D 288 " model vdw 2.205 3.120 nonbonded pdb=" NE2 GLN B 322 " pdb=" OE2 GLU C 236 " model vdw 2.245 3.120 nonbonded pdb=" O THR A 153 " pdb=" OG1 THR A 154 " model vdw 2.255 3.040 nonbonded pdb=" O THR B 153 " pdb=" OG1 THR B 154 " model vdw 2.258 3.040 nonbonded pdb=" N GLU B 315 " pdb=" OE1 GLU B 315 " model vdw 2.262 3.120 ... (remaining 76818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 55 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 or (resid 59 and (name N or name CA or nam \ e C or name O or name CB )) or resid 60 through 61 or (resid 62 and (name N or n \ ame CA or name C or name O or name CB )) or resid 63 or (resid 64 and (name N or \ name CA or name C or name O or name CB )) or (resid 77 through 92 and (name N o \ r name CA or name C or name O or name CB )) or resid 93 through 190 or (resid 19 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 192 through \ 193 or (resid 194 and (name N or name CA or name C or name O or name CB )) or re \ sid 195 through 196 or (resid 197 and (name N or name CA or name C or name O or \ name CB )) or resid 198 or (resid 199 through 203 and (name N or name CA or name \ C or name O or name CB )) or resid 204 through 229 or (resid 230 through 231 an \ d (name N or name CA or name C or name O or name CB )) or resid 232 through 250 \ or (resid 251 and (name N or name CA or name C or name O or name CB )) or resid \ 252 or (resid 253 and (name N or name CA or name C or name O or name CB )) or re \ sid 254 through 286 or (resid 287 through 288 and (name N or name CA or name C o \ r name O or name CB )) or resid 289 through 312 or (resid 313 and (name N or nam \ e CA or name C or name O or name CB )) or resid 314 through 353 or (resid 354 an \ d (name N or name CA or name C or name O or name CB )) or resid 355 through 370 \ or (resid 371 and (name N or name CA or name C or name O or name CB )) or resid \ 372 through 374 or (resid 375 through 381 and (name N or name CA or name C or na \ me O or name CB )))) selection = (chain 'B' and (resid 55 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 61 or (resid 62 and (name N or nam \ e CA or name C or name O or name CB )) or resid 63 through 64 or resid 77 throug \ h 121 or (resid 122 and (name N or name CA or name C or name O or name CB )) or \ resid 123 through 193 or (resid 194 and (name N or name CA or name C or name O o \ r name CB )) or resid 195 through 200 or (resid 201 through 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 23 \ 0 or (resid 231 and (name N or name CA or name C or name O or name CB )) or resi \ d 232 through 250 or (resid 251 and (name N or name CA or name C or name O or na \ me CB )) or resid 252 through 302 or (resid 303 and (name N or name CA or name C \ or name O or name CB )) or resid 304 through 357 or (resid 358 and (name N or n \ ame CA or name C or name O or name CB )) or resid 359 through 361 or (resid 362 \ through 364 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 5 through 374 or (resid 375 through 381 and (name N or name CA or name C or name \ O or name CB )))) selection = (chain 'C' and (resid 55 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 90 or (resid 91 through 92 and (na \ me N or name CA or name C or name O or name CB )) or resid 93 through 121 or (re \ sid 122 and (name N or name CA or name C or name O or name CB )) or resid 123 th \ rough 190 or (resid 191 and (name N or name CA or name C or name O or name CB )) \ or resid 192 through 216 or (resid 217 and (name N or name CA or name C or name \ O or name CB )) or resid 218 through 252 or (resid 253 and (name N or name CA o \ r name C or name O or name CB )) or resid 254 through 286 or (resid 287 through \ 288 and (name N or name CA or name C or name O or name CB )) or resid 289 throug \ h 312 or (resid 313 and (name N or name CA or name C or name O or name CB )) or \ resid 314 through 353 or (resid 354 and (name N or name CA or name C or name O o \ r name CB )) or resid 355 through 361 or (resid 362 through 364 and (name N or n \ ame CA or name C or name O or name CB )) or resid 365 through 370 or (resid 371 \ and (name N or name CA or name C or name O or name CB )) or resid 372 through 38 \ 1)) selection = (chain 'D' and (resid 55 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 or (resid 59 and (name N or name CA or nam \ e C or name O or name CB )) or resid 60 or (resid 61 through 62 and (name N or n \ ame CA or name C or name O or name CB )) or resid 63 through 64 or (resid 77 thr \ ough 92 and (name N or name CA or name C or name O or name CB )) or resid 93 thr \ ough 121 or (resid 122 and (name N or name CA or name C or name O or name CB )) \ or resid 123 through 190 or (resid 191 and (name N or name CA or name C or name \ O or name CB )) or resid 192 through 193 or (resid 194 and (name N or name CA or \ name C or name O or name CB )) or resid 195 through 196 or (resid 197 and (name \ N or name CA or name C or name O or name CB )) or resid 198 or (resid 199 throu \ gh 203 and (name N or name CA or name C or name O or name CB )) or resid 204 thr \ ough 216 or (resid 217 and (name N or name CA or name C or name O or name CB )) \ or resid 218 through 229 or (resid 230 through 231 and (name N or name CA or nam \ e C or name O or name CB )) or resid 232 through 250 or (resid 251 and (name N o \ r name CA or name C or name O or name CB )) or resid 252 or (resid 253 and (name \ N or name CA or name C or name O or name CB )) or resid 254 through 286 or (res \ id 287 through 288 and (name N or name CA or name C or name O or name CB )) or r \ esid 289 through 312 or (resid 313 and (name N or name CA or name C or name O or \ name CB )) or resid 314 through 353 or (resid 354 and (name N or name CA or nam \ e C or name O or name CB )) or resid 355 through 357 or (resid 358 and (name N o \ r name CA or name C or name O or name CB )) or resid 359 through 361 or (resid 3 \ 62 through 364 and (name N or name CA or name C or name O or name CB )) or resid \ 365 through 370 or (resid 371 and (name N or name CA or name C or name O or nam \ e CB )) or resid 372 through 374 or (resid 375 through 381 and (name N or name C \ A or name C or name O or name CB )))) } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.460 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9991 Z= 0.203 Angle : 0.619 7.444 13613 Z= 0.373 Chirality : 0.043 0.296 1602 Planarity : 0.003 0.036 1688 Dihedral : 13.728 69.878 3417 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.38 % Favored : 93.98 % Rotamer: Outliers : 0.30 % Allowed : 14.29 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.25), residues: 1263 helix: 2.66 (0.25), residues: 406 sheet: 0.25 (0.33), residues: 238 loop : -0.54 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 120 TYR 0.010 0.001 TYR B 58 PHE 0.033 0.001 PHE D 98 TRP 0.014 0.001 TRP A 91 HIS 0.002 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9991) covalent geometry : angle 0.61881 (13613) hydrogen bonds : bond 0.15402 ( 510) hydrogen bonds : angle 7.35289 ( 1515) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 0.346 Fit side-chains REVERT: A 186 PHE cc_start: 0.8004 (t80) cc_final: 0.7783 (t80) REVERT: A 191 MET cc_start: 0.8440 (tmm) cc_final: 0.7673 (tmm) REVERT: A 292 TRP cc_start: 0.8828 (t-100) cc_final: 0.8517 (t-100) REVERT: B 100 MET cc_start: 0.8580 (tmm) cc_final: 0.8332 (tmm) REVERT: D 96 LEU cc_start: 0.8922 (mm) cc_final: 0.8566 (mt) REVERT: D 137 ASN cc_start: 0.8644 (m-40) cc_final: 0.8387 (t0) REVERT: D 215 MET cc_start: 0.8024 (tpt) cc_final: 0.7737 (tpt) outliers start: 3 outliers final: 3 residues processed: 142 average time/residue: 0.0821 time to fit residues: 17.2608 Evaluate side-chains 120 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain D residue 201 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS B 233 HIS C 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.139286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.108602 restraints weight = 17821.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.108958 restraints weight = 15308.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.110833 restraints weight = 12430.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.111473 restraints weight = 9830.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.111740 restraints weight = 9187.224| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9991 Z= 0.154 Angle : 0.616 7.797 13613 Z= 0.326 Chirality : 0.045 0.155 1602 Planarity : 0.004 0.032 1688 Dihedral : 5.310 45.520 1371 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.75 % Favored : 94.85 % Rotamer: Outliers : 2.20 % Allowed : 15.88 % Favored : 81.92 % 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: 1.11 (0.24), residues: 1263 helix: 2.86 (0.23), residues: 401 sheet: 0.60 (0.34), residues: 230 loop : -0.65 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 324 TYR 0.011 0.001 TYR B 58 PHE 0.020 0.002 PHE D 98 TRP 0.027 0.001 TRP A 91 HIS 0.005 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9991) covalent geometry : angle 0.61609 (13613) hydrogen bonds : bond 0.04340 ( 510) hydrogen bonds : angle 4.97688 ( 1515) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7357 (tm) REVERT: A 305 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: B 96 LEU cc_start: 0.8668 (mm) cc_final: 0.8403 (mm) REVERT: B 215 MET cc_start: 0.7704 (mmm) cc_final: 0.7436 (mmm) REVERT: B 298 GLN cc_start: 0.8888 (tp40) cc_final: 0.8667 (tp40) REVERT: B 301 LYS cc_start: 0.9161 (mmmm) cc_final: 0.8843 (mtmm) REVERT: C 223 MET cc_start: 0.7659 (ptp) cc_final: 0.7422 (ptp) REVERT: C 313 MET cc_start: 0.7190 (ppp) cc_final: 0.6932 (ppp) REVERT: D 93 PHE cc_start: 0.8094 (t80) cc_final: 0.7760 (t80) REVERT: D 96 LEU cc_start: 0.8864 (mm) cc_final: 0.8530 (mt) outliers start: 22 outliers final: 10 residues processed: 155 average time/residue: 0.0656 time to fit residues: 15.8380 Evaluate side-chains 128 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 298 GLN Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.137409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.103694 restraints weight = 18225.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.104174 restraints weight = 12597.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.104523 restraints weight = 11503.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104983 restraints weight = 10482.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.105326 restraints weight = 9928.145| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9991 Z= 0.238 Angle : 0.657 8.946 13613 Z= 0.348 Chirality : 0.046 0.157 1602 Planarity : 0.004 0.032 1688 Dihedral : 5.231 29.520 1365 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.62 % Favored : 93.98 % Rotamer: Outliers : 3.90 % Allowed : 17.08 % Favored : 79.02 % 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: 1.01 (0.24), residues: 1263 helix: 2.81 (0.23), residues: 409 sheet: 0.23 (0.34), residues: 224 loop : -0.62 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 201 TYR 0.017 0.002 TYR B 58 PHE 0.025 0.002 PHE D 98 TRP 0.027 0.001 TRP A 91 HIS 0.003 0.001 HIS D 210 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 9991) covalent geometry : angle 0.65656 (13613) hydrogen bonds : bond 0.04175 ( 510) hydrogen bonds : angle 4.73409 ( 1515) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 96 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7337 (tm) REVERT: A 292 TRP cc_start: 0.9015 (t-100) cc_final: 0.8479 (t-100) REVERT: B 96 LEU cc_start: 0.8717 (mm) cc_final: 0.8509 (mm) REVERT: B 100 MET cc_start: 0.8208 (tmm) cc_final: 0.7933 (tmm) REVERT: B 215 MET cc_start: 0.7702 (mmm) cc_final: 0.7474 (mmm) REVERT: B 301 LYS cc_start: 0.9170 (mmmm) cc_final: 0.8918 (mtmm) REVERT: C 223 MET cc_start: 0.7816 (ptp) cc_final: 0.7548 (ptp) REVERT: C 313 MET cc_start: 0.7305 (ppp) cc_final: 0.7048 (ppp) REVERT: C 322 GLN cc_start: 0.6914 (mp10) cc_final: 0.6433 (mp10) REVERT: D 96 LEU cc_start: 0.8853 (mm) cc_final: 0.8510 (mt) REVERT: D 137 ASN cc_start: 0.8311 (t0) cc_final: 0.8013 (t0) outliers start: 39 outliers final: 23 residues processed: 156 average time/residue: 0.0732 time to fit residues: 17.8547 Evaluate side-chains 139 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 221 CYS Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 298 GLN Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 64 optimal weight: 20.0000 chunk 82 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 121 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.148990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.117859 restraints weight = 17342.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.119387 restraints weight = 14126.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.121128 restraints weight = 12015.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121965 restraints weight = 8946.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.122269 restraints weight = 8452.560| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9991 Z= 0.125 Angle : 0.587 8.919 13613 Z= 0.306 Chirality : 0.044 0.153 1602 Planarity : 0.003 0.037 1688 Dihedral : 4.784 29.205 1365 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.67 % Favored : 94.93 % Rotamer: Outliers : 4.10 % Allowed : 18.08 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.24), residues: 1263 helix: 3.08 (0.24), residues: 403 sheet: 0.36 (0.34), residues: 224 loop : -0.58 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 324 TYR 0.015 0.001 TYR D 349 PHE 0.023 0.001 PHE D 98 TRP 0.026 0.001 TRP A 91 HIS 0.004 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9991) covalent geometry : angle 0.58731 (13613) hydrogen bonds : bond 0.03636 ( 510) hydrogen bonds : angle 4.44982 ( 1515) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 96 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7445 (tm) REVERT: A 152 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 292 TRP cc_start: 0.8788 (t-100) cc_final: 0.8318 (t-100) REVERT: B 100 MET cc_start: 0.7960 (tmm) cc_final: 0.7683 (tmm) REVERT: C 100 MET cc_start: 0.7623 (ptp) cc_final: 0.7415 (ptp) REVERT: C 223 MET cc_start: 0.7668 (ptp) cc_final: 0.7462 (ptp) REVERT: D 96 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8482 (mt) outliers start: 41 outliers final: 24 residues processed: 167 average time/residue: 0.0729 time to fit residues: 18.7996 Evaluate side-chains 145 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 221 CYS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 8 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.150572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.118382 restraints weight = 17544.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.120331 restraints weight = 13227.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.122419 restraints weight = 9897.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.123830 restraints weight = 8237.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.124532 restraints weight = 7683.170| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9991 Z= 0.121 Angle : 0.588 10.027 13613 Z= 0.303 Chirality : 0.043 0.179 1602 Planarity : 0.003 0.035 1688 Dihedral : 4.641 28.502 1365 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.83 % Favored : 94.85 % Rotamer: Outliers : 3.80 % Allowed : 18.68 % Favored : 77.52 % 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: 1.23 (0.24), residues: 1263 helix: 3.09 (0.23), residues: 404 sheet: 0.37 (0.34), residues: 227 loop : -0.55 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 324 TYR 0.015 0.001 TYR C 102 PHE 0.028 0.001 PHE D 98 TRP 0.020 0.001 TRP D 114 HIS 0.004 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9991) covalent geometry : angle 0.58836 (13613) hydrogen bonds : bond 0.03477 ( 510) hydrogen bonds : angle 4.32489 ( 1515) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 96 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7318 (tm) REVERT: A 100 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7649 (tpp) REVERT: A 152 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 292 TRP cc_start: 0.8843 (t-100) cc_final: 0.8366 (t-100) REVERT: B 100 MET cc_start: 0.8121 (tmm) cc_final: 0.7795 (tmm) REVERT: B 301 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8744 (mtmm) REVERT: C 192 PHE cc_start: 0.8209 (t80) cc_final: 0.7910 (t80) REVERT: C 223 MET cc_start: 0.7683 (ptp) cc_final: 0.7462 (ptp) REVERT: D 96 LEU cc_start: 0.8786 (mm) cc_final: 0.8436 (mt) REVERT: D 98 PHE cc_start: 0.7264 (t80) cc_final: 0.6481 (m-80) REVERT: D 220 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8263 (tm) outliers start: 38 outliers final: 30 residues processed: 160 average time/residue: 0.0734 time to fit residues: 18.4020 Evaluate side-chains 152 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 51 optimal weight: 0.0030 chunk 2 optimal weight: 10.0000 chunk 31 optimal weight: 0.0870 overall best weight: 0.5768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 298 GLN ** 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 = 0.4193 r_free = 0.4193 target = 0.151652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.119720 restraints weight = 17592.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.121184 restraints weight = 14026.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.123147 restraints weight = 11637.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.123902 restraints weight = 8960.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.124568 restraints weight = 8744.238| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9991 Z= 0.115 Angle : 0.583 11.151 13613 Z= 0.298 Chirality : 0.043 0.195 1602 Planarity : 0.003 0.036 1688 Dihedral : 4.525 28.437 1365 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.43 % Favored : 95.33 % Rotamer: Outliers : 3.80 % Allowed : 19.08 % Favored : 77.12 % 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: 1.26 (0.24), residues: 1263 helix: 3.09 (0.23), residues: 404 sheet: 0.43 (0.34), residues: 227 loop : -0.53 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 225 TYR 0.012 0.001 TYR D 349 PHE 0.033 0.001 PHE D 98 TRP 0.014 0.001 TRP D 114 HIS 0.006 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9991) covalent geometry : angle 0.58341 (13613) hydrogen bonds : bond 0.03314 ( 510) hydrogen bonds : angle 4.26474 ( 1515) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7276 (tm) REVERT: A 100 MET cc_start: 0.7957 (mmp) cc_final: 0.7753 (tpp) REVERT: A 152 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7573 (tm-30) REVERT: A 163 THR cc_start: 0.8891 (t) cc_final: 0.8589 (t) REVERT: B 98 PHE cc_start: 0.7150 (m-80) cc_final: 0.6257 (m-80) REVERT: B 100 MET cc_start: 0.8125 (tmm) cc_final: 0.7835 (tmm) REVERT: B 298 GLN cc_start: 0.8753 (tp40) cc_final: 0.8338 (mm-40) REVERT: B 301 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8433 (mtmm) REVERT: C 100 MET cc_start: 0.7697 (ptp) cc_final: 0.7460 (ptp) REVERT: C 176 GLN cc_start: 0.8664 (tt0) cc_final: 0.8423 (tt0) REVERT: C 192 PHE cc_start: 0.8251 (t80) cc_final: 0.8026 (t80) REVERT: C 223 MET cc_start: 0.7611 (ptp) cc_final: 0.7398 (ptp) REVERT: D 93 PHE cc_start: 0.8133 (t80) cc_final: 0.7818 (t80) REVERT: D 96 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8408 (mt) outliers start: 38 outliers final: 27 residues processed: 168 average time/residue: 0.0752 time to fit residues: 19.4440 Evaluate side-chains 157 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 80 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.149081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.117129 restraints weight = 17540.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.118125 restraints weight = 15564.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.119681 restraints weight = 12472.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.121031 restraints weight = 9969.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.121169 restraints weight = 9165.475| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9991 Z= 0.169 Angle : 0.616 11.659 13613 Z= 0.316 Chirality : 0.044 0.193 1602 Planarity : 0.003 0.034 1688 Dihedral : 4.718 28.104 1365 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.70 % Favored : 94.06 % Rotamer: Outliers : 5.59 % Allowed : 17.68 % Favored : 76.72 % 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: 1.19 (0.24), residues: 1263 helix: 3.11 (0.23), residues: 403 sheet: 0.23 (0.33), residues: 234 loop : -0.56 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 201 TYR 0.013 0.001 TYR B 58 PHE 0.014 0.001 PHE D 224 TRP 0.014 0.001 TRP D 114 HIS 0.006 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9991) covalent geometry : angle 0.61561 (13613) hydrogen bonds : bond 0.03470 ( 510) hydrogen bonds : angle 4.31669 ( 1515) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 133 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7276 (tm) REVERT: A 329 THR cc_start: 0.8067 (p) cc_final: 0.7823 (t) REVERT: B 100 MET cc_start: 0.8047 (tmm) cc_final: 0.7772 (tmm) REVERT: B 194 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8326 (tmtt) REVERT: B 301 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8650 (mtmm) REVERT: C 176 GLN cc_start: 0.8763 (tt0) cc_final: 0.8497 (tt0) REVERT: C 223 MET cc_start: 0.7668 (ptp) cc_final: 0.7425 (ptp) REVERT: D 93 PHE cc_start: 0.8072 (t80) cc_final: 0.7702 (t80) REVERT: D 96 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8446 (mt) REVERT: D 220 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8475 (tm) outliers start: 56 outliers final: 38 residues processed: 173 average time/residue: 0.0727 time to fit residues: 19.3954 Evaluate side-chains 162 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 221 CYS Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 321 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 GLN D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.147553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.115929 restraints weight = 17334.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.117058 restraints weight = 14990.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.118832 restraints weight = 12194.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.119700 restraints weight = 9362.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.119928 restraints weight = 8759.307| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9991 Z= 0.166 Angle : 0.630 12.014 13613 Z= 0.323 Chirality : 0.045 0.200 1602 Planarity : 0.003 0.036 1688 Dihedral : 4.726 28.012 1365 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.23 % Favored : 94.54 % Rotamer: Outliers : 5.00 % Allowed : 18.98 % Favored : 76.02 % 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: 1.16 (0.24), residues: 1263 helix: 3.08 (0.23), residues: 403 sheet: 0.15 (0.33), residues: 235 loop : -0.55 (0.27), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.013 0.001 TYR B 58 PHE 0.025 0.001 PHE D 98 TRP 0.016 0.001 TRP D 114 HIS 0.007 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9991) covalent geometry : angle 0.62983 (13613) hydrogen bonds : bond 0.03474 ( 510) hydrogen bonds : angle 4.32716 ( 1515) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7270 (tm) REVERT: A 98 PHE cc_start: 0.8100 (t80) cc_final: 0.7872 (t80) REVERT: A 292 TRP cc_start: 0.8846 (t-100) cc_final: 0.8391 (t-100) REVERT: A 329 THR cc_start: 0.8081 (p) cc_final: 0.7859 (t) REVERT: B 100 MET cc_start: 0.8036 (tmm) cc_final: 0.7757 (tmm) REVERT: B 194 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8334 (tmtt) REVERT: B 298 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8107 (mm-40) REVERT: B 301 LYS cc_start: 0.8976 (mtmm) cc_final: 0.8495 (mtmm) REVERT: C 100 MET cc_start: 0.7675 (ptp) cc_final: 0.7443 (ptp) REVERT: C 176 GLN cc_start: 0.8756 (tt0) cc_final: 0.8469 (tt0) REVERT: D 93 PHE cc_start: 0.8044 (t80) cc_final: 0.7648 (t80) REVERT: D 96 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8426 (mt) REVERT: D 137 ASN cc_start: 0.7836 (t0) cc_final: 0.7547 (t0) REVERT: D 220 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8566 (tm) outliers start: 50 outliers final: 39 residues processed: 165 average time/residue: 0.0705 time to fit residues: 17.7852 Evaluate side-chains 166 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 221 CYS Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 321 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 123 optimal weight: 0.2980 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.148887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.117496 restraints weight = 17229.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118417 restraints weight = 14683.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.120296 restraints weight = 12094.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.121075 restraints weight = 9323.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.121216 restraints weight = 9011.715| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9991 Z= 0.139 Angle : 0.629 11.695 13613 Z= 0.320 Chirality : 0.045 0.212 1602 Planarity : 0.003 0.036 1688 Dihedral : 4.615 27.764 1365 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.99 % Favored : 94.77 % Rotamer: Outliers : 4.60 % Allowed : 19.38 % Favored : 76.02 % 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: 1.16 (0.24), residues: 1263 helix: 3.02 (0.23), residues: 404 sheet: 0.16 (0.33), residues: 238 loop : -0.52 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 324 TYR 0.011 0.001 TYR B 58 PHE 0.023 0.001 PHE D 98 TRP 0.020 0.001 TRP D 114 HIS 0.008 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9991) covalent geometry : angle 0.62894 (13613) hydrogen bonds : bond 0.03415 ( 510) hydrogen bonds : angle 4.30639 ( 1515) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.8159 (t80) cc_final: 0.7959 (t80) REVERT: A 100 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7342 (tpp) REVERT: B 100 MET cc_start: 0.8051 (tmm) cc_final: 0.7751 (tmm) REVERT: B 194 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8361 (tmtt) REVERT: B 298 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8006 (mm-40) REVERT: B 301 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8432 (mtmm) REVERT: C 176 GLN cc_start: 0.8754 (tt0) cc_final: 0.8485 (tt0) REVERT: C 223 MET cc_start: 0.7710 (ptp) cc_final: 0.7484 (ptp) REVERT: D 96 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8423 (mt) REVERT: D 137 ASN cc_start: 0.7849 (t0) cc_final: 0.7461 (t0) REVERT: D 220 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8551 (tm) outliers start: 46 outliers final: 34 residues processed: 166 average time/residue: 0.0746 time to fit residues: 19.0270 Evaluate side-chains 161 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 221 CYS Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 115 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.148344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.116490 restraints weight = 17312.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.116945 restraints weight = 16001.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118870 restraints weight = 12767.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.120141 restraints weight = 10005.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.120343 restraints weight = 9267.655| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9991 Z= 0.175 Angle : 0.656 11.504 13613 Z= 0.336 Chirality : 0.045 0.204 1602 Planarity : 0.004 0.037 1688 Dihedral : 4.638 27.717 1363 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.86 % Favored : 93.90 % Rotamer: Outliers : 4.20 % Allowed : 20.58 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.07 (0.24), residues: 1263 helix: 2.98 (0.23), residues: 403 sheet: -0.03 (0.32), residues: 252 loop : -0.53 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 201 TYR 0.018 0.001 TYR D 102 PHE 0.021 0.002 PHE D 98 TRP 0.019 0.001 TRP D 114 HIS 0.008 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9991) covalent geometry : angle 0.65648 (13613) hydrogen bonds : bond 0.03540 ( 510) hydrogen bonds : angle 4.41961 ( 1515) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7383 (tpp) REVERT: B 100 MET cc_start: 0.8067 (tmm) cc_final: 0.7719 (tmm) REVERT: B 194 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8352 (tmtt) REVERT: B 301 LYS cc_start: 0.8977 (mtmm) cc_final: 0.8666 (mtmm) REVERT: C 176 GLN cc_start: 0.8772 (tt0) cc_final: 0.8476 (tt0) REVERT: D 96 LEU cc_start: 0.8742 (mm) cc_final: 0.8422 (mt) REVERT: D 137 ASN cc_start: 0.7935 (t0) cc_final: 0.7548 (t0) outliers start: 42 outliers final: 37 residues processed: 156 average time/residue: 0.0761 time to fit residues: 18.2383 Evaluate side-chains 164 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 221 CYS Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.150373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.119500 restraints weight = 17309.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.120059 restraints weight = 14481.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.122599 restraints weight = 11696.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.122842 restraints weight = 9468.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.123089 restraints weight = 9061.251| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9991 Z= 0.127 Angle : 0.632 11.382 13613 Z= 0.319 Chirality : 0.044 0.214 1602 Planarity : 0.003 0.038 1688 Dihedral : 4.436 27.615 1363 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.51 % Favored : 95.25 % Rotamer: Outliers : 3.60 % Allowed : 21.38 % Favored : 75.02 % 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: 1.12 (0.25), residues: 1263 helix: 2.99 (0.23), residues: 403 sheet: 0.08 (0.32), residues: 254 loop : -0.52 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 240 TYR 0.010 0.001 TYR B 58 PHE 0.031 0.001 PHE D 98 TRP 0.021 0.001 TRP D 114 HIS 0.011 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9991) covalent geometry : angle 0.63191 (13613) hydrogen bonds : bond 0.03339 ( 510) hydrogen bonds : angle 4.29746 ( 1515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.79 seconds wall clock time: 23 minutes 56.34 seconds (1436.34 seconds total)