Starting phenix.real_space_refine on Wed Sep 17 07:47:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bkk_44643/09_2025/9bkk_44643_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bkk_44643/09_2025/9bkk_44643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bkk_44643/09_2025/9bkk_44643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bkk_44643/09_2025/9bkk_44643.map" model { file = "/net/cci-nas-00/data/ceres_data/9bkk_44643/09_2025/9bkk_44643_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bkk_44643/09_2025/9bkk_44643_neut.cif" } resolution = 2.51 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= 0.001 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 4362 2.51 5 N 1156 2.21 5 O 1235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6809 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1599 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 199} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 4, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2497 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'ARG:plan': 8, 'GLN:plan1': 2, 'ASN:plan1': 3, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 407 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2228 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 1.66, per 1000 atoms: 0.24 Number of scatterers: 6809 At special positions: 0 Unit cell: (84.15, 90.1, 126.65, 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 56 16.00 O 1235 8.00 N 1156 7.00 C 4362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 365.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 47.8% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.569A pdb=" N ASN A 29 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.905A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.666A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.742A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 25 removed outlier: 3.531A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 39 through 69 Processing helix chain 'R' and resid 74 through 105 Proline residue: R 96 - end of helix Proline residue: R 101 - end of helix Processing helix chain 'R' and resid 110 through 145 removed outlier: 3.575A pdb=" N VAL R 133 " --> pdb=" O THR R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 152 Processing helix chain 'R' and resid 154 through 173 Processing helix chain 'R' and resid 174 through 179 removed outlier: 3.762A pdb=" N ILE R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 217 Processing helix chain 'R' and resid 218 through 238 removed outlier: 3.828A pdb=" N MET R 225 " --> pdb=" O PRO R 221 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR R 229 " --> pdb=" O MET R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 348 removed outlier: 3.671A pdb=" N MET R 314 " --> pdb=" O ARG R 310 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE R 323 " --> pdb=" O VAL R 319 " (cutoff:3.500A) Proline residue: R 328 - end of helix removed outlier: 8.237A pdb=" N ALA R 341 " --> pdb=" O ALA R 337 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SER R 342 " --> pdb=" O TYR R 338 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 371 removed outlier: 3.877A pdb=" N SER R 353 " --> pdb=" O GLY R 349 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE R 354 " --> pdb=" O THR R 350 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER R 363 " --> pdb=" O SER R 359 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS R 364 " --> pdb=" O TYR R 360 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 385 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.749A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.595A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.598A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.900A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.659A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.521A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.370A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.816A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 183 through 186 400 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1198 1.32 - 1.44: 1778 1.44 - 1.57: 3886 1.57 - 1.69: 1 1.69 - 1.82: 82 Bond restraints: 6945 Sorted by residual: bond pdb=" C MET R 327 " pdb=" O MET R 327 " ideal model delta sigma weight residual 1.241 1.194 0.047 9.80e-03 1.04e+04 2.29e+01 bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.595 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" N VAL B 158 " pdb=" CA VAL B 158 " ideal model delta sigma weight residual 1.459 1.511 -0.052 1.26e-02 6.30e+03 1.69e+01 bond pdb=" N VAL R 183 " pdb=" CA VAL R 183 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.66e+01 bond pdb=" N ILE B 157 " pdb=" CA ILE B 157 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.19e-02 7.06e+03 1.33e+01 ... (remaining 6940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6507 1.71 - 3.43: 2434 3.43 - 5.14: 433 5.14 - 6.85: 58 6.85 - 8.56: 8 Bond angle restraints: 9440 Sorted by residual: angle pdb=" CA ASP A 347 " pdb=" CB ASP A 347 " pdb=" CG ASP A 347 " ideal model delta sigma weight residual 112.60 120.10 -7.50 1.00e+00 1.00e+00 5.63e+01 angle pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " pdb=" CG PHE B 151 " ideal model delta sigma weight residual 113.80 120.73 -6.93 1.00e+00 1.00e+00 4.80e+01 angle pdb=" N LEU B 152 " pdb=" CA LEU B 152 " pdb=" C LEU B 152 " ideal model delta sigma weight residual 113.12 104.89 8.23 1.25e+00 6.40e-01 4.34e+01 angle pdb=" N LYS B 301 " pdb=" CA LYS B 301 " pdb=" C LYS B 301 " ideal model delta sigma weight residual 113.72 105.47 8.25 1.30e+00 5.92e-01 4.03e+01 angle pdb=" CA PHE B 292 " pdb=" CB PHE B 292 " pdb=" CG PHE B 292 " ideal model delta sigma weight residual 113.80 119.76 -5.96 1.00e+00 1.00e+00 3.55e+01 ... (remaining 9435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.83: 3696 13.83 - 27.66: 314 27.66 - 41.48: 66 41.48 - 55.31: 20 55.31 - 69.14: 13 Dihedral angle restraints: 4109 sinusoidal: 1506 harmonic: 2603 Sorted by residual: dihedral pdb=" C ASP A 347 " pdb=" N ASP A 347 " pdb=" CA ASP A 347 " pdb=" CB ASP A 347 " ideal model delta harmonic sigma weight residual -122.60 -137.47 14.87 0 2.50e+00 1.60e-01 3.54e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" C LYS A 293 " pdb=" N LYS A 293 " pdb=" CA LYS A 293 " pdb=" CB LYS A 293 " ideal model delta harmonic sigma weight residual -122.60 -136.92 14.32 0 2.50e+00 1.60e-01 3.28e+01 ... (remaining 4106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 808 0.101 - 0.202: 270 0.202 - 0.303: 24 0.303 - 0.404: 7 0.404 - 0.505: 3 Chirality restraints: 1112 Sorted by residual: chirality pdb=" CA ASP A 347 " pdb=" N ASP A 347 " pdb=" C ASP A 347 " pdb=" CB ASP A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" CB THR B 321 " pdb=" CA THR B 321 " pdb=" OG1 THR B 321 " pdb=" CG2 THR B 321 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.33e+00 chirality pdb=" CA LYS A 293 " pdb=" N LYS A 293 " pdb=" C LYS A 293 " pdb=" CB LYS A 293 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.70e+00 ... (remaining 1109 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 277 " -0.134 2.00e-02 2.50e+03 7.00e-02 1.23e+02 pdb=" CG TRP A 277 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 277 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 277 " 0.069 2.00e-02 2.50e+03 pdb=" NE1 TRP A 277 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP A 277 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP A 277 " 0.102 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 277 " -0.071 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 277 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP A 277 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " -0.093 2.00e-02 2.50e+03 4.97e-02 6.18e+01 pdb=" CG TRP B 332 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " 0.047 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " 0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " 0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " 0.075 2.00e-02 2.50e+03 4.45e-02 4.95e+01 pdb=" CG TRP A 281 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " -0.066 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " -0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " -0.059 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " 0.057 2.00e-02 2.50e+03 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2442 2.89 - 3.39: 6643 3.39 - 3.90: 11499 3.90 - 4.40: 13396 4.40 - 4.90: 22504 Nonbonded interactions: 56484 Sorted by model distance: nonbonded pdb=" O TRP P 5 " pdb=" NH1 ARG R 336 " model vdw 2.388 3.120 nonbonded pdb=" O MET A 25 " pdb=" ND2 ASN A 29 " model vdw 2.430 3.120 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.431 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.456 3.040 nonbonded pdb=" O THR R 74 " pdb=" N ASN R 77 " model vdw 2.470 3.120 ... (remaining 56479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.870 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 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 0.107 6947 Z= 0.791 Angle : 1.754 8.564 9442 Z= 1.211 Chirality : 0.097 0.505 1112 Planarity : 0.012 0.100 1183 Dihedral : 12.285 69.136 2408 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.92 % Allowed : 4.49 % Favored : 94.59 % Rotamer: Outliers : 2.54 % Allowed : 5.07 % Favored : 92.39 % Cbeta Deviations : 0.24 % 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: -1.67 (0.26), residues: 868 helix: -1.29 (0.23), residues: 384 sheet: 1.39 (0.48), residues: 108 loop : -1.57 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.086 0.012 TYR R 176 PHE 0.052 0.008 PHE B 278 TRP 0.134 0.019 TRP A 277 HIS 0.016 0.004 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.01217 ( 6945) covalent geometry : angle 1.75397 ( 9440) SS BOND : bond 0.01739 ( 1) SS BOND : angle 3.11046 ( 2) hydrogen bonds : bond 0.20191 ( 400) hydrogen bonds : angle 8.38829 ( 1152) Misc. bond : bond 0.10741 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.6626 (mtmm) cc_final: 0.6390 (mttt) REVERT: A 211 LYS cc_start: 0.7444 (mtpt) cc_final: 0.6752 (mttt) REVERT: A 280 ARG cc_start: 0.6407 (ttp-110) cc_final: 0.6043 (ttt-90) REVERT: A 338 LYS cc_start: 0.5288 (mtpt) cc_final: 0.5070 (mttt) REVERT: A 371 ASN cc_start: 0.6838 (m-40) cc_final: 0.6278 (m-40) REVERT: A 386 MET cc_start: 0.6013 (ttp) cc_final: 0.5640 (ptp) REVERT: B 59 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: B 277 SER cc_start: 0.7346 (t) cc_final: 0.6991 (m) REVERT: R 69 ASN cc_start: 0.5960 (t0) cc_final: 0.5413 (m-40) REVERT: R 148 GLN cc_start: 0.6204 (mp10) cc_final: 0.5799 (mm-40) REVERT: R 160 LYS cc_start: 0.4549 (mmtp) cc_final: 0.4236 (tmtt) REVERT: R 194 ASN cc_start: 0.6196 (m-40) cc_final: 0.5955 (m-40) REVERT: R 217 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6391 (tt) REVERT: R 225 MET cc_start: 0.7046 (mtp) cc_final: 0.6846 (mtm) REVERT: R 235 GLU cc_start: 0.5738 (mm-30) cc_final: 0.5183 (tt0) REVERT: R 310 ARG cc_start: 0.5341 (ttm-80) cc_final: 0.5069 (ptm-80) REVERT: R 344 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6559 (mt-10) REVERT: R 348 SER cc_start: 0.6946 (t) cc_final: 0.6497 (m) outliers start: 18 outliers final: 2 residues processed: 197 average time/residue: 0.5955 time to fit residues: 122.9821 Evaluate side-chains 125 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain R residue 217 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 267 GLN B 88 ASN G 18 GLN R 131 ASN R 333 ASN R 366 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.213547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.170727 restraints weight = 7335.367| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.10 r_work: 0.4038 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6947 Z= 0.136 Angle : 0.628 9.517 9442 Z= 0.335 Chirality : 0.044 0.157 1112 Planarity : 0.005 0.067 1183 Dihedral : 6.221 66.513 957 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.38 % Allowed : 14.08 % Favored : 82.54 % 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: 0.62 (0.28), residues: 868 helix: 1.46 (0.26), residues: 389 sheet: 0.21 (0.37), residues: 186 loop : -0.82 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 283 TYR 0.010 0.001 TYR R 176 PHE 0.013 0.002 PHE B 151 TRP 0.023 0.002 TRP B 169 HIS 0.008 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6945) covalent geometry : angle 0.62745 ( 9440) SS BOND : bond 0.00520 ( 1) SS BOND : angle 2.29708 ( 2) hydrogen bonds : bond 0.04634 ( 400) hydrogen bonds : angle 4.95268 ( 1152) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 271 ASN cc_start: 0.5882 (m-40) cc_final: 0.5616 (m-40) REVERT: A 274 LYS cc_start: 0.6696 (tttt) cc_final: 0.6343 (ttmp) REVERT: A 280 ARG cc_start: 0.6800 (ttp-110) cc_final: 0.6368 (tmt90) REVERT: A 343 LYS cc_start: 0.7650 (tmtt) cc_final: 0.7450 (tmmt) REVERT: A 371 ASN cc_start: 0.7399 (m-40) cc_final: 0.7128 (m-40) REVERT: B 146 LEU cc_start: 0.7787 (mp) cc_final: 0.7533 (mm) REVERT: R 69 ASN cc_start: 0.6362 (t0) cc_final: 0.5198 (m-40) REVERT: R 160 LYS cc_start: 0.5751 (mmtp) cc_final: 0.5342 (tmtt) REVERT: R 194 ASN cc_start: 0.6503 (m-40) cc_final: 0.6230 (m-40) REVERT: R 202 ASN cc_start: 0.5621 (p0) cc_final: 0.5201 (p0) outliers start: 24 outliers final: 8 residues processed: 149 average time/residue: 0.5810 time to fit residues: 90.9751 Evaluate side-chains 114 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 233 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 350 THR Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN B 259 GLN G 18 GLN R 210 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.204156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.159368 restraints weight = 7117.483| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.12 r_work: 0.3907 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6947 Z= 0.146 Angle : 0.616 9.051 9442 Z= 0.325 Chirality : 0.045 0.222 1112 Planarity : 0.004 0.052 1183 Dihedral : 5.487 68.346 952 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.24 % Allowed : 16.62 % Favored : 80.14 % 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: 1.09 (0.29), residues: 868 helix: 1.93 (0.26), residues: 389 sheet: 0.28 (0.37), residues: 186 loop : -0.57 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 73 TYR 0.020 0.002 TYR B 59 PHE 0.014 0.002 PHE B 292 TRP 0.017 0.002 TRP B 169 HIS 0.005 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6945) covalent geometry : angle 0.61535 ( 9440) SS BOND : bond 0.00551 ( 1) SS BOND : angle 2.34836 ( 2) hydrogen bonds : bond 0.04528 ( 400) hydrogen bonds : angle 4.79041 ( 1152) Misc. bond : bond 0.00067 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.284 Fit side-chains REVERT: A 271 ASN cc_start: 0.6023 (m-40) cc_final: 0.5530 (m-40) REVERT: A 274 LYS cc_start: 0.6776 (tttt) cc_final: 0.6429 (ttmp) REVERT: A 280 ARG cc_start: 0.6939 (ttp-110) cc_final: 0.6684 (ttp80) REVERT: A 343 LYS cc_start: 0.7770 (tmtt) cc_final: 0.7508 (tmmt) REVERT: A 371 ASN cc_start: 0.7569 (m-40) cc_final: 0.7289 (m-40) REVERT: B 226 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: R 45 ILE cc_start: 0.5841 (pt) cc_final: 0.5433 (mt) REVERT: R 160 LYS cc_start: 0.5816 (mmtp) cc_final: 0.5418 (tmtt) REVERT: R 194 ASN cc_start: 0.6337 (m-40) cc_final: 0.6123 (m-40) REVERT: R 233 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6748 (m) REVERT: R 235 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5801 (tt0) outliers start: 23 outliers final: 13 residues processed: 128 average time/residue: 0.6381 time to fit residues: 85.6637 Evaluate side-chains 113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 233 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 350 THR Chi-restraints excluded: chain R residue 361 THR Chi-restraints excluded: chain R residue 362 SER Chi-restraints excluded: chain R residue 384 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 254 ASN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.203468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.158750 restraints weight = 7209.751| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.13 r_work: 0.3904 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6947 Z= 0.126 Angle : 0.554 5.952 9442 Z= 0.295 Chirality : 0.043 0.255 1112 Planarity : 0.004 0.045 1183 Dihedral : 5.312 68.434 952 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.66 % Allowed : 17.04 % Favored : 79.30 % 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: 1.36 (0.29), residues: 868 helix: 2.26 (0.26), residues: 385 sheet: 0.32 (0.36), residues: 186 loop : -0.49 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 73 TYR 0.011 0.001 TYR R 176 PHE 0.013 0.002 PHE B 199 TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6945) covalent geometry : angle 0.55317 ( 9440) SS BOND : bond 0.00504 ( 1) SS BOND : angle 2.30726 ( 2) hydrogen bonds : bond 0.04054 ( 400) hydrogen bonds : angle 4.60189 ( 1152) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.282 Fit side-chains REVERT: A 271 ASN cc_start: 0.6041 (m-40) cc_final: 0.5440 (m-40) REVERT: A 274 LYS cc_start: 0.6802 (tttt) cc_final: 0.6426 (ttmp) REVERT: A 280 ARG cc_start: 0.6944 (ttp-110) cc_final: 0.6620 (ttp80) REVERT: A 314 GLU cc_start: 0.6218 (mt-10) cc_final: 0.5476 (mp0) REVERT: A 343 LYS cc_start: 0.7862 (tmtt) cc_final: 0.7484 (tmmt) REVERT: A 371 ASN cc_start: 0.7490 (m-40) cc_final: 0.7192 (m-40) REVERT: A 373 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.5762 (mmt-90) REVERT: B 226 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6077 (mp0) REVERT: G 19 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5847 (mm) REVERT: R 45 ILE cc_start: 0.5870 (pt) cc_final: 0.5498 (mt) REVERT: R 160 LYS cc_start: 0.5797 (mmtp) cc_final: 0.5439 (tmtt) REVERT: R 194 ASN cc_start: 0.6265 (m-40) cc_final: 0.6044 (m-40) REVERT: R 235 GLU cc_start: 0.6308 (mm-30) cc_final: 0.5815 (tt0) REVERT: R 314 MET cc_start: 0.6322 (tpp) cc_final: 0.6094 (tpp) REVERT: R 346 ARG cc_start: 0.6244 (mmt180) cc_final: 0.5765 (tpm170) outliers start: 26 outliers final: 8 residues processed: 128 average time/residue: 0.6196 time to fit residues: 83.1495 Evaluate side-chains 113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 8 optimal weight: 0.0770 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 254 ASN B 75 GLN R 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.200633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.155321 restraints weight = 7127.132| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.10 r_work: 0.3867 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6947 Z= 0.151 Angle : 0.589 6.966 9442 Z= 0.313 Chirality : 0.043 0.141 1112 Planarity : 0.004 0.043 1183 Dihedral : 5.508 73.083 952 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.08 % Allowed : 18.17 % Favored : 77.75 % 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: 1.21 (0.28), residues: 868 helix: 2.11 (0.26), residues: 386 sheet: 0.26 (0.38), residues: 175 loop : -0.54 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.019 0.002 TYR R 179 PHE 0.015 0.002 PHE A 219 TRP 0.015 0.002 TRP B 169 HIS 0.009 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6945) covalent geometry : angle 0.58774 ( 9440) SS BOND : bond 0.00603 ( 1) SS BOND : angle 2.43137 ( 2) hydrogen bonds : bond 0.04346 ( 400) hydrogen bonds : angle 4.73229 ( 1152) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.292 Fit side-chains REVERT: A 271 ASN cc_start: 0.6237 (m-40) cc_final: 0.5628 (m-40) REVERT: A 274 LYS cc_start: 0.6844 (tttt) cc_final: 0.6498 (ttmp) REVERT: A 343 LYS cc_start: 0.8005 (tmtt) cc_final: 0.7735 (ttpt) REVERT: A 371 ASN cc_start: 0.7455 (m-40) cc_final: 0.7139 (m-40) REVERT: A 373 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5637 (mmt-90) REVERT: B 19 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7656 (mtp-110) REVERT: B 217 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6769 (ppp) REVERT: B 226 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6194 (mp0) REVERT: G 19 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6108 (mm) REVERT: R 45 ILE cc_start: 0.5794 (pt) cc_final: 0.5492 (mt) REVERT: R 129 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7566 (m) REVERT: R 160 LYS cc_start: 0.6001 (mmtp) cc_final: 0.5661 (tmtt) REVERT: R 194 ASN cc_start: 0.6358 (m-40) cc_final: 0.6124 (m-40) REVERT: R 233 SER cc_start: 0.7119 (OUTLIER) cc_final: 0.6775 (m) REVERT: R 235 GLU cc_start: 0.6460 (mm-30) cc_final: 0.6029 (tt0) REVERT: R 338 TYR cc_start: 0.7190 (m-80) cc_final: 0.6851 (m-10) REVERT: R 346 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5772 (tpm170) outliers start: 29 outliers final: 9 residues processed: 124 average time/residue: 0.6573 time to fit residues: 85.3943 Evaluate side-chains 111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 233 SER Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 346 ARG Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 8 optimal weight: 0.0040 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 = 0.4471 r_free = 0.4471 target = 0.201661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.156488 restraints weight = 7145.586| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.10 r_work: 0.3881 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6947 Z= 0.136 Angle : 0.565 6.267 9442 Z= 0.298 Chirality : 0.042 0.136 1112 Planarity : 0.004 0.041 1183 Dihedral : 5.442 73.854 952 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.66 % Allowed : 18.59 % Favored : 77.75 % 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: 1.30 (0.28), residues: 868 helix: 2.24 (0.26), residues: 386 sheet: 0.23 (0.37), residues: 175 loop : -0.52 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 73 TYR 0.018 0.002 TYR R 179 PHE 0.012 0.002 PHE B 151 TRP 0.015 0.002 TRP B 169 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6945) covalent geometry : angle 0.56370 ( 9440) SS BOND : bond 0.00576 ( 1) SS BOND : angle 2.45044 ( 2) hydrogen bonds : bond 0.04076 ( 400) hydrogen bonds : angle 4.61861 ( 1152) Misc. bond : bond 0.00078 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6620 (mt) REVERT: A 265 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.6297 (mtp180) REVERT: A 271 ASN cc_start: 0.6283 (m-40) cc_final: 0.5701 (m-40) REVERT: A 274 LYS cc_start: 0.6835 (tttt) cc_final: 0.6494 (ttmp) REVERT: A 314 GLU cc_start: 0.6289 (mt-10) cc_final: 0.5856 (mp0) REVERT: A 343 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7685 (ttpt) REVERT: A 371 ASN cc_start: 0.7472 (m-40) cc_final: 0.7146 (m-40) REVERT: A 373 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5904 (tpp-160) REVERT: B 217 MET cc_start: 0.7203 (ptt) cc_final: 0.5783 (pmt) REVERT: B 219 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7545 (mmt90) REVERT: B 226 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: G 19 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6217 (mm) REVERT: R 45 ILE cc_start: 0.5820 (pt) cc_final: 0.5556 (mt) REVERT: R 93 PHE cc_start: 0.7073 (m-80) cc_final: 0.6859 (m-10) REVERT: R 129 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7455 (m) REVERT: R 160 LYS cc_start: 0.6004 (mmtp) cc_final: 0.5743 (tmtt) REVERT: R 194 ASN cc_start: 0.6376 (m-40) cc_final: 0.6162 (m-40) REVERT: R 235 GLU cc_start: 0.6577 (mm-30) cc_final: 0.5973 (mt-10) REVERT: R 338 TYR cc_start: 0.7119 (m-80) cc_final: 0.6803 (m-80) REVERT: R 346 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5613 (tpm170) outliers start: 26 outliers final: 11 residues processed: 123 average time/residue: 0.5971 time to fit residues: 77.0550 Evaluate side-chains 117 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 346 ARG Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 0.0170 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 40 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.204126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.159973 restraints weight = 7156.959| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.10 r_work: 0.3921 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6947 Z= 0.107 Angle : 0.523 7.101 9442 Z= 0.276 Chirality : 0.041 0.139 1112 Planarity : 0.004 0.040 1183 Dihedral : 5.180 70.346 952 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.38 % Allowed : 20.28 % Favored : 76.34 % 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 (0.28), residues: 868 helix: 2.58 (0.26), residues: 385 sheet: 0.20 (0.35), residues: 179 loop : -0.51 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.022 0.001 TYR B 59 PHE 0.012 0.001 PHE A 212 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 6945) covalent geometry : angle 0.52260 ( 9440) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.89861 ( 2) hydrogen bonds : bond 0.03603 ( 400) hydrogen bonds : angle 4.38134 ( 1152) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6595 (mt) REVERT: A 271 ASN cc_start: 0.6190 (m-40) cc_final: 0.5624 (m-40) REVERT: A 274 LYS cc_start: 0.6863 (tttt) cc_final: 0.6525 (ttmp) REVERT: A 314 GLU cc_start: 0.6267 (mt-10) cc_final: 0.5558 (mp0) REVERT: A 343 LYS cc_start: 0.7970 (tmtt) cc_final: 0.7655 (ttpt) REVERT: A 371 ASN cc_start: 0.7398 (m-40) cc_final: 0.7087 (m-40) REVERT: A 373 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.5881 (tpp-160) REVERT: B 19 ARG cc_start: 0.8077 (mmm160) cc_final: 0.7653 (mtp-110) REVERT: B 59 TYR cc_start: 0.7361 (m-80) cc_final: 0.6836 (m-80) REVERT: B 217 MET cc_start: 0.7122 (ptt) cc_final: 0.5649 (pmt) REVERT: B 219 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7483 (mmt90) REVERT: G 19 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.6082 (mm) REVERT: R 45 ILE cc_start: 0.5847 (pt) cc_final: 0.5600 (mt) REVERT: R 160 LYS cc_start: 0.6106 (mmtp) cc_final: 0.5795 (tmtt) REVERT: R 194 ASN cc_start: 0.6201 (m-40) cc_final: 0.5990 (m-40) REVERT: R 235 GLU cc_start: 0.6472 (mm-30) cc_final: 0.5862 (mt-10) REVERT: R 346 ARG cc_start: 0.6146 (mmt180) cc_final: 0.5621 (tpm170) outliers start: 24 outliers final: 10 residues processed: 124 average time/residue: 0.5669 time to fit residues: 73.9392 Evaluate side-chains 109 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 66 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.0870 chunk 85 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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 = 0.4500 r_free = 0.4500 target = 0.204738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.160597 restraints weight = 7241.796| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.10 r_work: 0.3929 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6947 Z= 0.106 Angle : 0.532 10.742 9442 Z= 0.277 Chirality : 0.040 0.143 1112 Planarity : 0.004 0.038 1183 Dihedral : 5.079 67.243 952 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.24 % Allowed : 20.14 % Favored : 76.62 % 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: 1.64 (0.28), residues: 868 helix: 2.68 (0.26), residues: 384 sheet: 0.24 (0.36), residues: 179 loop : -0.45 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 73 TYR 0.016 0.001 TYR B 59 PHE 0.012 0.001 PHE A 212 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 6945) covalent geometry : angle 0.53193 ( 9440) SS BOND : bond 0.00878 ( 1) SS BOND : angle 0.91835 ( 2) hydrogen bonds : bond 0.03549 ( 400) hydrogen bonds : angle 4.32874 ( 1152) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6602 (mt) REVERT: A 265 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6331 (mtp180) REVERT: A 271 ASN cc_start: 0.6228 (m-40) cc_final: 0.5639 (m-40) REVERT: A 274 LYS cc_start: 0.6926 (tttt) cc_final: 0.6605 (ttmp) REVERT: A 314 GLU cc_start: 0.6290 (mt-10) cc_final: 0.5889 (mp0) REVERT: A 343 LYS cc_start: 0.7991 (tmtt) cc_final: 0.7688 (ttpt) REVERT: A 371 ASN cc_start: 0.7411 (m-40) cc_final: 0.7096 (m-40) REVERT: A 373 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.5983 (tpp-160) REVERT: B 19 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7701 (mtp-110) REVERT: B 59 TYR cc_start: 0.7292 (m-80) cc_final: 0.6735 (m-80) REVERT: B 75 GLN cc_start: 0.7134 (mt0) cc_final: 0.6641 (mt0) REVERT: B 217 MET cc_start: 0.7138 (ptt) cc_final: 0.5763 (pmt) REVERT: G 19 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6075 (mm) REVERT: R 45 ILE cc_start: 0.5817 (pt) cc_final: 0.5596 (mt) REVERT: R 73 ARG cc_start: 0.7503 (tpp80) cc_final: 0.7263 (tpp80) REVERT: R 129 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7244 (m) REVERT: R 160 LYS cc_start: 0.6141 (mmtp) cc_final: 0.5821 (tmtt) REVERT: R 346 ARG cc_start: 0.6135 (OUTLIER) cc_final: 0.5622 (tpm170) outliers start: 23 outliers final: 8 residues processed: 116 average time/residue: 0.5848 time to fit residues: 71.2555 Evaluate side-chains 112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 346 ARG Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 chunk 39 optimal weight: 0.0370 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.0040 overall best weight: 0.8074 ------------------------------------------------------------------------------- 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 = 0.4489 r_free = 0.4489 target = 0.203240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.158623 restraints weight = 7184.194| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.11 r_work: 0.3905 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6947 Z= 0.115 Angle : 0.539 9.803 9442 Z= 0.283 Chirality : 0.041 0.135 1112 Planarity : 0.004 0.039 1183 Dihedral : 5.099 65.938 952 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.96 % Allowed : 21.41 % Favored : 75.63 % 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: 1.59 (0.28), residues: 868 helix: 2.61 (0.26), residues: 385 sheet: 0.22 (0.35), residues: 179 loop : -0.46 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 73 TYR 0.018 0.001 TYR B 59 PHE 0.012 0.001 PHE B 151 TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6945) covalent geometry : angle 0.53881 ( 9440) SS BOND : bond 0.00854 ( 1) SS BOND : angle 1.02965 ( 2) hydrogen bonds : bond 0.03684 ( 400) hydrogen bonds : angle 4.37160 ( 1152) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.256 Fit side-chains REVERT: A 43 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6643 (mt) REVERT: A 265 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.6322 (mtp180) REVERT: A 271 ASN cc_start: 0.6226 (m-40) cc_final: 0.5568 (m-40) REVERT: A 314 GLU cc_start: 0.6274 (mt-10) cc_final: 0.5585 (mp0) REVERT: A 343 LYS cc_start: 0.8001 (tmtt) cc_final: 0.7704 (ttpt) REVERT: A 371 ASN cc_start: 0.7404 (m-40) cc_final: 0.7080 (m-40) REVERT: A 373 ARG cc_start: 0.6262 (OUTLIER) cc_final: 0.5989 (tpp-160) REVERT: B 19 ARG cc_start: 0.8082 (mmm160) cc_final: 0.7683 (mtp-110) REVERT: B 59 TYR cc_start: 0.7312 (m-80) cc_final: 0.7104 (m-80) REVERT: G 19 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6033 (mm) REVERT: R 52 PHE cc_start: 0.5182 (t80) cc_final: 0.4575 (t80) REVERT: R 73 ARG cc_start: 0.7580 (tpp80) cc_final: 0.7367 (tpp80) REVERT: R 93 PHE cc_start: 0.6823 (m-10) cc_final: 0.6571 (m-10) REVERT: R 129 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7319 (m) REVERT: R 148 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7165 (mm-40) REVERT: R 160 LYS cc_start: 0.6187 (mmtp) cc_final: 0.5886 (tmtt) REVERT: R 346 ARG cc_start: 0.6112 (OUTLIER) cc_final: 0.5609 (tpm170) outliers start: 21 outliers final: 7 residues processed: 118 average time/residue: 0.6116 time to fit residues: 75.9422 Evaluate side-chains 111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 148 GLN Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 346 ARG Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.4442 r_free = 0.4442 target = 0.198170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.152513 restraints weight = 7105.227| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.11 r_work: 0.3834 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6947 Z= 0.204 Angle : 0.664 10.204 9442 Z= 0.347 Chirality : 0.045 0.153 1112 Planarity : 0.005 0.038 1183 Dihedral : 5.061 26.735 951 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.68 % Allowed : 21.69 % Favored : 75.63 % 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: 0.98 (0.28), residues: 868 helix: 1.98 (0.25), residues: 386 sheet: 0.01 (0.35), residues: 188 loop : -0.66 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 73 TYR 0.021 0.002 TYR B 59 PHE 0.017 0.002 PHE B 151 TRP 0.013 0.002 TRP B 211 HIS 0.005 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 6945) covalent geometry : angle 0.66350 ( 9440) SS BOND : bond 0.01395 ( 1) SS BOND : angle 1.35239 ( 2) hydrogen bonds : bond 0.04783 ( 400) hydrogen bonds : angle 4.79909 ( 1152) Misc. bond : bond 0.00158 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.294 Fit side-chains REVERT: A 265 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6347 (mtp180) REVERT: A 314 GLU cc_start: 0.6287 (mt-10) cc_final: 0.5631 (mp0) REVERT: A 343 LYS cc_start: 0.8024 (tmtt) cc_final: 0.7541 (ttpt) REVERT: A 371 ASN cc_start: 0.7525 (m-40) cc_final: 0.7175 (m-40) REVERT: B 19 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7647 (mtp-110) REVERT: B 59 TYR cc_start: 0.7339 (m-80) cc_final: 0.7115 (m-80) REVERT: B 294 CYS cc_start: 0.7886 (OUTLIER) cc_final: 0.6801 (m) REVERT: G 19 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6230 (mm) REVERT: R 52 PHE cc_start: 0.5466 (t80) cc_final: 0.4924 (t80) REVERT: R 73 ARG cc_start: 0.7555 (tpp80) cc_final: 0.7349 (tpp80) REVERT: R 93 PHE cc_start: 0.6886 (m-10) cc_final: 0.6675 (m-10) REVERT: R 160 LYS cc_start: 0.6029 (mmtp) cc_final: 0.5787 (tmtt) REVERT: R 205 MET cc_start: 0.5283 (ptp) cc_final: 0.4522 (ppp) REVERT: R 346 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5606 (tpm170) outliers start: 19 outliers final: 8 residues processed: 112 average time/residue: 0.6274 time to fit residues: 73.7558 Evaluate side-chains 106 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 346 ARG Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 0.0370 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.202223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.157789 restraints weight = 7169.479| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.09 r_work: 0.3898 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6947 Z= 0.117 Angle : 0.555 9.891 9442 Z= 0.290 Chirality : 0.041 0.137 1112 Planarity : 0.004 0.039 1183 Dihedral : 4.608 23.161 951 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.55 % Allowed : 22.82 % Favored : 75.63 % 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: 1.33 (0.28), residues: 868 helix: 2.39 (0.26), residues: 384 sheet: 0.07 (0.35), residues: 186 loop : -0.58 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 73 TYR 0.013 0.001 TYR B 59 PHE 0.011 0.001 PHE B 253 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6945) covalent geometry : angle 0.55538 ( 9440) SS BOND : bond 0.00972 ( 1) SS BOND : angle 0.43091 ( 2) hydrogen bonds : bond 0.03788 ( 400) hydrogen bonds : angle 4.46998 ( 1152) Misc. bond : bond 0.00051 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3749.53 seconds wall clock time: 64 minutes 23.41 seconds (3863.41 seconds total)