Starting phenix.real_space_refine on Fri Aug 22 18:48:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gdc_29946/08_2025/8gdc_29946_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gdc_29946/08_2025/8gdc_29946.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gdc_29946/08_2025/8gdc_29946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gdc_29946/08_2025/8gdc_29946.map" model { file = "/net/cci-nas-00/data/ceres_data/8gdc_29946/08_2025/8gdc_29946_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gdc_29946/08_2025/8gdc_29946_neut.cif" } 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1646 atoms to isotropic. 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 40 5.16 5 C 3631 2.51 5 N 966 2.21 5 O 1020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5657 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1457 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 2, 'TRANS': 204} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 9, 'ARG:plan': 5, 'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2174 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 304} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 5, 'ASP:plan': 14, 'ARG:plan': 10, 'GLU:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 145 Chain: "C" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 213 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 1788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 258, 1781 Classifications: {'peptide': 258} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 65} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 5, 'TRP:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 83 Conformer: "B" Number of residues, atoms: 258, 1781 Classifications: {'peptide': 258} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 65} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 5, 'TRP:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 83 bond proxies already assigned to first conformer: 1808 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.10, per 1000 atoms: 0.37 Number of scatterers: 5657 At special positions: 0 Unit cell: (84.15, 93.5, 108.8, 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 40 16.00 O 1020 8.00 N 966 7.00 C 3631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 130 " - pdb=" SG CYS R 208 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 420.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 41.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.702A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.420A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 213 through 216 removed outlier: 4.026A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 244 through 255 removed outlier: 3.543A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 332 through 340 Processing helix chain 'A' and resid 341 through 351 removed outlier: 3.651A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 removed outlier: 4.128A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'R' and resid 53 through 76 removed outlier: 4.227A pdb=" N LEU R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET R 70 " --> pdb=" O ASN R 66 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG R 75 " --> pdb=" O LEU R 71 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 105 removed outlier: 4.101A pdb=" N LEU R 95 " --> pdb=" O CYS R 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR R 98 " --> pdb=" O TRP R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 117 removed outlier: 4.054A pdb=" N VAL R 110 " --> pdb=" O THR R 106 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU R 115 " --> pdb=" O ILE R 111 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER R 116 " --> pdb=" O VAL R 112 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS R 117 " --> pdb=" O VAL R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 124 Processing helix chain 'R' and resid 128 through 161 removed outlier: 3.599A pdb=" N LEU R 135 " --> pdb=" O THR R 131 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR R 138 " --> pdb=" O GLY R 134 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER R 144 " --> pdb=" O PHE R 140 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU R 145 " --> pdb=" O GLY R 141 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA R 150 " --> pdb=" O PHE R 146 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE R 159 " --> pdb=" O ARG R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 169 removed outlier: 3.525A pdb=" N SER R 167 " --> pdb=" O HIS R 163 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS R 168 " --> pdb=" O TRP R 164 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET R 169 " --> pdb=" O TYR R 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 163 through 169' Processing helix chain 'R' and resid 180 through 190 removed outlier: 4.378A pdb=" N PHE R 188 " --> pdb=" O ALA R 184 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 262 removed outlier: 4.136A pdb=" N ALA R 241 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU R 242 " --> pdb=" O GLY R 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA R 262 " --> pdb=" O SER R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 284 removed outlier: 3.949A pdb=" N ILE R 276 " --> pdb=" O GLN R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 294 removed outlier: 4.057A pdb=" N SER R 292 " --> pdb=" O MET R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 307 removed outlier: 3.586A pdb=" N MET R 302 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS R 304 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 348 removed outlier: 3.530A pdb=" N ILE R 330 " --> pdb=" O ASN R 326 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL R 332 " --> pdb=" O PHE R 328 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG R 333 " --> pdb=" O LEU R 329 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN R 338 " --> pdb=" O LEU R 334 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Proline residue: R 343 - end of helix removed outlier: 3.796A pdb=" N TYR R 346 " --> pdb=" O ASP R 342 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU R 347 " --> pdb=" O PRO R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 353 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 3.605A pdb=" N LEU A 37 " --> pdb=" O ALA A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 3.600A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 225 removed outlier: 3.550A pdb=" N LEU A 266 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 52 removed outlier: 4.341A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 63 removed outlier: 3.700A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.999A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.827A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 200 through 202 removed outlier: 3.648A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.994A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AB2, first strand: chain 'R' and resid 199 through 201 239 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 919 1.28 - 1.42: 1528 1.42 - 1.55: 3253 1.55 - 1.68: 13 1.68 - 1.82: 54 Bond restraints: 5767 Sorted by residual: bond pdb=" CA ILE R 159 " pdb=" CB ILE R 159 " ideal model delta sigma weight residual 1.540 1.435 0.104 1.29e-02 6.01e+03 6.54e+01 bond pdb=" C PRO R 162 " pdb=" O PRO R 162 " ideal model delta sigma weight residual 1.237 1.152 0.086 1.29e-02 6.01e+03 4.41e+01 bond pdb=" C VAL R 112 " pdb=" O VAL R 112 " ideal model delta sigma weight residual 1.237 1.162 0.074 1.12e-02 7.97e+03 4.41e+01 bond pdb=" C LEU R 347 " pdb=" O LEU R 347 " ideal model delta sigma weight residual 1.236 1.180 0.056 8.80e-03 1.29e+04 4.00e+01 bond pdb=" CA ALA R 150 " pdb=" C ALA R 150 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.29e-02 6.01e+03 3.99e+01 ... (remaining 5762 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 7360 2.65 - 5.29: 405 5.29 - 7.94: 81 7.94 - 10.58: 28 10.58 - 13.23: 7 Bond angle restraints: 7881 Sorted by residual: angle pdb=" C ALA R 161 " pdb=" N PRO R 162 " pdb=" CA PRO R 162 " ideal model delta sigma weight residual 119.32 130.23 -10.91 1.14e+00 7.69e-01 9.15e+01 angle pdb=" N ILE R 147 " pdb=" CA ILE R 147 " pdb=" C ILE R 147 " ideal model delta sigma weight residual 112.96 103.95 9.01 1.00e+00 1.00e+00 8.12e+01 angle pdb=" N SER R 116 " pdb=" CA SER R 116 " pdb=" C SER R 116 " ideal model delta sigma weight residual 111.28 121.04 -9.76 1.09e+00 8.42e-01 8.01e+01 angle pdb=" N HIS R 168 " pdb=" CA HIS R 168 " pdb=" C HIS R 168 " ideal model delta sigma weight residual 112.92 123.81 -10.89 1.23e+00 6.61e-01 7.84e+01 angle pdb=" N ALA R 187 " pdb=" CA ALA R 187 " pdb=" C ALA R 187 " ideal model delta sigma weight residual 112.97 103.65 9.32 1.06e+00 8.90e-01 7.74e+01 ... (remaining 7876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 3028 16.68 - 33.37: 239 33.37 - 50.05: 49 50.05 - 66.74: 5 66.74 - 83.42: 3 Dihedral angle restraints: 3324 sinusoidal: 994 harmonic: 2330 Sorted by residual: dihedral pdb=" C TYR R 114 " pdb=" N TYR R 114 " pdb=" CA TYR R 114 " pdb=" CB TYR R 114 " ideal model delta harmonic sigma weight residual -122.60 -162.91 40.31 0 2.50e+00 1.60e-01 2.60e+02 dihedral pdb=" N TYR R 114 " pdb=" C TYR R 114 " pdb=" CA TYR R 114 " pdb=" CB TYR R 114 " ideal model delta harmonic sigma weight residual 122.80 163.01 -40.21 0 2.50e+00 1.60e-01 2.59e+02 dihedral pdb=" C TYR R 165 " pdb=" N TYR R 165 " pdb=" CA TYR R 165 " pdb=" CB TYR R 165 " ideal model delta harmonic sigma weight residual -122.60 -144.10 21.50 0 2.50e+00 1.60e-01 7.39e+01 ... (remaining 3321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.360: 942 0.360 - 0.719: 12 0.719 - 1.079: 2 1.079 - 1.438: 0 1.438 - 1.798: 1 Chirality restraints: 957 Sorted by residual: chirality pdb=" CA TYR R 114 " pdb=" N TYR R 114 " pdb=" C TYR R 114 " pdb=" CB TYR R 114 " both_signs ideal model delta sigma weight residual False 2.51 0.71 1.80 2.00e-01 2.50e+01 8.08e+01 chirality pdb=" CA ASN R 249 " pdb=" N ASN R 249 " pdb=" C ASN R 249 " pdb=" CB ASN R 249 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA TYR R 165 " pdb=" N TYR R 165 " pdb=" C TYR R 165 " pdb=" CB TYR R 165 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 954 not shown) Planarity restraints: 999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 P2E R 401 " -0.085 2.00e-02 2.50e+03 1.98e-01 3.93e+02 pdb=" C5 P2E R 401 " 0.251 2.00e-02 2.50e+03 pdb=" C6 P2E R 401 " -0.274 2.00e-02 2.50e+03 pdb=" C7 P2E R 401 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 P2E R 401 " 0.168 2.00e-02 2.50e+03 1.76e-01 3.11e+02 pdb=" C13 P2E R 401 " -0.149 2.00e-02 2.50e+03 pdb=" C14 P2E R 401 " -0.202 2.00e-02 2.50e+03 pdb=" C15 P2E R 401 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 238 " -0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C GLY R 238 " 0.085 2.00e-02 2.50e+03 pdb=" O GLY R 238 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU R 239 " -0.029 2.00e-02 2.50e+03 ... (remaining 996 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1707 2.81 - 3.33: 4952 3.33 - 3.86: 8581 3.86 - 4.38: 9420 4.38 - 4.90: 16948 Nonbonded interactions: 41608 Sorted by model distance: nonbonded pdb=" OG SER B 122 " pdb=" OE1 GLU B 138 " model vdw 2.289 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.319 3.040 nonbonded pdb=" O ASN A 269 " pdb=" OG1 THR A 324 " model vdw 2.324 3.040 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.325 3.040 nonbonded pdb=" N LEU R 284 " pdb=" N MET R 285 " model vdw 2.373 2.560 ... (remaining 41603 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 : 0.012 0.104 5768 Z= 0.750 Angle : 1.459 13.227 7883 Z= 0.942 Chirality : 0.122 1.798 957 Planarity : 0.012 0.198 999 Dihedral : 13.132 83.419 1807 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.62 % Allowed : 4.34 % Favored : 95.04 % Cbeta Deviations : 1.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.62 (0.27), residues: 787 helix: -1.68 (0.27), residues: 300 sheet: -2.44 (0.39), residues: 161 loop : -2.97 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 160 TYR 0.040 0.004 TYR R 114 PHE 0.027 0.003 PHE B 234 TRP 0.029 0.003 TRP R 164 HIS 0.011 0.003 HIS R 168 Details of bonding type rmsd covalent geometry : bond 0.01168 ( 5767) covalent geometry : angle 1.45874 ( 7881) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.99831 ( 2) hydrogen bonds : bond 0.18625 ( 239) hydrogen bonds : angle 7.29149 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.265 Fit side-chains REVERT: B 246 ASP cc_start: 0.8607 (t0) cc_final: 0.8346 (t70) REVERT: B 300 LEU cc_start: 0.7936 (tp) cc_final: 0.7720 (tt) outliers start: 3 outliers final: 3 residues processed: 89 average time/residue: 0.0808 time to fit residues: 9.5548 Evaluate side-chains 83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 GLN Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 333 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 103 GLN R 163 HIS A R 338 ASN ** R 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.172415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.150056 restraints weight = 7164.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.154126 restraints weight = 4278.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.156623 restraints weight = 2943.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158882 restraints weight = 2260.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.160013 restraints weight = 1809.663| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4039 r_free = 0.4039 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4039 r_free = 0.4039 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5768 Z= 0.132 Angle : 0.630 9.743 7883 Z= 0.325 Chirality : 0.044 0.244 957 Planarity : 0.004 0.045 999 Dihedral : 6.335 42.873 876 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.65 % Allowed : 9.92 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.29), residues: 787 helix: 0.03 (0.30), residues: 323 sheet: -1.92 (0.41), residues: 149 loop : -2.84 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 155 TYR 0.019 0.002 TYR B 105 PHE 0.013 0.002 PHE A 199 TRP 0.018 0.002 TRP R 207 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5767) covalent geometry : angle 0.62995 ( 7881) SS BOND : bond 0.00257 ( 1) SS BOND : angle 0.83606 ( 2) hydrogen bonds : bond 0.03625 ( 239) hydrogen bonds : angle 4.30345 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.203 Fit side-chains REVERT: A 196 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7434 (p90) REVERT: A 337 ASP cc_start: 0.7578 (t70) cc_final: 0.7321 (m-30) REVERT: B 95 LEU cc_start: 0.6607 (mt) cc_final: 0.6212 (mt) REVERT: B 103 CYS cc_start: 0.6831 (p) cc_final: 0.6460 (m) REVERT: B 246 ASP cc_start: 0.8396 (t0) cc_final: 0.8152 (t70) REVERT: B 300 LEU cc_start: 0.7708 (tp) cc_final: 0.7463 (tt) outliers start: 8 outliers final: 5 residues processed: 88 average time/residue: 0.0764 time to fit residues: 8.9736 Evaluate side-chains 83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 9.9990 chunk 77 optimal weight: 0.0770 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN R 168 HIS R 339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.173662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.148149 restraints weight = 13984.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.153825 restraints weight = 7152.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.156940 restraints weight = 4249.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.158869 restraints weight = 2781.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.160241 restraints weight = 2278.221| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4040 r_free = 0.4040 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4040 r_free = 0.4040 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5768 Z= 0.092 Angle : 0.523 9.227 7883 Z= 0.271 Chirality : 0.041 0.179 957 Planarity : 0.003 0.042 999 Dihedral : 5.047 37.722 869 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.45 % Allowed : 12.19 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.30), residues: 787 helix: 0.75 (0.31), residues: 322 sheet: -1.65 (0.42), residues: 151 loop : -2.60 (0.30), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 155 TYR 0.011 0.001 TYR B 105 PHE 0.010 0.001 PHE B 234 TRP 0.012 0.001 TRP B 63 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 5767) covalent geometry : angle 0.52269 ( 7881) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.55224 ( 2) hydrogen bonds : bond 0.02899 ( 239) hydrogen bonds : angle 3.72555 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.202 Fit side-chains REVERT: B 95 LEU cc_start: 0.6560 (mt) cc_final: 0.6157 (mt) REVERT: B 188 MET cc_start: 0.6670 (tpp) cc_final: 0.5892 (mmt) REVERT: B 300 LEU cc_start: 0.7655 (tp) cc_final: 0.7438 (tt) outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 0.0603 time to fit residues: 6.1940 Evaluate side-chains 70 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.171044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.147883 restraints weight = 9133.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.151980 restraints weight = 5184.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.155317 restraints weight = 3489.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.157298 restraints weight = 2566.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.158726 restraints weight = 2045.366| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5768 Z= 0.147 Angle : 0.571 9.310 7883 Z= 0.298 Chirality : 0.043 0.159 957 Planarity : 0.003 0.040 999 Dihedral : 5.251 40.667 869 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.07 % Allowed : 14.46 % Favored : 83.47 % 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 aren not related in a simple way. whole: -1.43 (0.30), residues: 787 helix: 0.70 (0.30), residues: 335 sheet: -1.55 (0.41), residues: 158 loop : -2.54 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 150 TYR 0.016 0.002 TYR B 105 PHE 0.015 0.002 PHE B 199 TRP 0.013 0.002 TRP B 63 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5767) covalent geometry : angle 0.57127 ( 7881) SS BOND : bond 0.00310 ( 1) SS BOND : angle 0.78019 ( 2) hydrogen bonds : bond 0.03508 ( 239) hydrogen bonds : angle 3.76600 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.203 Fit side-chains REVERT: B 61 MET cc_start: 0.6100 (ppp) cc_final: 0.5594 (ppp) REVERT: B 188 MET cc_start: 0.6819 (tpp) cc_final: 0.6086 (mmt) REVERT: B 300 LEU cc_start: 0.7577 (tp) cc_final: 0.7336 (tt) outliers start: 10 outliers final: 6 residues processed: 76 average time/residue: 0.0560 time to fit residues: 6.2576 Evaluate side-chains 74 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.172519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.150863 restraints weight = 9561.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154879 restraints weight = 5641.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157724 restraints weight = 3818.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.159233 restraints weight = 2864.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.160568 restraints weight = 2339.985| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5768 Z= 0.107 Angle : 0.515 8.813 7883 Z= 0.265 Chirality : 0.041 0.141 957 Planarity : 0.003 0.038 999 Dihedral : 4.927 37.650 869 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.07 % Allowed : 15.70 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.31), residues: 787 helix: 1.15 (0.31), residues: 325 sheet: -1.37 (0.41), residues: 154 loop : -2.36 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 150 TYR 0.010 0.001 TYR B 105 PHE 0.010 0.001 PHE B 234 TRP 0.011 0.001 TRP R 273 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 5767) covalent geometry : angle 0.51492 ( 7881) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.60736 ( 2) hydrogen bonds : bond 0.02859 ( 239) hydrogen bonds : angle 3.56566 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.201 Fit side-chains REVERT: A 196 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.6948 (p90) REVERT: B 188 MET cc_start: 0.6669 (tpp) cc_final: 0.6040 (mmt) REVERT: B 300 LEU cc_start: 0.7446 (tp) cc_final: 0.7223 (tt) REVERT: R 295 TRP cc_start: 0.8041 (m100) cc_final: 0.7676 (m100) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.0631 time to fit residues: 6.5769 Evaluate side-chains 74 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.171143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.148841 restraints weight = 9531.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.151516 restraints weight = 5731.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155470 restraints weight = 4147.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.158797 restraints weight = 2601.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.158991 restraints weight = 2018.706| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5768 Z= 0.145 Angle : 0.551 8.396 7883 Z= 0.282 Chirality : 0.042 0.155 957 Planarity : 0.003 0.039 999 Dihedral : 5.040 37.474 869 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.86 % Allowed : 17.15 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.31), residues: 787 helix: 1.03 (0.31), residues: 330 sheet: -1.45 (0.41), residues: 161 loop : -2.28 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.012 0.001 TYR B 105 PHE 0.013 0.002 PHE B 199 TRP 0.016 0.001 TRP R 273 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5767) covalent geometry : angle 0.55066 ( 7881) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.58781 ( 2) hydrogen bonds : bond 0.03267 ( 239) hydrogen bonds : angle 3.76969 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.187 Fit side-chains REVERT: A 20 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6614 (t0) REVERT: A 196 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.6916 (p90) REVERT: A 337 ASP cc_start: 0.7376 (m-30) cc_final: 0.7145 (m-30) REVERT: B 188 MET cc_start: 0.6673 (tpp) cc_final: 0.6078 (mmt) REVERT: B 300 LEU cc_start: 0.7530 (tp) cc_final: 0.7322 (tt) REVERT: R 295 TRP cc_start: 0.8126 (m100) cc_final: 0.7717 (m100) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 0.0605 time to fit residues: 6.9904 Evaluate side-chains 83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 76 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 0.0670 chunk 75 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.173048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.150183 restraints weight = 11512.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.154586 restraints weight = 6447.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.157463 restraints weight = 4223.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.159758 restraints weight = 3084.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.160908 restraints weight = 2424.576| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5768 Z= 0.095 Angle : 0.509 9.162 7883 Z= 0.257 Chirality : 0.041 0.134 957 Planarity : 0.003 0.038 999 Dihedral : 4.683 35.575 869 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.69 % Allowed : 16.53 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.31), residues: 787 helix: 1.44 (0.31), residues: 323 sheet: -1.40 (0.40), residues: 159 loop : -2.25 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.009 0.001 TYR B 105 PHE 0.010 0.001 PHE B 234 TRP 0.014 0.001 TRP R 273 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 5767) covalent geometry : angle 0.50886 ( 7881) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.65598 ( 2) hydrogen bonds : bond 0.02624 ( 239) hydrogen bonds : angle 3.56852 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.158 Fit side-chains REVERT: A 20 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6546 (t70) REVERT: A 196 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.6965 (p90) REVERT: A 337 ASP cc_start: 0.7198 (m-30) cc_final: 0.6957 (m-30) REVERT: B 61 MET cc_start: 0.6024 (ppp) cc_final: 0.5781 (ppp) REVERT: B 155 ASN cc_start: 0.6559 (OUTLIER) cc_final: 0.6085 (t0) REVERT: B 188 MET cc_start: 0.6339 (tpp) cc_final: 0.5879 (mmt) REVERT: B 300 LEU cc_start: 0.7429 (tp) cc_final: 0.7223 (tt) REVERT: R 295 TRP cc_start: 0.8005 (m100) cc_final: 0.7604 (m100) outliers start: 13 outliers final: 6 residues processed: 82 average time/residue: 0.0609 time to fit residues: 7.1610 Evaluate side-chains 80 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 209 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.0030 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.172430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.149793 restraints weight = 9077.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.154184 restraints weight = 5137.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157195 restraints weight = 3404.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.158853 restraints weight = 2506.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.160539 restraints weight = 2030.408| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5768 Z= 0.108 Angle : 0.524 8.160 7883 Z= 0.265 Chirality : 0.041 0.139 957 Planarity : 0.003 0.040 999 Dihedral : 4.622 35.330 869 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.07 % Allowed : 18.39 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.31), residues: 787 helix: 1.52 (0.31), residues: 323 sheet: -1.34 (0.40), residues: 160 loop : -2.21 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.010 0.001 TYR B 105 PHE 0.009 0.001 PHE B 235 TRP 0.013 0.001 TRP R 273 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 5767) covalent geometry : angle 0.52444 ( 7881) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.59183 ( 2) hydrogen bonds : bond 0.02788 ( 239) hydrogen bonds : angle 3.54009 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.163 Fit side-chains REVERT: A 20 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6564 (t70) REVERT: A 196 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7584 (p90) REVERT: A 337 ASP cc_start: 0.7254 (m-30) cc_final: 0.7010 (m-30) REVERT: B 61 MET cc_start: 0.6095 (ppp) cc_final: 0.5865 (ppp) REVERT: B 155 ASN cc_start: 0.6654 (OUTLIER) cc_final: 0.6115 (t0) REVERT: B 188 MET cc_start: 0.6473 (tpp) cc_final: 0.5907 (mmt) REVERT: R 295 TRP cc_start: 0.8045 (m100) cc_final: 0.7624 (m100) outliers start: 10 outliers final: 5 residues processed: 76 average time/residue: 0.0612 time to fit residues: 6.4923 Evaluate side-chains 79 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 0.7980 chunk 65 optimal weight: 0.0050 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 53 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.173984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.150389 restraints weight = 9134.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.155024 restraints weight = 5040.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.158064 restraints weight = 3295.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.160457 restraints weight = 2408.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.161625 restraints weight = 1886.149| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5768 Z= 0.086 Angle : 0.506 7.985 7883 Z= 0.251 Chirality : 0.040 0.129 957 Planarity : 0.003 0.037 999 Dihedral : 4.421 31.578 869 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.86 % Allowed : 20.04 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.31), residues: 787 helix: 1.74 (0.31), residues: 325 sheet: -1.16 (0.41), residues: 160 loop : -2.08 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 49 TYR 0.007 0.001 TYR B 105 PHE 0.009 0.001 PHE B 278 TRP 0.012 0.001 TRP R 273 HIS 0.002 0.001 HIS R 168 Details of bonding type rmsd covalent geometry : bond 0.00184 ( 5767) covalent geometry : angle 0.50590 ( 7881) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.55144 ( 2) hydrogen bonds : bond 0.02415 ( 239) hydrogen bonds : angle 3.42162 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.226 Fit side-chains REVERT: A 20 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6532 (t0) REVERT: A 196 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.6838 (p90) REVERT: A 337 ASP cc_start: 0.7294 (m-30) cc_final: 0.7061 (m-30) REVERT: B 155 ASN cc_start: 0.6628 (OUTLIER) cc_final: 0.6065 (t0) REVERT: B 188 MET cc_start: 0.6307 (tpp) cc_final: 0.5844 (mmt) REVERT: R 295 TRP cc_start: 0.8036 (m100) cc_final: 0.7658 (m100) outliers start: 9 outliers final: 5 residues processed: 76 average time/residue: 0.0666 time to fit residues: 7.0254 Evaluate side-chains 77 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 14 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.173160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.148766 restraints weight = 9586.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153636 restraints weight = 5229.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.157082 restraints weight = 3380.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.159297 restraints weight = 2442.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.160528 restraints weight = 1914.241| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4044 r_free = 0.4044 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4044 r_free = 0.4044 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5768 Z= 0.104 Angle : 0.533 7.963 7883 Z= 0.264 Chirality : 0.041 0.135 957 Planarity : 0.003 0.037 999 Dihedral : 4.439 31.255 869 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.86 % Allowed : 20.45 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.31), residues: 787 helix: 1.83 (0.31), residues: 323 sheet: -1.16 (0.41), residues: 160 loop : -2.09 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.009 0.001 TYR B 105 PHE 0.011 0.001 PHE B 234 TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 5767) covalent geometry : angle 0.53310 ( 7881) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.58892 ( 2) hydrogen bonds : bond 0.02619 ( 239) hydrogen bonds : angle 3.41740 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.200 Fit side-chains REVERT: A 20 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6559 (t70) REVERT: A 196 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7450 (p90) REVERT: B 155 ASN cc_start: 0.6649 (OUTLIER) cc_final: 0.6016 (t0) REVERT: B 188 MET cc_start: 0.6252 (tpp) cc_final: 0.5842 (mmt) REVERT: R 295 TRP cc_start: 0.8056 (m100) cc_final: 0.7679 (m100) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 0.0562 time to fit residues: 6.2716 Evaluate side-chains 77 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 209 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.173271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.148634 restraints weight = 9462.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153583 restraints weight = 5093.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.156778 restraints weight = 3275.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.159282 restraints weight = 2386.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.160965 restraints weight = 1843.212| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5768 Z= 0.105 Angle : 0.531 7.886 7883 Z= 0.264 Chirality : 0.041 0.136 957 Planarity : 0.003 0.036 999 Dihedral : 4.420 31.320 869 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.07 % Allowed : 20.25 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.31), residues: 787 helix: 1.89 (0.31), residues: 323 sheet: -1.13 (0.41), residues: 160 loop : -2.06 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 49 TYR 0.009 0.001 TYR B 105 PHE 0.010 0.001 PHE B 234 TRP 0.016 0.001 TRP B 339 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 5767) covalent geometry : angle 0.53126 ( 7881) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.63662 ( 2) hydrogen bonds : bond 0.02642 ( 239) hydrogen bonds : angle 3.41269 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1135.94 seconds wall clock time: 20 minutes 8.43 seconds (1208.43 seconds total)