Starting phenix.real_space_refine on Sat May 10 20:00:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bkk_44643/05_2025/9bkk_44643_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bkk_44643/05_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_44643/05_2025/9bkk_44643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bkk_44643/05_2025/9bkk_44643.map" model { file = "/net/cci-nas-00/data/ceres_data/9bkk_44643/05_2025/9bkk_44643_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bkk_44643/05_2025/9bkk_44643_neut.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} 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: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'ASN%COO:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 8} 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, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 4.98, per 1000 atoms: 0.73 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: 1.92 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.71 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: 2.06 Time building geometry restraints manager: 2.21 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.410 Find NCS groups from input model: 0.060 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:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- 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 : 6.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.134 0.019 TRP A 277 HIS 0.016 0.004 HIS B 225 PHE 0.052 0.008 PHE B 278 TYR 0.086 0.012 TYR R 176 ARG 0.007 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.20191 ( 400) hydrogen bonds : angle 8.38829 ( 1152) SS BOND : bond 0.01739 ( 1) SS BOND : angle 3.11046 ( 2) covalent geometry : bond 0.01217 ( 6945) covalent geometry : angle 1.75397 ( 9440) 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 : 0.801 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: 1.1144 time to fit residues: 231.1795 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 : 0.709 ------------------------------------------------------------------------------- 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 72 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 B 259 GLN G 18 GLN 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 = 0.4490 r_free = 0.4490 target = 0.204932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.160197 restraints weight = 7046.173| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.12 r_work: 0.3909 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6947 Z= 0.183 Angle : 0.703 10.703 9442 Z= 0.373 Chirality : 0.047 0.166 1112 Planarity : 0.005 0.068 1183 Dihedral : 6.433 72.795 957 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.94 % Allowed : 14.08 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 868 helix: 1.18 (0.26), residues: 388 sheet: 0.25 (0.38), residues: 186 loop : -0.87 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 169 HIS 0.007 0.003 HIS A 220 PHE 0.019 0.002 PHE B 292 TYR 0.022 0.002 TYR R 176 ARG 0.007 0.001 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 400) hydrogen bonds : angle 5.16577 ( 1152) SS BOND : bond 0.00671 ( 1) SS BOND : angle 2.60739 ( 2) covalent geometry : bond 0.00397 ( 6945) covalent geometry : angle 0.70203 ( 9440) Misc. bond : bond 0.00091 ( 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 153 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 THR cc_start: 0.7907 (p) cc_final: 0.7673 (t) REVERT: A 211 LYS cc_start: 0.7483 (mtpt) cc_final: 0.7153 (mmtt) REVERT: A 271 ASN cc_start: 0.6025 (m-40) cc_final: 0.5621 (m-40) REVERT: A 274 LYS cc_start: 0.6696 (tttt) cc_final: 0.6337 (ttmp) REVERT: A 280 ARG cc_start: 0.6894 (ttp-110) cc_final: 0.6472 (tmt90) REVERT: A 343 LYS cc_start: 0.7600 (tmtt) cc_final: 0.7359 (tmmt) REVERT: A 371 ASN cc_start: 0.7590 (m-40) cc_final: 0.7285 (m-40) REVERT: A 386 MET cc_start: 0.6933 (ttp) cc_final: 0.6676 (ptp) REVERT: R 45 ILE cc_start: 0.5722 (pt) cc_final: 0.5339 (mt) REVERT: R 69 ASN cc_start: 0.6445 (t0) cc_final: 0.5342 (m-40) REVERT: R 160 LYS cc_start: 0.5682 (mmtp) cc_final: 0.5219 (tmtt) REVERT: R 194 ASN cc_start: 0.6545 (m-40) cc_final: 0.6267 (m-40) REVERT: R 202 ASN cc_start: 0.5549 (p0) cc_final: 0.5099 (p0) outliers start: 28 outliers final: 10 residues processed: 141 average time/residue: 1.1600 time to fit residues: 172.5139 Evaluate side-chains 107 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 B residue 267 ASP 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 359 SER 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 21 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 23 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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 G 18 GLN R 131 ASN R 210 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.206492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.162309 restraints weight = 7138.021| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.11 r_work: 0.3939 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3890 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 : 0.559 8.942 9442 Z= 0.298 Chirality : 0.043 0.259 1112 Planarity : 0.004 0.051 1183 Dihedral : 5.340 68.923 952 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.10 % Allowed : 16.34 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 868 helix: 2.07 (0.26), residues: 384 sheet: 0.23 (0.36), residues: 187 loop : -0.60 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.002 PHE B 241 TYR 0.009 0.001 TYR R 338 ARG 0.004 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 400) hydrogen bonds : angle 4.62914 ( 1152) SS BOND : bond 0.00433 ( 1) SS BOND : angle 2.24749 ( 2) covalent geometry : bond 0.00228 ( 6945) covalent geometry : angle 0.55835 ( 9440) Misc. bond : bond 0.00038 ( 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 139 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7290 (mtpt) cc_final: 0.7087 (mmtt) REVERT: A 271 ASN cc_start: 0.5970 (m-40) cc_final: 0.5510 (m-40) REVERT: A 274 LYS cc_start: 0.6738 (tttt) cc_final: 0.6376 (ttmp) REVERT: A 280 ARG cc_start: 0.6868 (ttp-110) cc_final: 0.6615 (ttp80) REVERT: A 343 LYS cc_start: 0.7721 (tmtt) cc_final: 0.7475 (tmmt) REVERT: A 371 ASN cc_start: 0.7556 (m-40) cc_final: 0.7266 (m-40) REVERT: B 217 MET cc_start: 0.7120 (ptt) cc_final: 0.6763 (pp-130) REVERT: R 45 ILE cc_start: 0.5858 (pt) cc_final: 0.5463 (mt) REVERT: R 160 LYS cc_start: 0.5772 (mmtp) cc_final: 0.5362 (tmtt) REVERT: R 194 ASN cc_start: 0.6279 (m-40) cc_final: 0.6070 (m-40) REVERT: R 235 GLU cc_start: 0.6337 (mm-30) cc_final: 0.5788 (tt0) outliers start: 22 outliers final: 7 residues processed: 128 average time/residue: 1.1458 time to fit residues: 154.6085 Evaluate side-chains 109 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 R residue 114 CYS Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 52 optimal weight: 0.0970 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 0.0870 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.0158 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.202919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.157999 restraints weight = 7172.857| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.13 r_work: 0.3894 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4302 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 : 0.552 6.504 9442 Z= 0.293 Chirality : 0.042 0.134 1112 Planarity : 0.004 0.046 1183 Dihedral : 5.300 69.783 952 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.66 % Allowed : 17.32 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.28), residues: 868 helix: 2.25 (0.26), residues: 380 sheet: 0.17 (0.35), residues: 187 loop : -0.61 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.002 PHE B 151 TYR 0.019 0.001 TYR R 179 ARG 0.005 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 400) hydrogen bonds : angle 4.62135 ( 1152) SS BOND : bond 0.00541 ( 1) SS BOND : angle 2.29469 ( 2) covalent geometry : bond 0.00265 ( 6945) covalent geometry : angle 0.55073 ( 9440) 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 132 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.6333 (mtp180) REVERT: A 271 ASN cc_start: 0.6069 (m-40) cc_final: 0.5456 (m-40) REVERT: A 274 LYS cc_start: 0.6774 (tttt) cc_final: 0.6436 (ttmp) REVERT: A 280 ARG cc_start: 0.6934 (ttp-110) cc_final: 0.6494 (ttt90) REVERT: A 314 GLU cc_start: 0.6297 (mt-10) cc_final: 0.5541 (mp0) REVERT: A 343 LYS cc_start: 0.7878 (tmtt) cc_final: 0.7499 (tmmt) REVERT: A 371 ASN cc_start: 0.7501 (m-40) cc_final: 0.7206 (m-40) REVERT: A 373 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.5721 (mmt-90) REVERT: B 42 ARG cc_start: 0.5094 (mmp-170) cc_final: 0.4833 (mmp-170) REVERT: R 45 ILE cc_start: 0.5914 (pt) cc_final: 0.5546 (mt) REVERT: R 129 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7443 (m) REVERT: R 160 LYS cc_start: 0.5860 (mmtp) cc_final: 0.5488 (tmtt) REVERT: R 194 ASN cc_start: 0.6316 (m-40) cc_final: 0.6094 (m-40) REVERT: R 235 GLU cc_start: 0.6386 (mm-30) cc_final: 0.5909 (tt0) REVERT: R 238 GLN cc_start: 0.6103 (OUTLIER) cc_final: 0.5902 (tt0) REVERT: R 314 MET cc_start: 0.6324 (tpp) cc_final: 0.6114 (tpp) REVERT: R 346 ARG cc_start: 0.6325 (OUTLIER) cc_final: 0.5806 (tpm170) outliers start: 26 outliers final: 9 residues processed: 123 average time/residue: 1.2486 time to fit residues: 161.2493 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 : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 265 ARG 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 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 238 GLN Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 346 ARG 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 40 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 R 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.203098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.158233 restraints weight = 7089.101| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.12 r_work: 0.3899 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4531 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= 0.120 Angle : 0.539 6.119 9442 Z= 0.285 Chirality : 0.042 0.135 1112 Planarity : 0.004 0.042 1183 Dihedral : 5.189 69.111 952 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.38 % Allowed : 18.59 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 868 helix: 2.36 (0.26), residues: 385 sheet: 0.13 (0.35), residues: 188 loop : -0.45 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.010 0.001 HIS A 220 PHE 0.015 0.002 PHE A 219 TYR 0.012 0.001 TYR R 179 ARG 0.005 0.000 ARG R 73 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 400) hydrogen bonds : angle 4.54634 ( 1152) SS BOND : bond 0.00496 ( 1) SS BOND : angle 2.25143 ( 2) covalent geometry : bond 0.00255 ( 6945) covalent geometry : angle 0.53757 ( 9440) Misc. bond : bond 0.00056 ( 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 128 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 271 ASN cc_start: 0.6029 (m-40) cc_final: 0.5422 (m-40) REVERT: A 274 LYS cc_start: 0.6846 (tttt) cc_final: 0.6479 (ttmp) REVERT: A 314 GLU cc_start: 0.6268 (mt-10) cc_final: 0.5608 (mp0) REVERT: A 343 LYS cc_start: 0.7897 (tmtt) cc_final: 0.7534 (tmmt) REVERT: A 371 ASN cc_start: 0.7523 (m-40) cc_final: 0.7218 (m-40) REVERT: A 373 ARG cc_start: 0.6039 (OUTLIER) cc_final: 0.5591 (mmt-90) REVERT: A 381 ASP cc_start: 0.7679 (t0) cc_final: 0.7471 (t70) REVERT: B 19 ARG cc_start: 0.8097 (mmm160) cc_final: 0.7700 (mtp-110) REVERT: B 42 ARG cc_start: 0.5040 (mmp-170) cc_final: 0.4735 (mmp-170) REVERT: R 45 ILE cc_start: 0.5860 (pt) cc_final: 0.5498 (mt) REVERT: R 160 LYS cc_start: 0.5911 (mmtp) cc_final: 0.5630 (tmtt) REVERT: R 194 ASN cc_start: 0.6190 (m-40) cc_final: 0.5988 (m-40) REVERT: R 235 GLU cc_start: 0.6321 (mm-30) cc_final: 0.5818 (tt0) REVERT: R 346 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.5734 (tpm170) outliers start: 24 outliers final: 9 residues processed: 120 average time/residue: 1.2986 time to fit residues: 163.3403 Evaluate side-chains 106 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 R residue 172 ILE Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 346 ARG 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 45 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 11 optimal weight: 0.2980 chunk 74 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4478 r_free = 0.4478 target = 0.203024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158044 restraints weight = 7123.431| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.13 r_work: 0.3898 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6947 Z= 0.118 Angle : 0.533 6.370 9442 Z= 0.283 Chirality : 0.041 0.138 1112 Planarity : 0.004 0.040 1183 Dihedral : 5.155 68.169 952 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.82 % Allowed : 19.30 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.28), residues: 868 helix: 2.38 (0.26), residues: 386 sheet: 0.21 (0.35), residues: 188 loop : -0.40 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.019 0.002 PHE A 222 TYR 0.019 0.001 TYR R 179 ARG 0.006 0.000 ARG R 73 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 400) hydrogen bonds : angle 4.45566 ( 1152) SS BOND : bond 0.00962 ( 1) SS BOND : angle 1.43986 ( 2) covalent geometry : bond 0.00245 ( 6945) covalent geometry : angle 0.53220 ( 9440) Misc. bond : bond 0.00049 ( 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 126 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.6101 (m-40) cc_final: 0.5493 (m-40) REVERT: A 274 LYS cc_start: 0.6865 (tttt) cc_final: 0.6532 (ttmp) REVERT: A 314 GLU cc_start: 0.6237 (mt-10) cc_final: 0.5643 (mp0) REVERT: A 343 LYS cc_start: 0.7891 (tmtt) cc_final: 0.7531 (tmmt) REVERT: A 371 ASN cc_start: 0.7489 (m-40) cc_final: 0.7175 (m-40) REVERT: A 373 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5759 (tpp-160) REVERT: B 42 ARG cc_start: 0.4932 (mmp-170) cc_final: 0.4676 (mmp-170) REVERT: B 226 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: G 19 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5871 (mm) REVERT: R 45 ILE cc_start: 0.5748 (pt) cc_final: 0.5435 (mt) REVERT: R 118 THR cc_start: 0.7008 (m) cc_final: 0.6800 (m) REVERT: R 129 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7348 (m) REVERT: R 160 LYS cc_start: 0.6006 (mmtp) cc_final: 0.5735 (tmtt) REVERT: R 194 ASN cc_start: 0.6178 (m-40) cc_final: 0.5960 (m-40) REVERT: R 223 VAL cc_start: 0.6743 (t) cc_final: 0.6525 (t) REVERT: R 235 GLU cc_start: 0.6429 (mm-30) cc_final: 0.5927 (tt0) REVERT: R 338 TYR cc_start: 0.6998 (m-80) cc_final: 0.6652 (m-80) REVERT: R 346 ARG cc_start: 0.6327 (OUTLIER) cc_final: 0.5764 (tpm170) outliers start: 20 outliers final: 7 residues processed: 119 average time/residue: 1.3289 time to fit residues: 166.6278 Evaluate side-chains 118 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 43 ILE 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 G residue 19 LEU Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 346 ARG 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 52 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 57 optimal weight: 0.0770 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.204763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.160194 restraints weight = 7129.064| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.12 r_work: 0.3921 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6947 Z= 0.109 Angle : 0.537 7.134 9442 Z= 0.284 Chirality : 0.041 0.140 1112 Planarity : 0.004 0.035 1183 Dihedral : 4.999 64.848 952 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.54 % Allowed : 19.30 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.29), residues: 868 helix: 2.52 (0.26), residues: 386 sheet: 0.24 (0.35), residues: 188 loop : -0.36 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.019 0.001 PHE A 222 TYR 0.009 0.001 TYR R 338 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 400) hydrogen bonds : angle 4.34079 ( 1152) SS BOND : bond 0.01338 ( 1) SS BOND : angle 1.40921 ( 2) covalent geometry : bond 0.00224 ( 6945) covalent geometry : angle 0.53645 ( 9440) Misc. bond : bond 0.00034 ( 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 128 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7043 (mtm110) cc_final: 0.6831 (ptm160) REVERT: A 43 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6652 (mt) REVERT: A 271 ASN cc_start: 0.6115 (m-40) cc_final: 0.5508 (m-40) REVERT: A 274 LYS cc_start: 0.6841 (tttt) cc_final: 0.6521 (ttmp) REVERT: A 314 GLU cc_start: 0.6156 (mt-10) cc_final: 0.5620 (mp0) REVERT: A 343 LYS cc_start: 0.7925 (tmtt) cc_final: 0.7611 (ttpt) REVERT: A 371 ASN cc_start: 0.7459 (m-40) cc_final: 0.7149 (m-40) REVERT: A 373 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5905 (tpp-160) REVERT: B 19 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7671 (mtp-110) REVERT: B 146 LEU cc_start: 0.7821 (mp) cc_final: 0.7568 (mm) REVERT: B 217 MET cc_start: 0.7078 (ptt) cc_final: 0.5625 (pmt) REVERT: B 226 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6081 (mp0) REVERT: R 45 ILE cc_start: 0.5841 (pt) cc_final: 0.5525 (mt) REVERT: R 160 LYS cc_start: 0.6018 (mmtp) cc_final: 0.5716 (tmtt) REVERT: R 235 GLU cc_start: 0.6372 (mm-30) cc_final: 0.5751 (mt-10) REVERT: R 338 TYR cc_start: 0.6956 (m-80) cc_final: 0.6624 (m-80) REVERT: R 346 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5720 (tpm170) outliers start: 18 outliers final: 7 residues processed: 121 average time/residue: 1.1497 time to fit residues: 146.7492 Evaluate side-chains 112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 B residue 43 ILE 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 R residue 346 ARG 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 53 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** R 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.203091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.158096 restraints weight = 7113.080| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.10 r_work: 0.3903 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6947 Z= 0.123 Angle : 0.556 10.702 9442 Z= 0.291 Chirality : 0.041 0.134 1112 Planarity : 0.004 0.036 1183 Dihedral : 4.454 22.533 951 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.10 % Allowed : 19.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 868 helix: 2.45 (0.26), residues: 385 sheet: 0.25 (0.36), residues: 188 loop : -0.41 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.018 0.002 PHE R 93 TYR 0.010 0.001 TYR R 338 ARG 0.006 0.000 ARG R 73 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 400) hydrogen bonds : angle 4.43745 ( 1152) SS BOND : bond 0.00991 ( 1) SS BOND : angle 1.24584 ( 2) covalent geometry : bond 0.00261 ( 6945) covalent geometry : angle 0.55606 ( 9440) Misc. bond : bond 0.00061 ( 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 123 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6925 (ptm160) REVERT: A 43 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6676 (mt) REVERT: A 271 ASN cc_start: 0.6186 (m-40) cc_final: 0.5577 (m-40) REVERT: A 274 LYS cc_start: 0.6907 (tttt) cc_final: 0.6605 (ttmp) REVERT: A 314 GLU cc_start: 0.6201 (mt-10) cc_final: 0.5653 (mp0) REVERT: A 343 LYS cc_start: 0.8026 (tmtt) cc_final: 0.7720 (ttpt) REVERT: A 371 ASN cc_start: 0.7405 (m-40) cc_final: 0.7082 (m-40) REVERT: A 373 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.5977 (tpp-160) REVERT: B 19 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7666 (mtp-110) REVERT: B 219 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7360 (mmt90) REVERT: B 226 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6143 (mp0) REVERT: G 19 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.5997 (mm) REVERT: R 45 ILE cc_start: 0.5815 (pt) cc_final: 0.5546 (mt) REVERT: R 129 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7382 (m) REVERT: R 160 LYS cc_start: 0.6162 (mmtp) cc_final: 0.5865 (tmtt) REVERT: R 223 VAL cc_start: 0.6847 (t) cc_final: 0.6639 (t) REVERT: R 314 MET cc_start: 0.6306 (tpp) cc_final: 0.6102 (tpp) REVERT: R 338 TYR cc_start: 0.7225 (m-80) cc_final: 0.6921 (m-80) REVERT: R 346 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5731 (tpm170) outliers start: 22 outliers final: 7 residues processed: 117 average time/residue: 1.2242 time to fit residues: 150.6647 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 : 0.756 ------------------------------------------------------------------------------- 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 358 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 43 ILE 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 G residue 19 LEU Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 320 VAL 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 53 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.199060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.153594 restraints weight = 7161.444| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.12 r_work: 0.3848 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6947 Z= 0.185 Angle : 0.646 9.789 9442 Z= 0.336 Chirality : 0.045 0.141 1112 Planarity : 0.004 0.036 1183 Dihedral : 4.883 26.213 951 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.68 % Allowed : 20.42 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.28), residues: 868 helix: 2.02 (0.26), residues: 385 sheet: 0.18 (0.37), residues: 177 loop : -0.67 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.005 0.002 HIS A 220 PHE 0.017 0.002 PHE B 151 TYR 0.014 0.002 TYR R 338 ARG 0.006 0.001 ARG R 73 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 400) hydrogen bonds : angle 4.76077 ( 1152) SS BOND : bond 0.01602 ( 1) SS BOND : angle 2.82404 ( 2) covalent geometry : bond 0.00413 ( 6945) covalent geometry : angle 0.64456 ( 9440) Misc. bond : bond 0.00148 ( 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 115 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7225 (mtm110) cc_final: 0.6982 (ptm160) REVERT: A 43 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6746 (mt) REVERT: A 274 LYS cc_start: 0.6970 (tttt) cc_final: 0.6602 (ttmt) REVERT: A 314 GLU cc_start: 0.6209 (mt-10) cc_final: 0.5970 (mp0) REVERT: A 343 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7736 (ttpt) REVERT: B 19 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7742 (mtp-110) REVERT: B 219 ARG cc_start: 0.7841 (ttm170) cc_final: 0.7439 (mmt90) REVERT: B 226 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: G 19 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6239 (mm) REVERT: R 45 ILE cc_start: 0.5886 (pt) cc_final: 0.5622 (mt) REVERT: R 52 PHE cc_start: 0.5315 (t80) cc_final: 0.4739 (t80) REVERT: R 73 ARG cc_start: 0.7514 (tpp80) cc_final: 0.7309 (tpp80) REVERT: R 129 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7654 (m) REVERT: R 160 LYS cc_start: 0.5996 (mmtp) cc_final: 0.5746 (tmtt) REVERT: R 195 MET cc_start: 0.6350 (ptm) cc_final: 0.6117 (ptt) REVERT: R 338 TYR cc_start: 0.7316 (m-80) cc_final: 0.6922 (m-80) REVERT: R 346 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.5594 (tpm170) outliers start: 19 outliers final: 10 residues processed: 109 average time/residue: 1.2599 time to fit residues: 144.5126 Evaluate side-chains 108 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 B residue 43 ILE 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.0370 chunk 3 optimal weight: 0.0770 chunk 39 optimal weight: 0.0000 chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.3220 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.205335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.161273 restraints weight = 7313.672| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.13 r_work: 0.3941 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6947 Z= 0.103 Angle : 0.548 9.957 9442 Z= 0.284 Chirality : 0.041 0.146 1112 Planarity : 0.004 0.037 1183 Dihedral : 4.333 22.343 951 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.27 % Allowed : 21.97 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 868 helix: 2.52 (0.26), residues: 386 sheet: 0.13 (0.35), residues: 186 loop : -0.44 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.002 0.001 HIS B 142 PHE 0.018 0.001 PHE R 93 TYR 0.008 0.001 TYR R 338 ARG 0.007 0.001 ARG R 73 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 400) hydrogen bonds : angle 4.39117 ( 1152) SS BOND : bond 0.01050 ( 1) SS BOND : angle 2.17948 ( 2) covalent geometry : bond 0.00206 ( 6945) covalent geometry : angle 0.54690 ( 9440) Misc. bond : bond 0.00019 ( 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 112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 271 ASN cc_start: 0.6183 (m-40) cc_final: 0.5620 (m-40) REVERT: A 314 GLU cc_start: 0.6198 (mt-10) cc_final: 0.5993 (mp0) REVERT: A 343 LYS cc_start: 0.7974 (tmtt) cc_final: 0.7709 (ttpt) REVERT: A 371 ASN cc_start: 0.7375 (m-40) cc_final: 0.7053 (m-40) REVERT: A 373 ARG cc_start: 0.6181 (mmp80) cc_final: 0.5915 (tpp-160) REVERT: B 19 ARG cc_start: 0.8078 (mmm160) cc_final: 0.7699 (mtp-110) REVERT: B 146 LEU cc_start: 0.7838 (mp) cc_final: 0.7608 (mm) REVERT: B 219 ARG cc_start: 0.7816 (ttm170) cc_final: 0.7399 (mmt90) REVERT: R 45 ILE cc_start: 0.5813 (pt) cc_final: 0.5573 (mt) REVERT: R 52 PHE cc_start: 0.5224 (t80) cc_final: 0.4607 (t80) REVERT: R 160 LYS cc_start: 0.6084 (mmtp) cc_final: 0.5768 (tmtt) REVERT: R 346 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5580 (tpm170) REVERT: R 376 ARG cc_start: 0.6567 (mtm180) cc_final: 0.5931 (mtm-85) outliers start: 9 outliers final: 3 residues processed: 106 average time/residue: 1.3529 time to fit residues: 150.8066 Evaluate side-chains 102 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 346 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 57 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.203798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.159370 restraints weight = 7260.193| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.12 r_work: 0.3922 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.5564 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= 0.113 Angle : 0.554 9.747 9442 Z= 0.290 Chirality : 0.042 0.226 1112 Planarity : 0.004 0.037 1183 Dihedral : 4.369 22.338 951 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.85 % Allowed : 22.96 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 868 helix: 2.56 (0.26), residues: 385 sheet: 0.06 (0.35), residues: 188 loop : -0.42 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 220 PHE 0.017 0.002 PHE A 222 TYR 0.006 0.001 TYR A 391 ARG 0.005 0.000 ARG R 73 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 400) hydrogen bonds : angle 4.36695 ( 1152) SS BOND : bond 0.01239 ( 1) SS BOND : angle 1.99748 ( 2) covalent geometry : bond 0.00234 ( 6945) covalent geometry : angle 0.55365 ( 9440) Misc. bond : bond 0.00045 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6874.89 seconds wall clock time: 118 minutes 50.08 seconds (7130.08 seconds total)