Starting phenix.real_space_refine on Sun Apr 5 08:33:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uan_63986/04_2026/9uan_63986.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uan_63986/04_2026/9uan_63986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uan_63986/04_2026/9uan_63986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uan_63986/04_2026/9uan_63986.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uan_63986/04_2026/9uan_63986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uan_63986/04_2026/9uan_63986.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5748 2.51 5 N 1523 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8962 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2321 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 288, 2315 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 288, 2315 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 2365 Chain: "B" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1819 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2565 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 384 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1776 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'CLR': 1, 'LTD': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS A 220 " occ=0.22 ... (10 atoms not shown) pdb=" SG BCYS A 220 " occ=0.78 Time building chain proxies: 2.44, per 1000 atoms: 0.27 Number of scatterers: 8962 At special positions: 0 Unit cell: (86.355, 123.975, 127.395, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1632 8.00 N 1523 7.00 C 5748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " 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: 0.67 Conformation dependent library (CDL) restraints added in 449.1 milliseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 37.6% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 32 through 64 removed outlier: 3.828A pdb=" N PHE A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 72 through 100 removed outlier: 4.210A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 107 through 142 Processing helix chain 'A' and resid 152 through 174 removed outlier: 3.536A pdb=" N TRP A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 231 removed outlier: 4.192A pdb=" N MET A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 239 through 274 removed outlier: 3.767A pdb=" N ILE A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Proline residue: A 262 - end of helix Processing helix chain 'A' and resid 280 through 306 removed outlier: 4.459A pdb=" N ALA A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 309 through 321 Processing helix chain 'B' and resid 6 through 32 removed outlier: 4.154A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.940A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.840A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 183 through 203 removed outlier: 3.810A pdb=" N THR B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.629A pdb=" N PHE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 242 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 25 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.524A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 29 through 42 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.619A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 31 removed outlier: 3.718A pdb=" N SER E 30 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.686A pdb=" N LYS E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AA2, first strand: chain 'B' and resid 106 through 111 removed outlier: 6.120A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.067A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.389A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 105 removed outlier: 5.838A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.678A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.886A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 232 through 234 removed outlier: 3.747A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG C 251 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS C 250 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 252 " --> pdb=" O MET C 262 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 285 through 286 removed outlier: 4.200A pdb=" N TRP C 297 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.024A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 59 removed outlier: 4.102A pdb=" N TYR E 58 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 96 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 186 through 189 removed outlier: 5.726A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2400 1.33 - 1.46: 2420 1.46 - 1.59: 4250 1.59 - 1.71: 0 1.71 - 1.84: 85 Bond restraints: 9155 Sorted by residual: bond pdb=" CG1 ILE A 225 " pdb=" CD1 ILE A 225 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.42e+00 bond pdb=" CA LYS A 275 " pdb=" CB LYS A 275 " ideal model delta sigma weight residual 1.518 1.540 -0.023 2.08e-02 2.31e+03 1.22e+00 bond pdb=" CB GLN B 146 " pdb=" CG GLN B 146 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" SD MET B 53 " pdb=" CE MET B 53 " ideal model delta sigma weight residual 1.791 1.764 0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" C TRP A 274 " pdb=" N LYS A 275 " ideal model delta sigma weight residual 1.325 1.337 -0.012 1.14e-02 7.69e+03 1.13e+00 ... (remaining 9150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 11986 1.54 - 3.07: 328 3.07 - 4.61: 69 4.61 - 6.14: 22 6.14 - 7.68: 8 Bond angle restraints: 12413 Sorted by residual: angle pdb=" C GLU E 234 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " ideal model delta sigma weight residual 120.06 124.27 -4.21 1.19e+00 7.06e-01 1.25e+01 angle pdb=" N MET B 53 " pdb=" CA MET B 53 " pdb=" CB MET B 53 " ideal model delta sigma weight residual 110.16 115.24 -5.08 1.48e+00 4.57e-01 1.18e+01 angle pdb=" CA GLU E 41 " pdb=" CB GLU E 41 " pdb=" CG GLU E 41 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" C LYS A 275 " pdb=" CA LYS A 275 " pdb=" CB LYS A 275 " ideal model delta sigma weight residual 115.79 111.78 4.01 1.19e+00 7.06e-01 1.13e+01 angle pdb=" CB GLN B 146 " pdb=" CG GLN B 146 " pdb=" CD GLN B 146 " ideal model delta sigma weight residual 112.60 117.57 -4.97 1.70e+00 3.46e-01 8.53e+00 ... (remaining 12408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.89: 5083 19.89 - 39.79: 383 39.79 - 59.68: 46 59.68 - 79.58: 10 79.58 - 99.47: 5 Dihedral angle restraints: 5527 sinusoidal: 2226 harmonic: 3301 Sorted by residual: dihedral pdb=" CB CYS A 31 " pdb=" SG CYS A 31 " pdb=" SG CYS A 279 " pdb=" CB CYS A 279 " ideal model delta sinusoidal sigma weight residual -86.00 -156.80 70.80 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY C 216 " pdb=" C GLY C 216 " pdb=" N MET C 217 " pdb=" CA MET C 217 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 908 0.036 - 0.073: 351 0.073 - 0.109: 122 0.109 - 0.146: 33 0.146 - 0.182: 5 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CBB Y01 A 601 " pdb=" CAC Y01 A 601 " pdb=" CAO Y01 A 601 " pdb=" CBE Y01 A 601 " both_signs ideal model delta sigma weight residual False 2.58 2.39 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA PHE A 41 " pdb=" N PHE A 41 " pdb=" C PHE A 41 " pdb=" CB PHE A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 1416 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO E 236 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 41 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.02e+00 pdb=" N PRO A 42 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 42 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 42 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 212 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO B 213 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " -0.026 5.00e-02 4.00e+02 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.98: 4371 2.98 - 3.46: 8813 3.46 - 3.94: 13626 3.94 - 4.42: 15395 4.42 - 4.90: 26141 Nonbonded interactions: 68346 Sorted by model distance: nonbonded pdb=" O PHE B 192 " pdb=" OE1 GLU B 196 " model vdw 2.495 3.040 nonbonded pdb=" O ASP D 48 " pdb=" OD1 ASP D 48 " model vdw 2.520 3.040 nonbonded pdb=" O ARG D 13 " pdb=" OE1 GLU D 17 " model vdw 2.535 3.040 nonbonded pdb=" O ALA A 294 " pdb=" OD1 ASN A 297 " model vdw 2.536 3.040 nonbonded pdb=" N GLN B 146 " pdb=" OE1 GLN B 146 " model vdw 2.536 3.120 ... (remaining 68341 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=0.22 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: 2.390 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9158 Z= 0.146 Angle : 0.659 7.681 12419 Z= 0.346 Chirality : 0.045 0.182 1419 Planarity : 0.004 0.057 1554 Dihedral : 13.727 99.472 3390 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.11 % Allowed : 0.42 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.25), residues: 1121 helix: 1.42 (0.27), residues: 381 sheet: -0.95 (0.33), residues: 244 loop : -1.78 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 19 TYR 0.024 0.001 TYR A 116 PHE 0.027 0.002 PHE C 234 TRP 0.019 0.002 TRP A 51 HIS 0.010 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9155) covalent geometry : angle 0.65946 (12413) SS BOND : bond 0.00311 ( 3) SS BOND : angle 0.67775 ( 6) hydrogen bonds : bond 0.12238 ( 416) hydrogen bonds : angle 5.26827 ( 1168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.253 Fit side-chains REVERT: A 40 PHE cc_start: 0.5532 (m-80) cc_final: 0.5257 (m-80) REVERT: A 91 LEU cc_start: 0.7666 (tp) cc_final: 0.7237 (mt) REVERT: A 201 MET cc_start: 0.6788 (ppp) cc_final: 0.6564 (ppp) REVERT: B 244 ASN cc_start: 0.8580 (m-40) cc_final: 0.8092 (m-40) REVERT: C 175 GLN cc_start: 0.8409 (pm20) cc_final: 0.8160 (pm20) REVERT: E 64 LYS cc_start: 0.8308 (tppp) cc_final: 0.8062 (tptp) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.0859 time to fit residues: 19.5104 Evaluate side-chains 133 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 57 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.203941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.156992 restraints weight = 20847.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158463 restraints weight = 26780.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.161882 restraints weight = 6980.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.161864 restraints weight = 4789.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.162705 restraints weight = 3995.770| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9158 Z= 0.130 Angle : 0.606 8.924 12419 Z= 0.309 Chirality : 0.044 0.233 1419 Planarity : 0.004 0.054 1554 Dihedral : 7.853 98.236 1403 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.05 % Allowed : 10.08 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.25), residues: 1121 helix: 1.68 (0.27), residues: 378 sheet: -0.90 (0.33), residues: 250 loop : -1.80 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 22 TYR 0.020 0.001 TYR A 116 PHE 0.020 0.001 PHE A 257 TRP 0.014 0.001 TRP A 51 HIS 0.005 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9155) covalent geometry : angle 0.60558 (12413) SS BOND : bond 0.00299 ( 3) SS BOND : angle 0.80722 ( 6) hydrogen bonds : bond 0.04181 ( 416) hydrogen bonds : angle 4.55317 ( 1168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7872 (tp) cc_final: 0.7372 (mt) REVERT: A 211 LEU cc_start: 0.7716 (mm) cc_final: 0.7493 (mm) REVERT: B 244 ASN cc_start: 0.8484 (m-40) cc_final: 0.8068 (m-40) REVERT: C 184 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8366 (m) outliers start: 10 outliers final: 6 residues processed: 161 average time/residue: 0.0988 time to fit residues: 21.7929 Evaluate side-chains 149 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 31 optimal weight: 0.0370 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS C 75 GLN C 88 ASN C 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.185285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144670 restraints weight = 20000.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146036 restraints weight = 29477.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145373 restraints weight = 6989.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148361 restraints weight = 4258.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147399 restraints weight = 2952.897| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9158 Z= 0.274 Angle : 0.734 9.191 12419 Z= 0.384 Chirality : 0.049 0.217 1419 Planarity : 0.005 0.060 1554 Dihedral : 8.201 97.707 1403 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.52 % Allowed : 11.97 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 1121 helix: 1.38 (0.27), residues: 380 sheet: -1.19 (0.32), residues: 262 loop : -1.91 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 15 TYR 0.026 0.002 TYR E 190 PHE 0.018 0.002 PHE B 192 TRP 0.019 0.002 TRP E 46 HIS 0.010 0.002 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00665 ( 9155) covalent geometry : angle 0.73349 (12413) SS BOND : bond 0.00560 ( 3) SS BOND : angle 0.76061 ( 6) hydrogen bonds : bond 0.05161 ( 416) hydrogen bonds : angle 4.80865 ( 1168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7903 (tp) cc_final: 0.7347 (mt) REVERT: A 167 MET cc_start: 0.7359 (mmm) cc_final: 0.7146 (mmp) REVERT: A 248 THR cc_start: 0.8777 (t) cc_final: 0.7219 (p) REVERT: B 80 ASN cc_start: 0.7258 (p0) cc_final: 0.7023 (p0) REVERT: B 244 ASN cc_start: 0.8698 (m-40) cc_final: 0.8475 (m-40) outliers start: 24 outliers final: 13 residues processed: 163 average time/residue: 0.0974 time to fit residues: 21.9190 Evaluate side-chains 148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 30.0000 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS B 57 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.188218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123649 restraints weight = 23262.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128399 restraints weight = 11406.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129560 restraints weight = 7053.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130694 restraints weight = 6501.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131266 restraints weight = 5724.695| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9158 Z= 0.135 Angle : 0.621 13.578 12419 Z= 0.316 Chirality : 0.044 0.234 1419 Planarity : 0.004 0.054 1554 Dihedral : 7.925 96.884 1403 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.10 % Allowed : 15.13 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.25), residues: 1121 helix: 1.62 (0.28), residues: 379 sheet: -1.21 (0.32), residues: 260 loop : -1.84 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.015 0.001 TYR A 305 PHE 0.013 0.001 PHE A 260 TRP 0.012 0.001 TRP C 211 HIS 0.010 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9155) covalent geometry : angle 0.62104 (12413) SS BOND : bond 0.00298 ( 3) SS BOND : angle 0.57078 ( 6) hydrogen bonds : bond 0.04225 ( 416) hydrogen bonds : angle 4.50621 ( 1168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7794 (tp) cc_final: 0.7248 (mt) REVERT: A 273 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8376 (p) REVERT: B 244 ASN cc_start: 0.8610 (m-40) cc_final: 0.8294 (m-40) REVERT: B 245 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8152 (pp) REVERT: E 230 MET cc_start: 0.7865 (ttm) cc_final: 0.7665 (ttm) outliers start: 20 outliers final: 10 residues processed: 159 average time/residue: 0.0981 time to fit residues: 21.5431 Evaluate side-chains 147 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.1980 chunk 78 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS B 209 HIS C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.191957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131869 restraints weight = 16470.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134629 restraints weight = 9155.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136870 restraints weight = 5821.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136795 restraints weight = 4467.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136957 restraints weight = 4484.914| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9158 Z= 0.111 Angle : 0.607 13.270 12419 Z= 0.302 Chirality : 0.043 0.176 1419 Planarity : 0.004 0.055 1554 Dihedral : 7.578 95.644 1403 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.79 % Allowed : 16.49 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.26), residues: 1121 helix: 1.75 (0.28), residues: 384 sheet: -0.93 (0.32), residues: 263 loop : -1.89 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.016 0.001 TYR A 116 PHE 0.010 0.001 PHE A 260 TRP 0.012 0.001 TRP C 211 HIS 0.007 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9155) covalent geometry : angle 0.60657 (12413) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.59358 ( 6) hydrogen bonds : bond 0.03694 ( 416) hydrogen bonds : angle 4.31479 ( 1168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7862 (tp) cc_final: 0.7273 (mt) REVERT: A 167 MET cc_start: 0.8193 (mmp) cc_final: 0.7937 (mmm) REVERT: A 212 LEU cc_start: 0.7953 (tt) cc_final: 0.7570 (mp) REVERT: B 244 ASN cc_start: 0.8566 (m-40) cc_final: 0.8298 (m-40) REVERT: B 245 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7808 (pp) REVERT: E 230 MET cc_start: 0.8061 (ttm) cc_final: 0.7860 (ttm) outliers start: 17 outliers final: 7 residues processed: 165 average time/residue: 0.0976 time to fit residues: 22.1257 Evaluate side-chains 143 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 0.1980 chunk 50 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.189821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127355 restraints weight = 24199.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130339 restraints weight = 10883.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132562 restraints weight = 6940.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133335 restraints weight = 5866.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133646 restraints weight = 5247.545| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9158 Z= 0.131 Angle : 0.616 13.323 12419 Z= 0.312 Chirality : 0.043 0.178 1419 Planarity : 0.004 0.056 1554 Dihedral : 7.253 94.120 1403 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.42 % Allowed : 17.33 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.26), residues: 1121 helix: 1.87 (0.28), residues: 379 sheet: -1.00 (0.31), residues: 275 loop : -1.80 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.016 0.001 TYR A 203 PHE 0.012 0.001 PHE E 79 TRP 0.017 0.001 TRP A 156 HIS 0.009 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9155) covalent geometry : angle 0.61592 (12413) SS BOND : bond 0.00284 ( 3) SS BOND : angle 0.56658 ( 6) hydrogen bonds : bond 0.03866 ( 416) hydrogen bonds : angle 4.30092 ( 1168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7812 (tp) cc_final: 0.7226 (mt) REVERT: A 212 LEU cc_start: 0.8011 (tt) cc_final: 0.7546 (mp) REVERT: B 71 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7152 (mm-30) REVERT: B 245 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7872 (pp) REVERT: C 17 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8295 (tm-30) REVERT: C 188 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6996 (mtm) REVERT: E 230 MET cc_start: 0.8214 (ttm) cc_final: 0.7996 (ttm) outliers start: 23 outliers final: 12 residues processed: 162 average time/residue: 0.0957 time to fit residues: 21.4180 Evaluate side-chains 156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 14 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS B 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.181344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116933 restraints weight = 26739.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121127 restraints weight = 11946.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124359 restraints weight = 7059.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124095 restraints weight = 6534.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124050 restraints weight = 5671.448| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 9158 Z= 0.293 Angle : 0.771 12.859 12419 Z= 0.398 Chirality : 0.051 0.425 1419 Planarity : 0.005 0.057 1554 Dihedral : 7.629 93.480 1403 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.47 % Allowed : 16.70 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.25), residues: 1121 helix: 1.44 (0.27), residues: 378 sheet: -1.35 (0.31), residues: 270 loop : -1.86 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 19 TYR 0.028 0.002 TYR E 190 PHE 0.017 0.002 PHE C 235 TRP 0.019 0.002 TRP A 156 HIS 0.009 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00710 ( 9155) covalent geometry : angle 0.77098 (12413) SS BOND : bond 0.00589 ( 3) SS BOND : angle 0.84506 ( 6) hydrogen bonds : bond 0.05213 ( 416) hydrogen bonds : angle 4.77862 ( 1168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7478 (tp) cc_final: 0.7200 (pp) REVERT: A 91 LEU cc_start: 0.7790 (tp) cc_final: 0.7219 (mt) REVERT: A 212 LEU cc_start: 0.8029 (tt) cc_final: 0.7618 (mp) REVERT: B 80 ASN cc_start: 0.7310 (p0) cc_final: 0.7096 (p0) REVERT: B 244 ASN cc_start: 0.8849 (m-40) cc_final: 0.8445 (m-40) REVERT: C 17 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 59 TYR cc_start: 0.8298 (m-80) cc_final: 0.7871 (m-80) REVERT: C 188 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7214 (mtm) REVERT: E 230 MET cc_start: 0.8356 (ttm) cc_final: 0.8069 (ttm) outliers start: 33 outliers final: 24 residues processed: 156 average time/residue: 0.0951 time to fit residues: 20.6316 Evaluate side-chains 160 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.187043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.137500 restraints weight = 12831.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134884 restraints weight = 11127.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136344 restraints weight = 10019.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137530 restraints weight = 5708.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141543 restraints weight = 4820.491| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9158 Z= 0.139 Angle : 0.676 14.802 12419 Z= 0.335 Chirality : 0.046 0.409 1419 Planarity : 0.004 0.048 1554 Dihedral : 7.125 92.873 1403 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.52 % Allowed : 18.70 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.26), residues: 1121 helix: 1.69 (0.28), residues: 378 sheet: -1.22 (0.31), residues: 278 loop : -1.86 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.015 0.001 TYR E 227 PHE 0.021 0.001 PHE A 260 TRP 0.012 0.001 TRP A 51 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9155) covalent geometry : angle 0.67560 (12413) SS BOND : bond 0.00271 ( 3) SS BOND : angle 0.59190 ( 6) hydrogen bonds : bond 0.04085 ( 416) hydrogen bonds : angle 4.46518 ( 1168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7281 (tp) cc_final: 0.7049 (pp) REVERT: A 212 LEU cc_start: 0.7888 (tt) cc_final: 0.7461 (mp) REVERT: B 244 ASN cc_start: 0.8545 (m-40) cc_final: 0.8253 (m-40) REVERT: B 245 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7836 (pp) REVERT: C 17 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8199 (tm-30) REVERT: C 59 TYR cc_start: 0.8148 (m-80) cc_final: 0.7838 (m-80) REVERT: C 175 GLN cc_start: 0.8537 (pm20) cc_final: 0.8237 (pm20) REVERT: C 188 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6970 (mtm) REVERT: E 230 MET cc_start: 0.8270 (ttm) cc_final: 0.8029 (ttm) outliers start: 24 outliers final: 17 residues processed: 160 average time/residue: 0.1002 time to fit residues: 22.0742 Evaluate side-chains 160 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 30.0000 chunk 98 optimal weight: 0.0670 chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.183979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.140632 restraints weight = 20958.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140745 restraints weight = 28276.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142691 restraints weight = 6819.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145817 restraints weight = 4068.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145604 restraints weight = 2856.637| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9158 Z= 0.195 Angle : 0.721 14.393 12419 Z= 0.360 Chirality : 0.048 0.404 1419 Planarity : 0.004 0.053 1554 Dihedral : 7.202 92.354 1403 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.26 % Allowed : 18.17 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.26), residues: 1121 helix: 1.62 (0.28), residues: 378 sheet: -1.34 (0.32), residues: 268 loop : -1.83 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 19 TYR 0.020 0.002 TYR E 190 PHE 0.019 0.001 PHE A 260 TRP 0.014 0.002 TRP A 156 HIS 0.008 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 9155) covalent geometry : angle 0.72063 (12413) SS BOND : bond 0.00425 ( 3) SS BOND : angle 0.57353 ( 6) hydrogen bonds : bond 0.04441 ( 416) hydrogen bonds : angle 4.53101 ( 1168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7298 (tp) cc_final: 0.7064 (pp) REVERT: A 212 LEU cc_start: 0.7836 (tt) cc_final: 0.7411 (mp) REVERT: B 80 ASN cc_start: 0.7169 (p0) cc_final: 0.6938 (p0) REVERT: B 244 ASN cc_start: 0.8713 (m-40) cc_final: 0.8381 (m-40) REVERT: C 17 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 59 TYR cc_start: 0.8326 (m-80) cc_final: 0.7923 (m-80) REVERT: C 175 GLN cc_start: 0.8533 (pm20) cc_final: 0.8228 (pm20) REVERT: C 188 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7188 (mtm) REVERT: E 230 MET cc_start: 0.8363 (ttm) cc_final: 0.8080 (ttm) outliers start: 31 outliers final: 22 residues processed: 156 average time/residue: 0.0972 time to fit residues: 21.0181 Evaluate side-chains 165 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.187209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121867 restraints weight = 25364.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125529 restraints weight = 11820.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128618 restraints weight = 7596.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130159 restraints weight = 6107.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130304 restraints weight = 5375.590| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9158 Z= 0.138 Angle : 0.696 14.816 12419 Z= 0.341 Chirality : 0.046 0.432 1419 Planarity : 0.004 0.048 1554 Dihedral : 6.974 91.720 1403 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.73 % Allowed : 18.70 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.26), residues: 1121 helix: 1.73 (0.28), residues: 378 sheet: -1.23 (0.31), residues: 278 loop : -1.84 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 19 TYR 0.012 0.001 TYR E 190 PHE 0.019 0.001 PHE A 260 TRP 0.012 0.001 TRP A 156 HIS 0.006 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9155) covalent geometry : angle 0.69574 (12413) SS BOND : bond 0.00274 ( 3) SS BOND : angle 0.51285 ( 6) hydrogen bonds : bond 0.04002 ( 416) hydrogen bonds : angle 4.40685 ( 1168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.7498 (tp) cc_final: 0.7146 (pp) REVERT: A 114 MET cc_start: 0.7573 (mmp) cc_final: 0.7197 (mmp) REVERT: A 212 LEU cc_start: 0.7902 (tt) cc_final: 0.7369 (mp) REVERT: B 244 ASN cc_start: 0.8618 (m-40) cc_final: 0.8284 (m-40) REVERT: B 245 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7827 (pp) REVERT: C 17 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8304 (tm-30) REVERT: C 59 TYR cc_start: 0.8149 (m-80) cc_final: 0.7786 (m-80) REVERT: C 188 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7084 (mtm) REVERT: E 230 MET cc_start: 0.8295 (ttm) cc_final: 0.8008 (ttm) outliers start: 26 outliers final: 19 residues processed: 162 average time/residue: 0.0989 time to fit residues: 21.9745 Evaluate side-chains 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.187177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.119608 restraints weight = 26483.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126291 restraints weight = 11894.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127749 restraints weight = 7475.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129117 restraints weight = 6154.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129896 restraints weight = 5358.695| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 9158 Z= 0.223 Angle : 0.976 59.181 12419 Z= 0.554 Chirality : 0.045 0.431 1419 Planarity : 0.004 0.049 1554 Dihedral : 6.979 91.708 1403 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.42 % Allowed : 19.12 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.26), residues: 1121 helix: 1.74 (0.28), residues: 378 sheet: -1.23 (0.31), residues: 278 loop : -1.83 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.012 0.001 TYR E 190 PHE 0.018 0.001 PHE A 260 TRP 0.011 0.001 TRP A 51 HIS 0.007 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9155) covalent geometry : angle 0.97667 (12413) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.50397 ( 6) hydrogen bonds : bond 0.03999 ( 416) hydrogen bonds : angle 4.40690 ( 1168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.15 seconds wall clock time: 32 minutes 36.07 seconds (1956.07 seconds total)