Starting phenix.real_space_refine on Tue Feb 13 23:56:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9m_31825/02_2024/7v9m_31825.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9m_31825/02_2024/7v9m_31825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9m_31825/02_2024/7v9m_31825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9m_31825/02_2024/7v9m_31825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9m_31825/02_2024/7v9m_31825.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9m_31825/02_2024/7v9m_31825.pdb" } resolution = 3.29 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= 0.022 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 45 5.16 5 C 5167 2.51 5 N 1419 2.21 5 O 1507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R ARG 91": "NH1" <-> "NH2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "R ARG 262": "NH1" <-> "NH2" Residue "R ARG 293": "NH1" <-> "NH2" Residue "R GLU 322": "OE1" <-> "OE2" Residue "Y GLU 22": "OE1" <-> "OE2" Residue "Y GLU 42": "OE1" <-> "OE2" Residue "Y ARG 62": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8138 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1867 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "R" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2125 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Time building chain proxies: 4.63, per 1000 atoms: 0.57 Number of scatterers: 8138 At special positions: 0 Unit cell: (81.12, 98.8, 134.16, 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 45 16.00 O 1507 8.00 N 1419 7.00 C 5167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.4 seconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 43.1% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 removed outlier: 4.464A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.520A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.842A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.628A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 19 Processing helix chain 'R' and resid 56 through 90 removed outlier: 3.715A pdb=" N SER R 60 " --> pdb=" O ALA R 56 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR R 61 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS R 73 " --> pdb=" O TYR R 69 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL R 82 " --> pdb=" O VAL R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 94 Processing helix chain 'R' and resid 95 through 122 Processing helix chain 'R' and resid 135 through 169 Processing helix chain 'R' and resid 174 through 202 removed outlier: 3.654A pdb=" N TRP R 179 " --> pdb=" O ARG R 175 " (cutoff:3.500A) Proline residue: R 189 - end of helix Processing helix chain 'R' and resid 206 through 210 removed outlier: 3.651A pdb=" N ASP R 210 " --> pdb=" O ALA R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 247 removed outlier: 3.901A pdb=" N TRP R 218 " --> pdb=" O THR R 214 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TRP R 219 " --> pdb=" O SER R 215 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE R 221 " --> pdb=" O TYR R 217 " (cutoff:3.500A) Proline residue: R 224 - end of helix Processing helix chain 'R' and resid 259 through 274 removed outlier: 3.951A pdb=" N LEU R 263 " --> pdb=" O GLN R 259 " (cutoff:3.500A) Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 275 through 277 No H-bonds generated for 'chain 'R' and resid 275 through 277' Processing helix chain 'R' and resid 278 through 283 removed outlier: 4.479A pdb=" N PHE R 283 " --> pdb=" O ILE R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 313 Proline residue: R 295 - end of helix removed outlier: 3.677A pdb=" N PHE R 303 " --> pdb=" O GLY R 299 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY R 305 " --> pdb=" O GLY R 301 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 328 Processing helix chain 'Y' and resid 7 through 24 removed outlier: 3.716A pdb=" N GLN Y 11 " --> pdb=" O ALA Y 7 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 45 removed outlier: 3.687A pdb=" N ALA Y 43 " --> pdb=" O ALA Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.916A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.327A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.788A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.768A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.673A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.634A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.500A 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: 6.548A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.942A 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: 3.703A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.576A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1203 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: 2.36 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2664 1.34 - 1.46: 1704 1.46 - 1.58: 3881 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 8309 Sorted by residual: bond pdb=" CG LEU B 190 " pdb=" CD1 LEU B 190 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.53e+00 bond pdb=" CB ILE R 109 " pdb=" CG2 ILE R 109 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.22e+00 bond pdb=" CG LEU R 80 " pdb=" CD2 LEU R 80 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.00e+00 bond pdb=" CB VAL R 65 " pdb=" CG2 VAL R 65 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 9.11e-01 bond pdb=" CB ASN R 232 " pdb=" CG ASN R 232 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.58e-01 ... (remaining 8304 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.64: 175 106.64 - 113.48: 4531 113.48 - 120.33: 3196 120.33 - 127.18: 3256 127.18 - 134.03: 97 Bond angle restraints: 11255 Sorted by residual: angle pdb=" N THR B 87 " pdb=" CA THR B 87 " pdb=" CB THR B 87 " ideal model delta sigma weight residual 113.65 108.87 4.78 1.47e+00 4.63e-01 1.06e+01 angle pdb=" CA TRP A 234 " pdb=" CB TRP A 234 " pdb=" CG TRP A 234 " ideal model delta sigma weight residual 113.60 119.29 -5.69 1.90e+00 2.77e-01 8.96e+00 angle pdb=" C SER N 112 " pdb=" N THR N 113 " pdb=" CA THR N 113 " ideal model delta sigma weight residual 121.54 126.89 -5.35 1.91e+00 2.74e-01 7.84e+00 angle pdb=" N VAL B 187 " pdb=" CA VAL B 187 " pdb=" C VAL B 187 " ideal model delta sigma weight residual 106.21 109.06 -2.85 1.07e+00 8.73e-01 7.07e+00 angle pdb=" C GLY R 185 " pdb=" N TRP R 186 " pdb=" CA TRP R 186 " ideal model delta sigma weight residual 121.64 116.13 5.51 2.13e+00 2.20e-01 6.70e+00 ... (remaining 11250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4549 17.78 - 35.57: 303 35.57 - 53.35: 37 53.35 - 71.14: 14 71.14 - 88.92: 10 Dihedral angle restraints: 4913 sinusoidal: 1928 harmonic: 2985 Sorted by residual: dihedral pdb=" CA GLY B 162 " pdb=" C GLY B 162 " pdb=" N ASP B 163 " pdb=" CA ASP B 163 " ideal model delta harmonic sigma weight residual 180.00 150.52 29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA THR N 114 " pdb=" C THR N 114 " pdb=" N TYR N 115 " pdb=" CA TYR N 115 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 4910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 839 0.042 - 0.083: 326 0.083 - 0.125: 84 0.125 - 0.167: 11 0.167 - 0.208: 3 Chirality restraints: 1263 Sorted by residual: chirality pdb=" CB ILE R 109 " pdb=" CA ILE R 109 " pdb=" CG1 ILE R 109 " pdb=" CG2 ILE R 109 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TRP R 155 " pdb=" N TRP R 155 " pdb=" C TRP R 155 " pdb=" CB TRP R 155 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA TRP A 234 " pdb=" N TRP A 234 " pdb=" C TRP A 234 " pdb=" CB TRP A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1260 not shown) Planarity restraints: 1433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO R 295 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PRO R 295 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO R 295 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU R 296 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 297 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLU R 297 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU R 297 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU R 298 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 67 " 0.062 9.50e-02 1.11e+02 3.66e-02 7.51e+00 pdb=" NE ARG N 67 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG N 67 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG N 67 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG N 67 " -0.013 2.00e-02 2.50e+03 ... (remaining 1430 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 599 2.74 - 3.28: 8493 3.28 - 3.82: 13576 3.82 - 4.36: 16288 4.36 - 4.90: 28315 Nonbonded interactions: 67271 Sorted by model distance: nonbonded pdb=" OG1 THR A 364 " pdb=" OD1 ASN A 371 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR A 55 " pdb=" ND2 ASN A 292 " model vdw 2.205 2.520 nonbonded pdb=" NH2 ARG N 67 " pdb=" OD2 ASP N 90 " model vdw 2.208 2.520 nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.259 2.520 nonbonded pdb=" NH1 ARG B 8 " pdb=" OE1 GLN N 120 " model vdw 2.271 2.520 ... (remaining 67266 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.890 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: 3.790 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.240 Find NCS groups from input model: 0.200 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 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 : 0.004 0.046 8309 Z= 0.272 Angle : 0.655 7.392 11255 Z= 0.386 Chirality : 0.046 0.208 1263 Planarity : 0.006 0.077 1433 Dihedral : 13.185 88.919 2979 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.23 % Allowed : 3.99 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.30 (0.26), residues: 1007 helix: 0.03 (0.24), residues: 387 sheet: 0.64 (0.36), residues: 226 loop : -0.81 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 234 HIS 0.005 0.001 HIS R 124 PHE 0.025 0.002 PHE R 306 TYR 0.028 0.003 TYR R 69 ARG 0.046 0.006 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 228 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7871 (tptp) cc_final: 0.7625 (tptp) REVERT: A 222 PHE cc_start: 0.7204 (m-80) cc_final: 0.6626 (m-80) REVERT: A 233 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7949 (mmmt) REVERT: A 265 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6877 (mtt180) REVERT: A 346 LEU cc_start: 0.8459 (mp) cc_final: 0.8245 (mt) REVERT: A 350 THR cc_start: 0.8534 (m) cc_final: 0.8296 (p) REVERT: A 392 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6839 (mm-30) REVERT: B 57 LYS cc_start: 0.7785 (pttm) cc_final: 0.7224 (pttm) REVERT: B 61 MET cc_start: 0.6441 (ppp) cc_final: 0.6132 (ppp) REVERT: B 95 LEU cc_start: 0.7648 (mt) cc_final: 0.7374 (mt) REVERT: B 118 ASP cc_start: 0.6522 (p0) cc_final: 0.6233 (p0) REVERT: B 119 ASN cc_start: 0.7614 (m-40) cc_final: 0.7371 (m-40) REVERT: B 135 VAL cc_start: 0.8174 (t) cc_final: 0.7889 (m) REVERT: B 137 ARG cc_start: 0.6827 (tpp-160) cc_final: 0.6539 (tpp-160) REVERT: B 187 VAL cc_start: 0.8104 (m) cc_final: 0.7732 (t) REVERT: B 189 SER cc_start: 0.7735 (p) cc_final: 0.7489 (t) REVERT: B 250 CYS cc_start: 0.7647 (m) cc_final: 0.7371 (m) REVERT: B 263 THR cc_start: 0.7836 (m) cc_final: 0.7524 (p) REVERT: B 298 ASP cc_start: 0.7284 (t0) cc_final: 0.6928 (t0) REVERT: B 300 LEU cc_start: 0.8101 (mt) cc_final: 0.7711 (mp) REVERT: B 333 ASP cc_start: 0.6763 (p0) cc_final: 0.6394 (p0) REVERT: N 32 TYR cc_start: 0.7346 (m-80) cc_final: 0.7110 (m-80) REVERT: R 106 THR cc_start: 0.7622 (p) cc_final: 0.7414 (t) REVERT: R 154 SER cc_start: 0.7802 (t) cc_final: 0.7601 (t) REVERT: R 231 VAL cc_start: 0.7613 (m) cc_final: 0.7403 (p) REVERT: R 268 LEU cc_start: 0.8022 (mt) cc_final: 0.7818 (mm) REVERT: R 279 ILE cc_start: 0.8013 (tp) cc_final: 0.7701 (tp) REVERT: R 290 LEU cc_start: 0.7419 (mp) cc_final: 0.7216 (mm) outliers start: 2 outliers final: 1 residues processed: 230 average time/residue: 0.2718 time to fit residues: 78.2276 Evaluate side-chains 199 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.0030 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.2980 overall best weight: 0.3528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8309 Z= 0.187 Angle : 0.577 8.038 11255 Z= 0.314 Chirality : 0.043 0.166 1263 Planarity : 0.004 0.037 1433 Dihedral : 6.083 69.828 1118 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.17 % Allowed : 10.83 % Favored : 87.00 % 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 (0.27), residues: 1007 helix: 1.25 (0.26), residues: 386 sheet: 0.42 (0.35), residues: 224 loop : -0.76 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.006 0.001 HIS B 54 PHE 0.022 0.002 PHE R 306 TYR 0.016 0.002 TYR R 69 ARG 0.004 0.000 ARG P 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7835 (tptp) cc_final: 0.7590 (tptp) REVERT: A 220 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.6235 (t70) REVERT: A 222 PHE cc_start: 0.7150 (m-80) cc_final: 0.6115 (m-80) REVERT: A 230 GLU cc_start: 0.7279 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 265 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6771 (mtt180) REVERT: A 342 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.8028 (ttp-110) REVERT: A 346 LEU cc_start: 0.8379 (mp) cc_final: 0.8124 (mm) REVERT: A 350 THR cc_start: 0.8470 (m) cc_final: 0.8228 (p) REVERT: A 392 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6798 (mm-30) REVERT: B 95 LEU cc_start: 0.7589 (mt) cc_final: 0.7326 (mt) REVERT: B 118 ASP cc_start: 0.6539 (p0) cc_final: 0.6199 (p0) REVERT: B 165 THR cc_start: 0.7866 (p) cc_final: 0.7637 (t) REVERT: B 197 ARG cc_start: 0.6370 (mtp180) cc_final: 0.6021 (mtp180) REVERT: B 219 ARG cc_start: 0.8301 (tpp80) cc_final: 0.7839 (mmt90) REVERT: B 283 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7220 (tpt170) REVERT: B 300 LEU cc_start: 0.8025 (mt) cc_final: 0.7727 (mp) REVERT: B 318 LEU cc_start: 0.7355 (tt) cc_final: 0.7142 (tp) REVERT: B 333 ASP cc_start: 0.6758 (p0) cc_final: 0.6493 (p0) REVERT: R 231 VAL cc_start: 0.7533 (m) cc_final: 0.7318 (p) REVERT: R 279 ILE cc_start: 0.7959 (tp) cc_final: 0.7627 (tp) REVERT: Y 21 MET cc_start: 0.6743 (tpp) cc_final: 0.6527 (tpp) outliers start: 19 outliers final: 12 residues processed: 199 average time/residue: 0.2569 time to fit residues: 65.1024 Evaluate side-chains 204 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 0.0070 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8309 Z= 0.207 Angle : 0.555 7.768 11255 Z= 0.300 Chirality : 0.043 0.175 1263 Planarity : 0.004 0.041 1433 Dihedral : 5.638 61.170 1118 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.62 % Allowed : 15.17 % Favored : 82.21 % 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: 0.48 (0.26), residues: 1007 helix: 1.53 (0.26), residues: 383 sheet: 0.25 (0.34), residues: 225 loop : -0.80 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.004 0.001 HIS B 266 PHE 0.021 0.002 PHE R 306 TYR 0.014 0.001 TYR B 105 ARG 0.008 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 196 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7858 (tptp) cc_final: 0.7586 (tptp) REVERT: A 220 HIS cc_start: 0.6799 (OUTLIER) cc_final: 0.6176 (t70) REVERT: A 222 PHE cc_start: 0.7140 (m-80) cc_final: 0.6236 (m-80) REVERT: A 265 ARG cc_start: 0.7007 (mtt180) cc_final: 0.6786 (mtt180) REVERT: A 346 LEU cc_start: 0.8297 (mp) cc_final: 0.8095 (mm) REVERT: A 350 THR cc_start: 0.8483 (m) cc_final: 0.8254 (p) REVERT: A 392 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6825 (mm-30) REVERT: B 49 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7166 (mtt180) REVERT: B 95 LEU cc_start: 0.7572 (mt) cc_final: 0.7304 (mt) REVERT: B 118 ASP cc_start: 0.6591 (p0) cc_final: 0.6283 (p0) REVERT: B 150 ARG cc_start: 0.7958 (mmt-90) cc_final: 0.7594 (mpt180) REVERT: B 186 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6532 (m-30) REVERT: B 187 VAL cc_start: 0.8200 (m) cc_final: 0.7787 (t) REVERT: B 197 ARG cc_start: 0.6373 (mtp180) cc_final: 0.6060 (mtp180) REVERT: B 219 ARG cc_start: 0.8325 (tpp80) cc_final: 0.7739 (mmt90) REVERT: B 300 LEU cc_start: 0.8016 (mt) cc_final: 0.7634 (mp) REVERT: R 150 MET cc_start: 0.7539 (tpp) cc_final: 0.7306 (mmt) REVERT: R 279 ILE cc_start: 0.7941 (tp) cc_final: 0.7630 (tp) REVERT: R 292 ILE cc_start: 0.7997 (pt) cc_final: 0.7709 (mm) REVERT: Y 21 MET cc_start: 0.6785 (tpp) cc_final: 0.6526 (tpp) outliers start: 23 outliers final: 14 residues processed: 206 average time/residue: 0.2724 time to fit residues: 70.6097 Evaluate side-chains 200 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 25 optimal weight: 0.0770 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN R 124 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8309 Z= 0.182 Angle : 0.518 6.114 11255 Z= 0.281 Chirality : 0.042 0.171 1263 Planarity : 0.004 0.042 1433 Dihedral : 5.202 54.326 1118 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.62 % Allowed : 16.76 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.60 (0.27), residues: 1007 helix: 1.71 (0.26), residues: 388 sheet: 0.15 (0.33), residues: 225 loop : -0.74 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.018 0.002 PHE R 306 TYR 0.014 0.001 TYR N 32 ARG 0.008 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7889 (tptp) cc_final: 0.7579 (tptp) REVERT: A 220 HIS cc_start: 0.6776 (OUTLIER) cc_final: 0.6092 (t70) REVERT: A 222 PHE cc_start: 0.7137 (m-80) cc_final: 0.6243 (m-80) REVERT: A 265 ARG cc_start: 0.7014 (mtt180) cc_final: 0.6770 (mtt180) REVERT: A 350 THR cc_start: 0.8468 (m) cc_final: 0.8257 (p) REVERT: A 392 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6786 (mm-30) REVERT: B 46 ARG cc_start: 0.5797 (mpp-170) cc_final: 0.5164 (mtp180) REVERT: B 49 ARG cc_start: 0.7554 (mtt90) cc_final: 0.7064 (mtt180) REVERT: B 118 ASP cc_start: 0.6581 (p0) cc_final: 0.6217 (p0) REVERT: B 150 ARG cc_start: 0.7966 (mmt-90) cc_final: 0.7645 (mpt180) REVERT: B 186 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6582 (m-30) REVERT: B 197 ARG cc_start: 0.6352 (mtp180) cc_final: 0.6093 (mtp180) REVERT: B 219 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7704 (mmt90) REVERT: B 300 LEU cc_start: 0.7958 (mt) cc_final: 0.7602 (mp) REVERT: R 150 MET cc_start: 0.7424 (tpp) cc_final: 0.7178 (mmt) REVERT: R 279 ILE cc_start: 0.7900 (tp) cc_final: 0.7596 (tp) REVERT: Y 21 MET cc_start: 0.6776 (tpp) cc_final: 0.6494 (tpp) outliers start: 23 outliers final: 19 residues processed: 209 average time/residue: 0.2727 time to fit residues: 71.7010 Evaluate side-chains 212 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8309 Z= 0.352 Angle : 0.589 8.402 11255 Z= 0.317 Chirality : 0.046 0.220 1263 Planarity : 0.004 0.050 1433 Dihedral : 5.298 49.546 1118 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.56 % Allowed : 16.19 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.26), residues: 1007 helix: 1.55 (0.26), residues: 382 sheet: -0.11 (0.33), residues: 219 loop : -0.93 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS Y 44 PHE 0.019 0.002 PHE B 241 TYR 0.016 0.002 TYR B 111 ARG 0.009 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 186 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7877 (tptp) cc_final: 0.7568 (tptp) REVERT: A 220 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.6075 (t70) REVERT: A 222 PHE cc_start: 0.7217 (m-80) cc_final: 0.6228 (m-80) REVERT: A 265 ARG cc_start: 0.7024 (mtt180) cc_final: 0.6813 (mtt180) REVERT: A 392 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6800 (mm-30) REVERT: B 46 ARG cc_start: 0.5920 (mpp-170) cc_final: 0.5422 (mtp180) REVERT: B 84 SER cc_start: 0.7352 (t) cc_final: 0.7124 (t) REVERT: B 95 LEU cc_start: 0.7546 (mt) cc_final: 0.7337 (mt) REVERT: B 118 ASP cc_start: 0.6592 (p0) cc_final: 0.6264 (p0) REVERT: B 186 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6600 (m-30) REVERT: B 197 ARG cc_start: 0.6375 (mtp180) cc_final: 0.5959 (mtp180) REVERT: B 219 ARG cc_start: 0.8344 (tpp80) cc_final: 0.7778 (mmt90) REVERT: B 253 PHE cc_start: 0.8502 (m-80) cc_final: 0.8164 (m-80) REVERT: B 300 LEU cc_start: 0.8027 (mt) cc_final: 0.7691 (mp) REVERT: B 316 SER cc_start: 0.7474 (t) cc_final: 0.7255 (p) REVERT: R 279 ILE cc_start: 0.7897 (tp) cc_final: 0.7578 (tp) REVERT: Y 21 MET cc_start: 0.6788 (tpp) cc_final: 0.6525 (tpp) outliers start: 40 outliers final: 30 residues processed: 206 average time/residue: 0.2858 time to fit residues: 74.4479 Evaluate side-chains 211 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain Y residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8309 Z= 0.201 Angle : 0.548 8.134 11255 Z= 0.294 Chirality : 0.043 0.196 1263 Planarity : 0.004 0.043 1433 Dihedral : 5.004 46.000 1118 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.88 % Allowed : 17.22 % Favored : 78.91 % 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: 0.36 (0.26), residues: 1007 helix: 1.69 (0.26), residues: 384 sheet: -0.15 (0.34), residues: 219 loop : -0.92 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.003 0.001 HIS B 266 PHE 0.016 0.002 PHE R 192 TYR 0.009 0.001 TYR N 32 ARG 0.010 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 180 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7885 (tptp) cc_final: 0.7566 (tptp) REVERT: A 220 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.6064 (t70) REVERT: A 222 PHE cc_start: 0.7195 (m-80) cc_final: 0.6172 (m-80) REVERT: A 233 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7911 (mmmt) REVERT: A 265 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6789 (mtt180) REVERT: A 392 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6764 (mm-30) REVERT: B 46 ARG cc_start: 0.5928 (mpp-170) cc_final: 0.5546 (mtp180) REVERT: B 49 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7233 (mtt180) REVERT: B 118 ASP cc_start: 0.6594 (p0) cc_final: 0.6255 (p0) REVERT: B 150 ARG cc_start: 0.7953 (mmt-90) cc_final: 0.7591 (mpt180) REVERT: B 186 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6515 (m-30) REVERT: B 187 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7762 (t) REVERT: B 197 ARG cc_start: 0.6394 (mtp180) cc_final: 0.6151 (mtp180) REVERT: B 219 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7761 (mmt90) REVERT: B 253 PHE cc_start: 0.8499 (m-80) cc_final: 0.8157 (m-80) REVERT: B 300 LEU cc_start: 0.7977 (mt) cc_final: 0.7643 (mp) REVERT: R 279 ILE cc_start: 0.7906 (tp) cc_final: 0.7606 (tp) REVERT: Y 21 MET cc_start: 0.6788 (tpp) cc_final: 0.6508 (tpp) outliers start: 34 outliers final: 27 residues processed: 196 average time/residue: 0.2746 time to fit residues: 67.8377 Evaluate side-chains 206 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8309 Z= 0.270 Angle : 0.571 8.176 11255 Z= 0.304 Chirality : 0.043 0.201 1263 Planarity : 0.004 0.045 1433 Dihedral : 4.996 43.345 1118 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.22 % Allowed : 17.67 % Favored : 78.11 % 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: 0.35 (0.26), residues: 1007 helix: 1.71 (0.26), residues: 383 sheet: -0.18 (0.34), residues: 219 loop : -0.94 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.004 0.001 HIS R 277 PHE 0.017 0.002 PHE R 306 TYR 0.013 0.002 TYR B 111 ARG 0.011 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7878 (tptp) cc_final: 0.7547 (tptp) REVERT: A 220 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.6049 (t70) REVERT: A 222 PHE cc_start: 0.7208 (m-80) cc_final: 0.6265 (m-80) REVERT: A 233 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7928 (mmmt) REVERT: A 265 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6809 (mtt180) REVERT: A 392 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6761 (mm-30) REVERT: B 46 ARG cc_start: 0.6002 (mpp-170) cc_final: 0.5550 (mtp180) REVERT: B 49 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7173 (mtt180) REVERT: B 118 ASP cc_start: 0.6604 (p0) cc_final: 0.6260 (p0) REVERT: B 150 ARG cc_start: 0.7954 (mmt-90) cc_final: 0.7586 (mpt180) REVERT: B 186 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6594 (m-30) REVERT: B 187 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7679 (t) REVERT: B 197 ARG cc_start: 0.6382 (mtp180) cc_final: 0.6059 (mtp180) REVERT: B 219 ARG cc_start: 0.8323 (tpp80) cc_final: 0.7779 (mmt90) REVERT: B 253 PHE cc_start: 0.8462 (m-80) cc_final: 0.8117 (m-80) REVERT: B 300 LEU cc_start: 0.8022 (mt) cc_final: 0.7691 (mp) REVERT: R 279 ILE cc_start: 0.7913 (tp) cc_final: 0.7628 (tp) REVERT: Y 21 MET cc_start: 0.6808 (tpp) cc_final: 0.6539 (tpp) outliers start: 37 outliers final: 30 residues processed: 203 average time/residue: 0.2739 time to fit residues: 69.6856 Evaluate side-chains 216 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain Y residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 91 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8309 Z= 0.213 Angle : 0.557 8.499 11255 Z= 0.298 Chirality : 0.043 0.200 1263 Planarity : 0.004 0.051 1433 Dihedral : 4.860 41.242 1118 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.22 % Allowed : 18.93 % Favored : 76.85 % 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: 0.43 (0.27), residues: 1007 helix: 1.81 (0.26), residues: 384 sheet: -0.21 (0.33), residues: 219 loop : -0.89 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.003 0.001 HIS B 266 PHE 0.015 0.001 PHE R 306 TYR 0.012 0.001 TYR B 111 ARG 0.012 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7872 (tptp) cc_final: 0.7552 (tptp) REVERT: A 220 HIS cc_start: 0.6721 (OUTLIER) cc_final: 0.6046 (t70) REVERT: A 222 PHE cc_start: 0.7178 (m-80) cc_final: 0.6168 (m-80) REVERT: A 233 LYS cc_start: 0.8146 (mmtm) cc_final: 0.7821 (mmmt) REVERT: A 392 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6770 (mm-30) REVERT: B 49 ARG cc_start: 0.7712 (mtt90) cc_final: 0.7223 (mtt180) REVERT: B 150 ARG cc_start: 0.7951 (mmt-90) cc_final: 0.7597 (mpt180) REVERT: B 186 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: B 187 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7659 (t) REVERT: B 197 ARG cc_start: 0.6374 (mtp180) cc_final: 0.6048 (mtp180) REVERT: B 219 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7774 (mmt90) REVERT: B 253 PHE cc_start: 0.8420 (m-80) cc_final: 0.8117 (m-80) REVERT: B 300 LEU cc_start: 0.7986 (mt) cc_final: 0.7667 (mp) REVERT: R 279 ILE cc_start: 0.7887 (tp) cc_final: 0.7622 (tp) REVERT: Y 21 MET cc_start: 0.6805 (tpp) cc_final: 0.6537 (tpp) outliers start: 37 outliers final: 31 residues processed: 205 average time/residue: 0.2788 time to fit residues: 72.0495 Evaluate side-chains 218 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8309 Z= 0.243 Angle : 0.567 8.158 11255 Z= 0.301 Chirality : 0.043 0.184 1263 Planarity : 0.004 0.056 1433 Dihedral : 4.859 40.205 1118 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.45 % Allowed : 18.93 % 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 (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: 0.33 (0.27), residues: 1007 helix: 1.66 (0.26), residues: 388 sheet: -0.26 (0.34), residues: 219 loop : -0.90 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.004 0.001 HIS B 266 PHE 0.016 0.002 PHE R 306 TYR 0.012 0.001 TYR B 105 ARG 0.013 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7867 (tptp) cc_final: 0.7547 (tptp) REVERT: A 220 HIS cc_start: 0.6720 (OUTLIER) cc_final: 0.6037 (t70) REVERT: A 222 PHE cc_start: 0.7193 (m-80) cc_final: 0.6165 (m-80) REVERT: A 392 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6774 (mm-30) REVERT: B 118 ASP cc_start: 0.6611 (p0) cc_final: 0.6298 (p0) REVERT: B 186 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6587 (m-30) REVERT: B 187 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7659 (t) REVERT: B 197 ARG cc_start: 0.6373 (mtp180) cc_final: 0.6036 (mtp180) REVERT: B 219 ARG cc_start: 0.8326 (tpp80) cc_final: 0.7782 (mmt90) REVERT: B 253 PHE cc_start: 0.8425 (m-80) cc_final: 0.8098 (m-80) REVERT: B 300 LEU cc_start: 0.8040 (mt) cc_final: 0.7740 (mp) REVERT: R 181 LEU cc_start: 0.7902 (tp) cc_final: 0.7685 (tp) REVERT: R 279 ILE cc_start: 0.7907 (tp) cc_final: 0.7630 (tp) REVERT: Y 21 MET cc_start: 0.6813 (tpp) cc_final: 0.6548 (tpp) outliers start: 39 outliers final: 31 residues processed: 202 average time/residue: 0.2690 time to fit residues: 70.2837 Evaluate side-chains 222 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain Y residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 98 optimal weight: 0.5980 chunk 90 optimal weight: 0.3980 chunk 78 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8309 Z= 0.222 Angle : 0.562 8.295 11255 Z= 0.298 Chirality : 0.043 0.219 1263 Planarity : 0.004 0.058 1433 Dihedral : 4.798 39.120 1118 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.22 % Allowed : 19.61 % Favored : 76.17 % 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: 0.37 (0.27), residues: 1007 helix: 1.71 (0.26), residues: 388 sheet: -0.30 (0.33), residues: 228 loop : -0.86 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.004 0.001 HIS B 266 PHE 0.015 0.002 PHE R 306 TYR 0.010 0.001 TYR B 105 ARG 0.014 0.000 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7869 (tptp) cc_final: 0.7546 (tptp) REVERT: A 220 HIS cc_start: 0.6702 (OUTLIER) cc_final: 0.6030 (t70) REVERT: A 222 PHE cc_start: 0.7164 (m-80) cc_final: 0.6172 (m-80) REVERT: A 392 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6774 (mm-30) REVERT: B 46 ARG cc_start: 0.6026 (mpp-170) cc_final: 0.5258 (mpp-170) REVERT: B 186 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6526 (m-30) REVERT: B 187 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7617 (t) REVERT: B 197 ARG cc_start: 0.6378 (mtp180) cc_final: 0.6033 (mtp180) REVERT: B 253 PHE cc_start: 0.8422 (m-80) cc_final: 0.8086 (m-80) REVERT: B 300 LEU cc_start: 0.8044 (mt) cc_final: 0.7739 (mp) REVERT: R 181 LEU cc_start: 0.7913 (tp) cc_final: 0.7698 (tp) REVERT: R 279 ILE cc_start: 0.7899 (tp) cc_final: 0.7627 (tp) REVERT: Y 21 MET cc_start: 0.6814 (tpp) cc_final: 0.6549 (tpp) outliers start: 37 outliers final: 31 residues processed: 203 average time/residue: 0.2557 time to fit residues: 66.3880 Evaluate side-chains 219 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain Y residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.140793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124729 restraints weight = 11116.016| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.10 r_work: 0.3479 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8309 Z= 0.248 Angle : 0.575 8.032 11255 Z= 0.304 Chirality : 0.043 0.211 1263 Planarity : 0.004 0.060 1433 Dihedral : 4.833 38.360 1118 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.99 % Allowed : 19.73 % Favored : 76.28 % 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: 0.34 (0.27), residues: 1007 helix: 1.69 (0.26), residues: 388 sheet: -0.32 (0.33), residues: 229 loop : -0.89 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.004 0.001 HIS B 266 PHE 0.015 0.002 PHE R 306 TYR 0.011 0.001 TYR B 111 ARG 0.014 0.001 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2266.32 seconds wall clock time: 41 minutes 51.40 seconds (2511.40 seconds total)