Starting phenix.real_space_refine on Tue Feb 3 18:37:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijr_60642/02_2026/9ijr_60642.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijr_60642/02_2026/9ijr_60642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ijr_60642/02_2026/9ijr_60642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijr_60642/02_2026/9ijr_60642.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ijr_60642/02_2026/9ijr_60642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijr_60642/02_2026/9ijr_60642.map" } resolution = 3.86 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= 0.002 sd= 0.033 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 S 18 5.16 5 C 3948 2.51 5 N 1027 2.21 5 O 1135 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6136 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2132 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 295, 2132 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 9, 'TYR:plan': 2, 'HIS:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 5, 'TRP:plan': 1, 'GLU:plan': 3, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 158 Chain: "C" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2427 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 325} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 363 Unresolved non-hydrogen angles: 446 Unresolved non-hydrogen dihedrals: 295 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 11, 'ASN:plan1': 5, 'ASP:plan': 13, 'GLU:plan': 20, 'GLN:plan1': 3, 'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 224 Chain: "H" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1543 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 218} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 7, 'ARG:plan': 5, 'PHE:plan': 2, 'ASP:plan': 5, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 120 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'EN6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.46, per 1000 atoms: 0.24 Number of scatterers: 6136 At special positions: 0 Unit cell: (76.544, 91.52, 133.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 5 15.00 F 3 9.00 O 1135 8.00 N 1027 7.00 C 3948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 162 " - pdb=" SG CYS H 227 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 306.6 milliseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 15 sheets defined 29.0% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 42 through 68 removed outlier: 4.271A pdb=" N VAL A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 100 removed outlier: 3.775A pdb=" N TYR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 109 through 139 removed outlier: 4.181A pdb=" N THR A 113 " --> pdb=" O HIS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.680A pdb=" N LEU A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 153' Processing helix chain 'A' and resid 154 through 179 Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.689A pdb=" N PHE A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 231 removed outlier: 4.303A pdb=" N HIS A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 263 through 289 removed outlier: 4.303A pdb=" N ARG A 269 " --> pdb=" O MET A 265 " (cutoff:3.500A) Proline residue: A 280 - end of helix removed outlier: 3.822A pdb=" N ILE A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 319 removed outlier: 5.048A pdb=" N SER A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 321 through 330 removed outlier: 3.956A pdb=" N GLY A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 Processing helix chain 'C' and resid 98 through 108 Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.533A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 493 removed outlier: 3.599A pdb=" N VAL C 40 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 39 " --> pdb=" O PHE C 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 26 through 29 removed outlier: 5.762A pdb=" N PHE C 27 " --> pdb=" O VAL C 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 85 removed outlier: 5.792A pdb=" N ASP C 78 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE C 61 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE C 80 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 82 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 55 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 76 through 85 removed outlier: 5.792A pdb=" N ASP C 78 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE C 61 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE C 80 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 82 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 55 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'C' and resid 183 through 184 removed outlier: 3.798A pdb=" N ALA C 184 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 183 through 184 removed outlier: 3.798A pdb=" N ALA C 184 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 207 through 208 removed outlier: 3.896A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 322 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE C 231 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU C 257 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 233 " --> pdb=" O MET C 255 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET C 255 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 235 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 207 through 208 removed outlier: 3.896A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 327 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 343 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.515A pdb=" N GLY H 13 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR H 120 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER H 53 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER H 55 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.515A pdb=" N GLY H 13 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR H 120 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER H 102 " --> pdb=" O SER H 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 143 through 146 Processing sheet with id=AB5, first strand: chain 'H' and resid 150 through 151 removed outlier: 6.956A pdb=" N LEU H 150 " --> pdb=" O GLU H 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'H' and resid 192 through 193 removed outlier: 3.620A pdb=" N SER H 192 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP H 174 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR H 188 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL H 172 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN H 229 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR H 236 " --> pdb=" O GLN H 229 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 801 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: 0.96 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 945 1.31 - 1.44: 1795 1.44 - 1.56: 3495 1.56 - 1.69: 21 1.69 - 1.82: 22 Bond restraints: 6278 Sorted by residual: bond pdb=" OG1 TPO A 491 " pdb=" P TPO A 491 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C22 EN6 A 601 " pdb=" N3 EN6 A 601 " ideal model delta sigma weight residual 1.344 1.453 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C1 EN6 A 601 " pdb=" N1 EN6 A 601 " ideal model delta sigma weight residual 1.410 1.319 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" O2P TPO A 491 " pdb=" P TPO A 491 " ideal model delta sigma weight residual 1.528 1.607 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" O3P TPO A 491 " pdb=" P TPO A 491 " ideal model delta sigma weight residual 1.528 1.605 -0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 6273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 8398 2.09 - 4.18: 178 4.18 - 6.27: 45 6.27 - 8.36: 9 8.36 - 10.44: 4 Bond angle restraints: 8634 Sorted by residual: angle pdb=" CA PRO A 183 " pdb=" N PRO A 183 " pdb=" CD PRO A 183 " ideal model delta sigma weight residual 112.00 102.21 9.79 1.40e+00 5.10e-01 4.89e+01 angle pdb=" OG1 TPO A 491 " pdb=" P TPO A 491 " pdb=" O1P TPO A 491 " ideal model delta sigma weight residual 100.43 110.87 -10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CB TPO A 491 " pdb=" OG1 TPO A 491 " pdb=" P TPO A 491 " ideal model delta sigma weight residual 119.31 108.90 10.41 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C LEU A 279 " pdb=" N PRO A 280 " pdb=" CA PRO A 280 " ideal model delta sigma weight residual 121.65 118.21 3.44 1.01e+00 9.80e-01 1.16e+01 angle pdb=" CA GLN H 229 " pdb=" CB GLN H 229 " pdb=" CG GLN H 229 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 ... (remaining 8629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 3502 33.95 - 67.89: 110 67.89 - 101.84: 7 101.84 - 135.79: 0 135.79 - 169.74: 1 Dihedral angle restraints: 3620 sinusoidal: 1061 harmonic: 2559 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 40.07 52.93 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CB CYS A 114 " pdb=" SG CYS A 114 " pdb=" SG CYS A 193 " pdb=" CB CYS A 193 " ideal model delta sinusoidal sigma weight residual 93.00 142.35 -49.35 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS H 162 " pdb=" SG CYS H 162 " pdb=" SG CYS H 227 " pdb=" CB CYS H 227 " ideal model delta sinusoidal sigma weight residual 93.00 50.28 42.72 1 1.00e+01 1.00e-02 2.55e+01 ... (remaining 3617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 768 0.047 - 0.093: 219 0.093 - 0.140: 57 0.140 - 0.186: 3 0.186 - 0.233: 1 Chirality restraints: 1048 Sorted by residual: chirality pdb=" CG LEU C 315 " pdb=" CB LEU C 315 " pdb=" CD1 LEU C 315 " pdb=" CD2 LEU C 315 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB VAL A 273 " pdb=" CA VAL A 273 " pdb=" CG1 VAL A 273 " pdb=" CG2 VAL A 273 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA ILE C 214 " pdb=" N ILE C 214 " pdb=" C ILE C 214 " pdb=" CB ILE C 214 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 1045 not shown) Planarity restraints: 1075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 182 " 0.065 5.00e-02 4.00e+02 9.21e-02 1.36e+01 pdb=" N PRO A 183 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 295 " -0.060 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO A 296 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 258 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO A 259 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " 0.038 5.00e-02 4.00e+02 ... (remaining 1072 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1004 2.76 - 3.29: 5865 3.29 - 3.83: 10086 3.83 - 4.36: 10392 4.36 - 4.90: 18566 Nonbonded interactions: 45913 Sorted by model distance: nonbonded pdb=" NH2 ARG A 139 " pdb=" O ASP A 260 " model vdw 2.222 3.120 nonbonded pdb=" N GLY C 179 " pdb=" OE2 GLU C 206 " model vdw 2.223 3.120 nonbonded pdb=" OG SER H 216 " pdb=" OE1 GLN H 218 " model vdw 2.259 3.040 nonbonded pdb=" O VAL C 53 " pdb=" OG SER C 86 " model vdw 2.273 3.040 nonbonded pdb=" O SER C 215 " pdb=" OG SER C 215 " model vdw 2.277 3.040 ... (remaining 45908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.010 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 : 0.006 0.124 6281 Z= 0.256 Angle : 0.794 10.444 8640 Z= 0.395 Chirality : 0.045 0.233 1048 Planarity : 0.006 0.092 1075 Dihedral : 17.007 169.735 1963 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.18 % Favored : 92.70 % Rotamer: Outliers : 0.93 % Allowed : 42.67 % Favored : 56.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.59 (0.30), residues: 852 helix: -0.35 (0.36), residues: 220 sheet: -0.63 (0.37), residues: 226 loop : -1.67 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 139 TYR 0.023 0.002 TYR A 78 PHE 0.014 0.001 PHE H 210 TRP 0.024 0.002 TRP H 39 HIS 0.015 0.002 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 6278) covalent geometry : angle 0.79294 ( 8634) SS BOND : bond 0.00366 ( 3) SS BOND : angle 1.42607 ( 6) hydrogen bonds : bond 0.20490 ( 270) hydrogen bonds : angle 7.94017 ( 801) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 209 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8768 (tt) cc_final: 0.8567 (tt) REVERT: A 129 MET cc_start: 0.7321 (tpt) cc_final: 0.6765 (tpt) REVERT: A 132 LEU cc_start: 0.8642 (tp) cc_final: 0.8411 (tt) REVERT: A 301 LEU cc_start: 0.8225 (mm) cc_final: 0.7966 (mm) REVERT: C 150 VAL cc_start: 0.7074 (OUTLIER) cc_final: 0.6716 (p) REVERT: C 160 LYS cc_start: 0.8059 (tppt) cc_final: 0.7690 (tppt) REVERT: C 229 LYS cc_start: 0.7828 (mptt) cc_final: 0.7563 (tptt) REVERT: C 295 HIS cc_start: 0.7751 (m-70) cc_final: 0.7539 (m-70) REVERT: C 299 ASN cc_start: 0.7861 (p0) cc_final: 0.7398 (p0) REVERT: C 300 LEU cc_start: 0.8496 (mt) cc_final: 0.8256 (mt) REVERT: C 320 SER cc_start: 0.8553 (t) cc_final: 0.8303 (p) REVERT: H 24 SER cc_start: 0.8074 (p) cc_final: 0.7808 (m) REVERT: H 56 SER cc_start: 0.8376 (m) cc_final: 0.7922 (p) REVERT: H 58 TYR cc_start: 0.7920 (m-10) cc_final: 0.7689 (m-80) REVERT: H 61 THR cc_start: 0.8849 (m) cc_final: 0.8581 (t) outliers start: 5 outliers final: 4 residues processed: 211 average time/residue: 0.0640 time to fit residues: 17.8869 Evaluate side-chains 205 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 200 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain H residue 48 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 172 GLN ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.129374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108064 restraints weight = 12681.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111751 restraints weight = 7101.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114211 restraints weight = 4640.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.115846 restraints weight = 3392.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.116967 restraints weight = 2710.038| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6281 Z= 0.146 Angle : 0.635 7.175 8640 Z= 0.325 Chirality : 0.043 0.160 1048 Planarity : 0.005 0.064 1075 Dihedral : 8.779 173.896 963 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 8.16 % Allowed : 37.11 % Favored : 54.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.30), residues: 852 helix: 0.37 (0.38), residues: 214 sheet: -0.39 (0.37), residues: 229 loop : -1.52 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 139 TYR 0.017 0.002 TYR C 208 PHE 0.016 0.001 PHE H 210 TRP 0.014 0.001 TRP H 39 HIS 0.005 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6278) covalent geometry : angle 0.63431 ( 8634) SS BOND : bond 0.00510 ( 3) SS BOND : angle 1.33627 ( 6) hydrogen bonds : bond 0.04182 ( 270) hydrogen bonds : angle 5.66117 ( 801) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.230 Fit side-chains REVERT: A 44 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8029 (p) REVERT: A 73 HIS cc_start: 0.6484 (OUTLIER) cc_final: 0.6159 (m-70) REVERT: A 129 MET cc_start: 0.7630 (tpt) cc_final: 0.7216 (tpt) REVERT: A 134 CYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7046 (t) REVERT: A 284 TYR cc_start: 0.7618 (t80) cc_final: 0.7344 (t80) REVERT: A 301 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8188 (mm) REVERT: C 22 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7661 (mt) REVERT: C 160 LYS cc_start: 0.8077 (tppt) cc_final: 0.7742 (tppt) REVERT: C 170 LYS cc_start: 0.8097 (tttp) cc_final: 0.7879 (tttp) REVERT: C 229 LYS cc_start: 0.8148 (mptt) cc_final: 0.7791 (tptt) REVERT: C 270 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8011 (pptt) REVERT: C 295 HIS cc_start: 0.8050 (m-70) cc_final: 0.7840 (m-70) REVERT: C 322 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7602 (mtmt) REVERT: H 6 GLN cc_start: 0.8213 (pp30) cc_final: 0.7771 (pp30) REVERT: H 56 SER cc_start: 0.8648 (m) cc_final: 0.8109 (p) REVERT: H 61 THR cc_start: 0.8726 (m) cc_final: 0.8470 (t) REVERT: H 105 PHE cc_start: 0.7616 (m-80) cc_final: 0.7295 (m-80) REVERT: H 175 TYR cc_start: 0.7383 (m-80) cc_final: 0.6773 (m-80) REVERT: H 237 PHE cc_start: 0.7705 (m-10) cc_final: 0.7424 (m-10) outliers start: 44 outliers final: 24 residues processed: 230 average time/residue: 0.0631 time to fit residues: 19.6098 Evaluate side-chains 237 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 214 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 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 = 0.3754 r_free = 0.3754 target = 0.130328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109557 restraints weight = 12381.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113132 restraints weight = 6831.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115519 restraints weight = 4443.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117101 restraints weight = 3240.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118051 restraints weight = 2589.442| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6281 Z= 0.174 Angle : 0.636 9.122 8640 Z= 0.323 Chirality : 0.042 0.141 1048 Planarity : 0.004 0.062 1075 Dihedral : 8.664 174.068 956 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.88 % Rotamer: Outliers : 9.65 % Allowed : 33.95 % Favored : 56.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.18 (0.30), residues: 852 helix: 0.50 (0.37), residues: 215 sheet: -0.70 (0.35), residues: 250 loop : -1.53 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.023 0.002 TYR C 208 PHE 0.013 0.002 PHE C 27 TRP 0.017 0.002 TRP H 39 HIS 0.005 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6278) covalent geometry : angle 0.63520 ( 8634) SS BOND : bond 0.00546 ( 3) SS BOND : angle 1.43367 ( 6) hydrogen bonds : bond 0.04036 ( 270) hydrogen bonds : angle 5.15160 ( 801) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 0.213 Fit side-chains REVERT: A 73 HIS cc_start: 0.6495 (OUTLIER) cc_final: 0.6182 (m-70) REVERT: A 129 MET cc_start: 0.7625 (tpt) cc_final: 0.7332 (tpt) REVERT: A 134 CYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7024 (t) REVERT: A 301 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8172 (mm) REVERT: C 11 LYS cc_start: 0.8610 (tptt) cc_final: 0.8319 (tppt) REVERT: C 22 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7705 (mt) REVERT: C 25 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.7905 (mmm160) REVERT: C 160 LYS cc_start: 0.8066 (tppt) cc_final: 0.7768 (tppt) REVERT: C 270 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7979 (pptt) REVERT: C 272 TYR cc_start: 0.7867 (m-10) cc_final: 0.7581 (m-10) REVERT: C 295 HIS cc_start: 0.8053 (m-70) cc_final: 0.7825 (m-70) REVERT: C 322 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7628 (mtmt) REVERT: C 326 LYS cc_start: 0.7811 (ttpp) cc_final: 0.7538 (ttpp) REVERT: H 6 GLN cc_start: 0.8439 (pp30) cc_final: 0.7903 (pp30) REVERT: H 56 SER cc_start: 0.8768 (m) cc_final: 0.8267 (p) REVERT: H 61 THR cc_start: 0.8688 (m) cc_final: 0.8363 (t) REVERT: H 200 ARG cc_start: 0.8354 (ttp80) cc_final: 0.7311 (tmt-80) REVERT: H 237 PHE cc_start: 0.7732 (m-10) cc_final: 0.7437 (m-10) outliers start: 52 outliers final: 26 residues processed: 234 average time/residue: 0.0644 time to fit residues: 20.1015 Evaluate side-chains 238 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 214 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.128043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106663 restraints weight = 12552.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110286 restraints weight = 6960.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.112769 restraints weight = 4543.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114273 restraints weight = 3326.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115473 restraints weight = 2688.978| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6281 Z= 0.164 Angle : 0.630 8.791 8640 Z= 0.316 Chirality : 0.042 0.147 1048 Planarity : 0.004 0.061 1075 Dihedral : 8.442 171.493 955 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.65 % Favored : 94.11 % Rotamer: Outliers : 9.83 % Allowed : 35.06 % Favored : 55.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.29), residues: 852 helix: 0.67 (0.37), residues: 214 sheet: -0.59 (0.35), residues: 241 loop : -1.61 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 139 TYR 0.021 0.002 TYR C 208 PHE 0.012 0.001 PHE C 27 TRP 0.023 0.002 TRP H 39 HIS 0.003 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6278) covalent geometry : angle 0.62868 ( 8634) SS BOND : bond 0.00766 ( 3) SS BOND : angle 1.65378 ( 6) hydrogen bonds : bond 0.03719 ( 270) hydrogen bonds : angle 4.99628 ( 801) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 0.134 Fit side-chains REVERT: A 63 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: A 73 HIS cc_start: 0.6527 (OUTLIER) cc_final: 0.6200 (m-70) REVERT: A 134 CYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7080 (t) REVERT: A 204 THR cc_start: 0.7388 (t) cc_final: 0.7111 (t) REVERT: A 301 LEU cc_start: 0.8428 (mm) cc_final: 0.8164 (mm) REVERT: C 22 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7672 (mt) REVERT: C 25 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.7885 (mmm160) REVERT: C 117 PHE cc_start: 0.8096 (m-10) cc_final: 0.7860 (m-10) REVERT: C 150 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7051 (p) REVERT: C 160 LYS cc_start: 0.8072 (tppt) cc_final: 0.7791 (tppt) REVERT: C 170 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7484 (tttp) REVERT: C 270 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7933 (pptt) REVERT: C 272 TYR cc_start: 0.7853 (m-10) cc_final: 0.7553 (m-10) REVERT: C 295 HIS cc_start: 0.8091 (m-70) cc_final: 0.7878 (m-70) REVERT: C 322 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7600 (mtmt) REVERT: C 326 LYS cc_start: 0.7823 (ttpp) cc_final: 0.7546 (ttpp) REVERT: H 56 SER cc_start: 0.8766 (m) cc_final: 0.8274 (p) REVERT: H 61 THR cc_start: 0.8700 (m) cc_final: 0.8384 (t) REVERT: H 105 PHE cc_start: 0.7627 (m-80) cc_final: 0.7367 (m-80) REVERT: H 237 PHE cc_start: 0.7773 (m-10) cc_final: 0.7456 (m-10) outliers start: 53 outliers final: 35 residues processed: 234 average time/residue: 0.0651 time to fit residues: 20.3571 Evaluate side-chains 247 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 235 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 81 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.109918 restraints weight = 12493.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.113629 restraints weight = 6826.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116055 restraints weight = 4385.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.117684 restraints weight = 3184.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.118783 restraints weight = 2526.829| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6281 Z= 0.126 Angle : 0.613 9.114 8640 Z= 0.302 Chirality : 0.042 0.145 1048 Planarity : 0.004 0.060 1075 Dihedral : 8.445 174.386 955 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.88 % Rotamer: Outliers : 9.83 % Allowed : 36.18 % Favored : 53.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.30), residues: 852 helix: 0.80 (0.38), residues: 215 sheet: -0.54 (0.35), residues: 241 loop : -1.57 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.018 0.001 TYR C 208 PHE 0.010 0.001 PHE C 27 TRP 0.021 0.002 TRP H 39 HIS 0.003 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6278) covalent geometry : angle 0.61168 ( 8634) SS BOND : bond 0.00471 ( 3) SS BOND : angle 1.40598 ( 6) hydrogen bonds : bond 0.03508 ( 270) hydrogen bonds : angle 4.82395 ( 801) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 0.145 Fit side-chains REVERT: A 63 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: A 72 HIS cc_start: 0.6183 (OUTLIER) cc_final: 0.5727 (p-80) REVERT: A 73 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.6166 (m-70) REVERT: A 134 CYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7064 (t) REVERT: A 204 THR cc_start: 0.7297 (t) cc_final: 0.7037 (t) REVERT: A 301 LEU cc_start: 0.8421 (mm) cc_final: 0.8154 (mm) REVERT: C 11 LYS cc_start: 0.8531 (tptt) cc_final: 0.8213 (tppt) REVERT: C 22 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7631 (mt) REVERT: C 25 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.7877 (mmm160) REVERT: C 117 PHE cc_start: 0.8053 (m-10) cc_final: 0.7843 (m-10) REVERT: C 150 VAL cc_start: 0.7504 (OUTLIER) cc_final: 0.7039 (p) REVERT: C 160 LYS cc_start: 0.8018 (tppt) cc_final: 0.7735 (tppt) REVERT: C 170 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7436 (tttp) REVERT: C 270 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7889 (pptt) REVERT: C 272 TYR cc_start: 0.7753 (m-10) cc_final: 0.7513 (m-10) REVERT: C 322 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7580 (mtmt) REVERT: C 323 VAL cc_start: 0.7299 (OUTLIER) cc_final: 0.6724 (t) REVERT: H 6 GLN cc_start: 0.8517 (pp30) cc_final: 0.7837 (pp30) REVERT: H 56 SER cc_start: 0.8750 (m) cc_final: 0.8221 (p) REVERT: H 60 TYR cc_start: 0.7520 (m-10) cc_final: 0.7195 (m-10) REVERT: H 61 THR cc_start: 0.8671 (m) cc_final: 0.8387 (t) REVERT: H 175 TYR cc_start: 0.7188 (m-80) cc_final: 0.6606 (m-80) REVERT: H 237 PHE cc_start: 0.7725 (m-10) cc_final: 0.7431 (m-10) outliers start: 53 outliers final: 33 residues processed: 232 average time/residue: 0.0616 time to fit residues: 19.1700 Evaluate side-chains 250 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 235 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.130297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109327 restraints weight = 12367.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112959 restraints weight = 6770.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115384 restraints weight = 4385.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117019 restraints weight = 3193.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.118119 restraints weight = 2542.130| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6281 Z= 0.141 Angle : 0.626 9.722 8640 Z= 0.308 Chirality : 0.042 0.152 1048 Planarity : 0.004 0.060 1075 Dihedral : 8.428 174.048 955 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.60 % Favored : 93.29 % Rotamer: Outliers : 9.09 % Allowed : 37.29 % Favored : 53.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.02 (0.30), residues: 852 helix: 0.72 (0.38), residues: 217 sheet: -0.44 (0.35), residues: 238 loop : -1.61 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.021 0.001 TYR C 208 PHE 0.013 0.001 PHE H 105 TRP 0.024 0.002 TRP H 39 HIS 0.003 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6278) covalent geometry : angle 0.62564 ( 8634) SS BOND : bond 0.00567 ( 3) SS BOND : angle 1.25608 ( 6) hydrogen bonds : bond 0.03576 ( 270) hydrogen bonds : angle 4.75927 ( 801) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.228 Fit side-chains REVERT: A 63 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: A 72 HIS cc_start: 0.6123 (OUTLIER) cc_final: 0.5687 (p-80) REVERT: A 73 HIS cc_start: 0.6447 (OUTLIER) cc_final: 0.6119 (m-70) REVERT: A 129 MET cc_start: 0.7762 (tpt) cc_final: 0.7439 (tpt) REVERT: A 134 CYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7071 (t) REVERT: A 289 SER cc_start: 0.6459 (t) cc_final: 0.6185 (t) REVERT: A 301 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8155 (mm) REVERT: C 25 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7881 (mmm160) REVERT: C 117 PHE cc_start: 0.8071 (m-10) cc_final: 0.7835 (m-10) REVERT: C 150 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7004 (p) REVERT: C 160 LYS cc_start: 0.8015 (tppt) cc_final: 0.7716 (tppt) REVERT: C 170 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7449 (tttp) REVERT: C 186 THR cc_start: 0.8247 (m) cc_final: 0.7675 (p) REVERT: C 270 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7921 (pptt) REVERT: C 272 TYR cc_start: 0.7831 (m-10) cc_final: 0.7593 (m-10) REVERT: C 320 SER cc_start: 0.8683 (t) cc_final: 0.8282 (m) REVERT: C 322 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7606 (mtmt) REVERT: C 323 VAL cc_start: 0.7318 (OUTLIER) cc_final: 0.6752 (t) REVERT: H 56 SER cc_start: 0.8762 (m) cc_final: 0.8272 (p) REVERT: H 60 TYR cc_start: 0.7526 (m-10) cc_final: 0.7249 (m-10) REVERT: H 61 THR cc_start: 0.8669 (m) cc_final: 0.8343 (t) REVERT: H 63 TYR cc_start: 0.7028 (m-10) cc_final: 0.6393 (m-80) REVERT: H 84 LEU cc_start: 0.7270 (tp) cc_final: 0.7030 (tp) REVERT: H 175 TYR cc_start: 0.7210 (m-80) cc_final: 0.6617 (m-80) REVERT: H 200 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8061 (tmm160) REVERT: H 237 PHE cc_start: 0.7764 (m-10) cc_final: 0.7438 (m-10) outliers start: 49 outliers final: 33 residues processed: 238 average time/residue: 0.0668 time to fit residues: 21.4571 Evaluate side-chains 260 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 235 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.0670 chunk 47 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 229 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 = 0.3697 r_free = 0.3697 target = 0.124810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103822 restraints weight = 12611.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.107439 restraints weight = 7004.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.109837 restraints weight = 4542.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111445 restraints weight = 3331.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112533 restraints weight = 2669.185| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6281 Z= 0.196 Angle : 0.667 10.507 8640 Z= 0.333 Chirality : 0.044 0.153 1048 Planarity : 0.004 0.060 1075 Dihedral : 8.505 171.291 955 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.71 % Favored : 93.05 % Rotamer: Outliers : 10.95 % Allowed : 36.55 % Favored : 52.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.29), residues: 852 helix: 0.59 (0.37), residues: 213 sheet: -0.49 (0.35), residues: 241 loop : -1.70 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 139 TYR 0.024 0.002 TYR C 208 PHE 0.015 0.002 PHE C 27 TRP 0.029 0.002 TRP H 39 HIS 0.005 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 6278) covalent geometry : angle 0.66621 ( 8634) SS BOND : bond 0.00732 ( 3) SS BOND : angle 1.38206 ( 6) hydrogen bonds : bond 0.03884 ( 270) hydrogen bonds : angle 4.92839 ( 801) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 0.220 Fit side-chains REVERT: A 63 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: A 72 HIS cc_start: 0.6201 (OUTLIER) cc_final: 0.5725 (p-80) REVERT: A 73 HIS cc_start: 0.6527 (OUTLIER) cc_final: 0.6175 (m-70) REVERT: A 129 MET cc_start: 0.7701 (tpt) cc_final: 0.7375 (tpt) REVERT: A 134 CYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7120 (t) REVERT: A 289 SER cc_start: 0.6744 (t) cc_final: 0.6327 (t) REVERT: A 298 LEU cc_start: 0.7927 (tp) cc_final: 0.7717 (tp) REVERT: A 301 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8166 (mm) REVERT: C 11 LYS cc_start: 0.8603 (tptt) cc_final: 0.8343 (tppt) REVERT: C 25 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.7842 (mmm160) REVERT: C 150 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7083 (p) REVERT: C 160 LYS cc_start: 0.8023 (tppt) cc_final: 0.7726 (tppt) REVERT: C 170 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7438 (tttp) REVERT: C 186 THR cc_start: 0.8234 (m) cc_final: 0.7601 (p) REVERT: C 205 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7639 (pttp) REVERT: C 270 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7968 (pptt) REVERT: C 272 TYR cc_start: 0.7950 (m-10) cc_final: 0.7693 (m-10) REVERT: C 320 SER cc_start: 0.8675 (t) cc_final: 0.8268 (m) REVERT: C 322 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7653 (mtmt) REVERT: H 56 SER cc_start: 0.8820 (m) cc_final: 0.8398 (p) REVERT: H 60 TYR cc_start: 0.7535 (m-10) cc_final: 0.7288 (m-10) REVERT: H 61 THR cc_start: 0.8648 (m) cc_final: 0.8344 (t) REVERT: H 84 LEU cc_start: 0.7258 (tp) cc_final: 0.7001 (tp) REVERT: H 200 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8075 (tmm160) REVERT: H 237 PHE cc_start: 0.7798 (m-10) cc_final: 0.7510 (m-10) outliers start: 59 outliers final: 43 residues processed: 244 average time/residue: 0.0694 time to fit residues: 22.5738 Evaluate side-chains 269 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 235 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 17 optimal weight: 0.0070 chunk 33 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 0.0370 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 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 = 0.3774 r_free = 0.3774 target = 0.130674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.109703 restraints weight = 12329.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113342 restraints weight = 6796.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115780 restraints weight = 4397.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.117396 restraints weight = 3202.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118431 restraints weight = 2549.246| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6281 Z= 0.117 Angle : 0.645 10.454 8640 Z= 0.315 Chirality : 0.043 0.147 1048 Planarity : 0.004 0.060 1075 Dihedral : 8.511 175.084 955 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.42 % Favored : 94.35 % Rotamer: Outliers : 9.65 % Allowed : 38.22 % Favored : 52.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.98 (0.30), residues: 852 helix: 0.91 (0.38), residues: 210 sheet: -0.37 (0.36), residues: 238 loop : -1.68 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.019 0.001 TYR C 208 PHE 0.013 0.001 PHE A 173 TRP 0.024 0.002 TRP H 39 HIS 0.003 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6278) covalent geometry : angle 0.64415 ( 8634) SS BOND : bond 0.00501 ( 3) SS BOND : angle 1.14059 ( 6) hydrogen bonds : bond 0.03446 ( 270) hydrogen bonds : angle 4.73103 ( 801) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 226 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 63 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: A 72 HIS cc_start: 0.6016 (OUTLIER) cc_final: 0.5524 (p-80) REVERT: A 73 HIS cc_start: 0.6428 (OUTLIER) cc_final: 0.6075 (m-70) REVERT: A 134 CYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7009 (t) REVERT: A 278 TRP cc_start: 0.8382 (t-100) cc_final: 0.7524 (t-100) REVERT: A 289 SER cc_start: 0.6538 (t) cc_final: 0.6196 (t) REVERT: A 301 LEU cc_start: 0.8398 (mm) cc_final: 0.8152 (mm) REVERT: C 11 LYS cc_start: 0.8538 (tptt) cc_final: 0.8208 (tppt) REVERT: C 25 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.7833 (mmm160) REVERT: C 150 VAL cc_start: 0.7440 (OUTLIER) cc_final: 0.6959 (p) REVERT: C 160 LYS cc_start: 0.7975 (tppt) cc_final: 0.7682 (tppt) REVERT: C 170 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7363 (tttp) REVERT: C 186 THR cc_start: 0.8226 (m) cc_final: 0.7632 (p) REVERT: C 245 ASN cc_start: 0.6683 (OUTLIER) cc_final: 0.6357 (m-40) REVERT: C 270 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7797 (pptt) REVERT: C 272 TYR cc_start: 0.7772 (m-10) cc_final: 0.7534 (m-10) REVERT: C 322 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7557 (mtmt) REVERT: H 56 SER cc_start: 0.8778 (m) cc_final: 0.8330 (p) REVERT: H 61 THR cc_start: 0.8611 (m) cc_final: 0.8341 (t) REVERT: H 84 LEU cc_start: 0.7157 (tp) cc_final: 0.6889 (tp) REVERT: H 175 TYR cc_start: 0.7164 (m-80) cc_final: 0.6592 (m-80) REVERT: H 200 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8070 (tmm160) REVERT: H 237 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7440 (m-10) outliers start: 52 outliers final: 38 residues processed: 250 average time/residue: 0.0729 time to fit residues: 24.3835 Evaluate side-chains 273 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 237 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 74 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.128777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107293 restraints weight = 12543.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111016 restraints weight = 6953.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.113471 restraints weight = 4511.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115118 restraints weight = 3300.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116092 restraints weight = 2638.797| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6281 Z= 0.134 Angle : 0.652 10.069 8640 Z= 0.321 Chirality : 0.044 0.172 1048 Planarity : 0.004 0.060 1075 Dihedral : 8.476 174.852 955 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.36 % Favored : 93.40 % Rotamer: Outliers : 9.83 % Allowed : 38.22 % Favored : 51.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.04 (0.30), residues: 852 helix: 0.76 (0.37), residues: 213 sheet: -0.40 (0.36), residues: 241 loop : -1.68 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.024 0.001 TYR A 185 PHE 0.012 0.001 PHE C 27 TRP 0.028 0.002 TRP A 192 HIS 0.002 0.000 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6278) covalent geometry : angle 0.65140 ( 8634) SS BOND : bond 0.00424 ( 3) SS BOND : angle 1.12204 ( 6) hydrogen bonds : bond 0.03679 ( 270) hydrogen bonds : angle 4.66813 ( 801) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 63 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: A 72 HIS cc_start: 0.6061 (OUTLIER) cc_final: 0.5557 (p-80) REVERT: A 73 HIS cc_start: 0.6469 (OUTLIER) cc_final: 0.6084 (m-70) REVERT: A 122 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8297 (t) REVERT: A 134 CYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7037 (t) REVERT: A 200 SER cc_start: 0.4673 (OUTLIER) cc_final: 0.4399 (p) REVERT: A 278 TRP cc_start: 0.8418 (t-100) cc_final: 0.7528 (t-100) REVERT: A 284 TYR cc_start: 0.7589 (t80) cc_final: 0.6919 (t80) REVERT: A 289 SER cc_start: 0.6752 (t) cc_final: 0.6400 (t) REVERT: A 301 LEU cc_start: 0.8418 (mm) cc_final: 0.8164 (mm) REVERT: C 11 LYS cc_start: 0.8528 (tptt) cc_final: 0.8267 (tppt) REVERT: C 25 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.7803 (mmm160) REVERT: C 150 VAL cc_start: 0.7459 (OUTLIER) cc_final: 0.6994 (p) REVERT: C 160 LYS cc_start: 0.8008 (tppt) cc_final: 0.7699 (tppt) REVERT: C 170 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7376 (tttp) REVERT: C 186 THR cc_start: 0.8211 (m) cc_final: 0.7598 (p) REVERT: C 245 ASN cc_start: 0.6738 (OUTLIER) cc_final: 0.6339 (m-40) REVERT: C 270 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7837 (pptt) REVERT: C 272 TYR cc_start: 0.7833 (m-10) cc_final: 0.7603 (m-10) REVERT: C 320 SER cc_start: 0.8666 (t) cc_final: 0.8281 (m) REVERT: C 322 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7617 (mtmt) REVERT: H 56 SER cc_start: 0.8810 (m) cc_final: 0.8339 (p) REVERT: H 61 THR cc_start: 0.8613 (m) cc_final: 0.8332 (t) REVERT: H 84 LEU cc_start: 0.7187 (tp) cc_final: 0.6895 (tp) REVERT: H 175 TYR cc_start: 0.7197 (m-80) cc_final: 0.6605 (m-80) REVERT: H 200 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8100 (tmm160) REVERT: H 237 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7465 (m-10) outliers start: 53 outliers final: 37 residues processed: 244 average time/residue: 0.0699 time to fit residues: 22.8817 Evaluate side-chains 270 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 237 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.104728 restraints weight = 12351.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108327 restraints weight = 6856.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.110770 restraints weight = 4466.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112402 restraints weight = 3270.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113527 restraints weight = 2614.602| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6281 Z= 0.197 Angle : 0.698 10.624 8640 Z= 0.349 Chirality : 0.045 0.173 1048 Planarity : 0.004 0.059 1075 Dihedral : 8.546 172.676 955 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.42 % Favored : 92.34 % Rotamer: Outliers : 9.83 % Allowed : 38.03 % Favored : 52.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.29), residues: 852 helix: 0.33 (0.36), residues: 220 sheet: -0.52 (0.35), residues: 248 loop : -1.67 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 139 TYR 0.026 0.002 TYR C 208 PHE 0.014 0.002 PHE C 27 TRP 0.032 0.003 TRP A 192 HIS 0.002 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 6278) covalent geometry : angle 0.69700 ( 8634) SS BOND : bond 0.00530 ( 3) SS BOND : angle 1.84567 ( 6) hydrogen bonds : bond 0.03960 ( 270) hydrogen bonds : angle 4.85888 ( 801) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: A 72 HIS cc_start: 0.6014 (OUTLIER) cc_final: 0.5517 (p-80) REVERT: A 73 HIS cc_start: 0.6519 (OUTLIER) cc_final: 0.6138 (m-70) REVERT: A 122 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8273 (t) REVERT: A 129 MET cc_start: 0.7711 (tpt) cc_final: 0.7471 (tpt) REVERT: A 134 CYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7018 (t) REVERT: A 135 ILE cc_start: 0.7858 (tt) cc_final: 0.7424 (pt) REVERT: A 278 TRP cc_start: 0.8438 (t-100) cc_final: 0.7529 (t-100) REVERT: A 284 TYR cc_start: 0.7665 (t80) cc_final: 0.7152 (t80) REVERT: A 289 SER cc_start: 0.6832 (t) cc_final: 0.6513 (t) REVERT: A 301 LEU cc_start: 0.8432 (mm) cc_final: 0.8183 (mm) REVERT: C 25 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.7824 (mmm160) REVERT: C 150 VAL cc_start: 0.7558 (OUTLIER) cc_final: 0.7089 (p) REVERT: C 170 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7420 (tttp) REVERT: C 186 THR cc_start: 0.8219 (m) cc_final: 0.7602 (p) REVERT: C 270 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7925 (pptt) REVERT: C 272 TYR cc_start: 0.7976 (m-10) cc_final: 0.7756 (m-10) REVERT: C 295 HIS cc_start: 0.8037 (m-70) cc_final: 0.7705 (m-70) REVERT: C 320 SER cc_start: 0.8654 (t) cc_final: 0.8258 (m) REVERT: C 322 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7628 (mtmt) REVERT: C 323 VAL cc_start: 0.7266 (OUTLIER) cc_final: 0.6701 (t) REVERT: H 56 SER cc_start: 0.8855 (m) cc_final: 0.8443 (p) REVERT: H 61 THR cc_start: 0.8579 (m) cc_final: 0.8288 (t) REVERT: H 84 LEU cc_start: 0.7273 (tp) cc_final: 0.6964 (tp) REVERT: H 212 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7831 (pt) REVERT: H 237 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7485 (m-10) outliers start: 53 outliers final: 40 residues processed: 245 average time/residue: 0.0754 time to fit residues: 24.5674 Evaluate side-chains 271 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 237 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 0.0060 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.128916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107681 restraints weight = 12343.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111380 restraints weight = 6858.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113873 restraints weight = 4454.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115476 restraints weight = 3243.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.116613 restraints weight = 2596.153| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6281 Z= 0.130 Angle : 0.673 10.067 8640 Z= 0.331 Chirality : 0.044 0.164 1048 Planarity : 0.004 0.060 1075 Dihedral : 8.573 176.713 955 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.36 % Favored : 93.40 % Rotamer: Outliers : 8.91 % Allowed : 39.15 % Favored : 51.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.30), residues: 852 helix: 0.58 (0.37), residues: 217 sheet: -0.41 (0.36), residues: 241 loop : -1.63 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.024 0.001 TYR C 208 PHE 0.012 0.001 PHE C 27 TRP 0.030 0.002 TRP A 192 HIS 0.002 0.000 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6278) covalent geometry : angle 0.67244 ( 8634) SS BOND : bond 0.00548 ( 3) SS BOND : angle 1.46197 ( 6) hydrogen bonds : bond 0.03657 ( 270) hydrogen bonds : angle 4.67623 ( 801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1228.99 seconds wall clock time: 21 minutes 49.88 seconds (1309.88 seconds total)