Starting phenix.real_space_refine on Tue Dec 31 08:40:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xt9_33443/12_2024/7xt9_33443_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xt9_33443/12_2024/7xt9_33443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xt9_33443/12_2024/7xt9_33443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xt9_33443/12_2024/7xt9_33443.map" model { file = "/net/cci-nas-00/data/ceres_data/7xt9_33443/12_2024/7xt9_33443_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xt9_33443/12_2024/7xt9_33443_trim.cif" } resolution = 3.2 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= -0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 4840 2.51 5 N 1276 2.21 5 O 1351 1.98 5 H 7351 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14875 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3928 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4793 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Chain: "R" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 161 Unusual residues: {'CLR': 4, 'PLM': 2, 'SRO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 7.16, per 1000 atoms: 0.48 Number of scatterers: 14875 At special positions: 0 Unit cell: (96.12, 102.6, 119.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 1351 8.00 N 1276 7.00 C 4840 6.00 H 7351 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 183 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.4 seconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 49.6% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.960A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.966A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.513A 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 351 removed outlier: 3.761A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 46 removed outlier: 4.528A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 46 removed outlier: 4.021A pdb=" N THR R 23 " --> pdb=" O VAL R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 51 removed outlier: 3.522A pdb=" N LYS R 51 " --> pdb=" O ARG R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 72 removed outlier: 4.029A pdb=" N PHE R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 83 Processing helix chain 'R' and resid 88 through 123 Processing helix chain 'R' and resid 124 through 126 No H-bonds generated for 'chain 'R' and resid 124 through 126' Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 133 through 159 Proline residue: R 148 - end of helix removed outlier: 3.816A pdb=" N ILE R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU R 154 " --> pdb=" O PHE R 150 " (cutoff:3.500A) Proline residue: R 155 - end of helix removed outlier: 3.578A pdb=" N GLN R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 174 removed outlier: 4.013A pdb=" N PHE R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 200 Processing helix chain 'R' and resid 200 through 233 Processing helix chain 'R' and resid 254 through 281 Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 282 through 285 removed outlier: 3.746A pdb=" N ASP R 285 " --> pdb=" O PRO R 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 282 through 285' Processing helix chain 'R' and resid 289 through 307 removed outlier: 3.607A pdb=" N ASN R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER R 304 " --> pdb=" O GLY R 300 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY R 305 " --> pdb=" O TYR R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 312 removed outlier: 3.649A pdb=" N ALA R 312 " --> pdb=" O PRO R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 328 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.655A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.439A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.647A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.105A 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: 3.693A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.666A 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 151 removed outlier: 3.600A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.110A 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: 6.935A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.326A 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: 3.502A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 259 " --> 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: 6.740A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1176 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: 5.21 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7319 1.03 - 1.23: 56 1.23 - 1.43: 3163 1.43 - 1.62: 4418 1.62 - 1.82: 80 Bond restraints: 15036 Sorted by residual: bond pdb=" CZ2 SRO R 407 " pdb=" CH2 SRO R 407 " ideal model delta sigma weight residual 1.386 1.522 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" CG SRO R 407 " pdb=" CD2 SRO R 407 " ideal model delta sigma weight residual 1.438 1.510 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C13 CLR R 404 " pdb=" C17 CLR R 404 " ideal model delta sigma weight residual 1.550 1.487 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C13 CLR R 402 " pdb=" C17 CLR R 402 " ideal model delta sigma weight residual 1.550 1.487 0.063 2.00e-02 2.50e+03 9.87e+00 bond pdb=" CD1 SRO R 407 " pdb=" NE1 SRO R 407 " ideal model delta sigma weight residual 1.377 1.315 0.062 2.00e-02 2.50e+03 9.73e+00 ... (remaining 15031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26853 2.08 - 4.15: 143 4.15 - 6.23: 18 6.23 - 8.31: 6 8.31 - 10.38: 1 Bond angle restraints: 27021 Sorted by residual: angle pdb=" CA PRO G 55 " pdb=" N PRO G 55 " pdb=" CD PRO G 55 " ideal model delta sigma weight residual 112.00 105.20 6.80 1.40e+00 5.10e-01 2.36e+01 angle pdb=" N PRO G 55 " pdb=" CD PRO G 55 " pdb=" CG PRO G 55 " ideal model delta sigma weight residual 103.20 97.04 6.16 1.50e+00 4.44e-01 1.69e+01 angle pdb=" CD1 SRO R 407 " pdb=" NE1 SRO R 407 " pdb=" CE2 SRO R 407 " ideal model delta sigma weight residual 109.10 119.48 -10.38 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C20 CLR R 403 " pdb=" C22 CLR R 403 " pdb=" C23 CLR R 403 " ideal model delta sigma weight residual 115.57 107.47 8.10 3.00e+00 1.11e-01 7.30e+00 angle pdb=" CG SRO R 407 " pdb=" CD1 SRO R 407 " pdb=" NE1 SRO R 407 " ideal model delta sigma weight residual 110.16 102.33 7.83 3.00e+00 1.11e-01 6.81e+00 ... (remaining 27016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 6895 24.08 - 48.16: 302 48.16 - 72.24: 57 72.24 - 96.33: 19 96.33 - 120.41: 3 Dihedral angle restraints: 7276 sinusoidal: 4047 harmonic: 3229 Sorted by residual: dihedral pdb=" C1 CLR R 402 " pdb=" C2 CLR R 402 " pdb=" C3 CLR R 402 " pdb=" O1 CLR R 402 " ideal model delta sinusoidal sigma weight residual 180.04 59.63 120.41 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" C1 CLR R 402 " pdb=" C2 CLR R 402 " pdb=" C3 CLR R 402 " pdb=" C4 CLR R 402 " ideal model delta sinusoidal sigma weight residual 57.41 -60.87 118.28 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C10 CLR R 402 " pdb=" C1 CLR R 402 " pdb=" C2 CLR R 402 " pdb=" C3 CLR R 402 " ideal model delta sinusoidal sigma weight residual -56.83 41.82 -98.65 1 3.00e+01 1.11e-03 1.23e+01 ... (remaining 7273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1047 0.068 - 0.136: 124 0.136 - 0.204: 12 0.204 - 0.271: 0 0.271 - 0.339: 4 Chirality restraints: 1187 Sorted by residual: chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 1184 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.043 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO G 55 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 202 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO R 203 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 203 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 203 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO B 39 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.014 5.00e-02 4.00e+02 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 812 2.19 - 2.80: 30374 2.80 - 3.40: 42406 3.40 - 4.00: 54476 4.00 - 4.60: 84912 Nonbonded interactions: 212980 Sorted by model distance: nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.593 2.450 nonbonded pdb=" HG1 THR B 274 " pdb=" O VAL B 315 " model vdw 1.600 2.450 nonbonded pdb=" OD1 ASP B 163 " pdb=" HG1 THR B 165 " model vdw 1.624 2.450 nonbonded pdb=" HH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 1.637 2.450 nonbonded pdb=" O ASP B 186 " pdb=" H CYS B 204 " model vdw 1.642 2.450 ... (remaining 212975 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.240 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.380 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 0.136 7685 Z= 0.288 Angle : 0.599 10.383 10421 Z= 0.318 Chirality : 0.046 0.339 1187 Planarity : 0.003 0.063 1294 Dihedral : 13.994 120.407 3017 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 2.46 (0.29), residues: 913 helix: 2.69 (0.26), residues: 426 sheet: 0.95 (0.41), residues: 169 loop : 0.63 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 298 HIS 0.002 0.000 HIS B 54 PHE 0.007 0.001 PHE B 234 TYR 0.009 0.001 TYR B 105 ARG 0.009 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.7744 (m-30) cc_final: 0.7491 (m-30) REVERT: G 32 LYS cc_start: 0.7453 (tptp) cc_final: 0.7164 (tptt) REVERT: G 36 ASP cc_start: 0.7606 (m-30) cc_final: 0.7336 (m-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.5648 time to fit residues: 99.2719 Evaluate side-chains 125 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS R 278 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7685 Z= 0.279 Angle : 0.540 7.098 10421 Z= 0.291 Chirality : 0.042 0.149 1187 Planarity : 0.004 0.035 1294 Dihedral : 6.377 51.878 1300 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.75 % Allowed : 5.37 % Favored : 93.88 % 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: 2.13 (0.29), residues: 913 helix: 2.47 (0.25), residues: 418 sheet: 0.55 (0.40), residues: 167 loop : 0.60 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS R 109 PHE 0.021 0.002 PHE R 275 TYR 0.013 0.002 TYR A 339 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8124 (m-30) cc_final: 0.7896 (m-30) REVERT: B 69 LEU cc_start: 0.8789 (mt) cc_final: 0.8516 (mm) REVERT: B 258 ASP cc_start: 0.7449 (t0) cc_final: 0.6961 (t0) REVERT: G 36 ASP cc_start: 0.7369 (m-30) cc_final: 0.7096 (m-30) REVERT: R 55 ASN cc_start: 0.8535 (m-40) cc_final: 0.8325 (m-40) outliers start: 6 outliers final: 6 residues processed: 132 average time/residue: 0.5568 time to fit residues: 94.3799 Evaluate side-chains 124 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7685 Z= 0.205 Angle : 0.486 5.693 10421 Z= 0.261 Chirality : 0.040 0.143 1187 Planarity : 0.004 0.033 1294 Dihedral : 5.866 58.893 1300 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.00 % Allowed : 7.87 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.09 (0.29), residues: 913 helix: 2.52 (0.25), residues: 417 sheet: 0.33 (0.40), residues: 170 loop : 0.60 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS R 109 PHE 0.016 0.001 PHE R 63 TYR 0.012 0.001 TYR A 339 ARG 0.007 0.000 ARG R 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7794 (ptpp) cc_final: 0.7527 (mtpt) REVERT: A 378 ASP cc_start: 0.8031 (m-30) cc_final: 0.7823 (m-30) REVERT: B 69 LEU cc_start: 0.8854 (mt) cc_final: 0.8583 (mm) REVERT: B 258 ASP cc_start: 0.7462 (t0) cc_final: 0.6931 (t0) REVERT: R 139 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7407 (mp) outliers start: 8 outliers final: 6 residues processed: 139 average time/residue: 0.5813 time to fit residues: 102.4540 Evaluate side-chains 132 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 0.2980 chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7685 Z= 0.271 Angle : 0.520 6.435 10421 Z= 0.280 Chirality : 0.041 0.147 1187 Planarity : 0.004 0.040 1294 Dihedral : 6.294 50.333 1300 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.62 % Allowed : 9.74 % Favored : 88.64 % 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: 1.71 (0.28), residues: 913 helix: 2.30 (0.25), residues: 417 sheet: -0.20 (0.38), residues: 181 loop : 0.52 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.005 0.001 HIS R 109 PHE 0.017 0.002 PHE R 91 TYR 0.015 0.001 TYR A 339 ARG 0.007 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7855 (ptpp) cc_final: 0.7580 (mtpt) REVERT: A 59 GLN cc_start: 0.7558 (tp40) cc_final: 0.7311 (tp40) REVERT: A 208 PHE cc_start: 0.6852 (OUTLIER) cc_final: 0.6451 (m-80) REVERT: A 378 ASP cc_start: 0.8092 (m-30) cc_final: 0.7859 (m-30) REVERT: B 69 LEU cc_start: 0.8902 (mt) cc_final: 0.8621 (mm) REVERT: B 258 ASP cc_start: 0.7466 (t0) cc_final: 0.6928 (t0) REVERT: R 139 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7424 (mp) outliers start: 13 outliers final: 9 residues processed: 137 average time/residue: 0.5660 time to fit residues: 98.2523 Evaluate side-chains 136 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 17 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7685 Z= 0.135 Angle : 0.454 5.139 10421 Z= 0.243 Chirality : 0.039 0.134 1187 Planarity : 0.004 0.053 1294 Dihedral : 5.460 49.091 1300 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.87 % Allowed : 10.86 % Favored : 88.26 % 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: 2.00 (0.29), residues: 913 helix: 2.60 (0.26), residues: 417 sheet: -0.15 (0.39), residues: 175 loop : 0.60 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 298 HIS 0.004 0.001 HIS R 109 PHE 0.013 0.001 PHE R 63 TYR 0.010 0.001 TYR A 339 ARG 0.009 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7788 (ptpp) cc_final: 0.7501 (mtpt) REVERT: A 59 GLN cc_start: 0.7527 (tp40) cc_final: 0.7285 (tp40) REVERT: A 208 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: B 69 LEU cc_start: 0.8919 (mt) cc_final: 0.8670 (mm) REVERT: B 153 ASP cc_start: 0.7600 (p0) cc_final: 0.7312 (p0) REVERT: B 258 ASP cc_start: 0.7444 (t0) cc_final: 0.6950 (t0) REVERT: B 333 ASP cc_start: 0.8516 (p0) cc_final: 0.8009 (p0) REVERT: R 139 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7356 (mp) REVERT: R 182 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.5696 (p90) outliers start: 7 outliers final: 4 residues processed: 134 average time/residue: 0.5780 time to fit residues: 98.3034 Evaluate side-chains 133 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 0.0570 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7685 Z= 0.192 Angle : 0.473 5.682 10421 Z= 0.254 Chirality : 0.039 0.138 1187 Planarity : 0.004 0.060 1294 Dihedral : 5.497 47.427 1300 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.12 % Allowed : 11.24 % Favored : 87.64 % 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: 1.92 (0.29), residues: 913 helix: 2.55 (0.25), residues: 417 sheet: -0.07 (0.39), residues: 173 loop : 0.45 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE R 275 TYR 0.012 0.001 TYR A 339 ARG 0.010 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7573 (tp40) cc_final: 0.7353 (tp40) REVERT: B 69 LEU cc_start: 0.8919 (mt) cc_final: 0.8668 (mm) REVERT: B 153 ASP cc_start: 0.7555 (p0) cc_final: 0.7300 (p0) REVERT: B 258 ASP cc_start: 0.7410 (t0) cc_final: 0.6980 (t0) REVERT: R 139 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7351 (mp) REVERT: R 182 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.5767 (p90) outliers start: 9 outliers final: 7 residues processed: 131 average time/residue: 0.5644 time to fit residues: 94.2790 Evaluate side-chains 131 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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: 0.7527 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7685 Z= 0.157 Angle : 0.455 4.949 10421 Z= 0.244 Chirality : 0.039 0.133 1187 Planarity : 0.004 0.068 1294 Dihedral : 5.201 46.656 1300 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.00 % Allowed : 11.61 % Favored : 87.39 % 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: 1.99 (0.29), residues: 913 helix: 2.67 (0.25), residues: 414 sheet: -0.12 (0.39), residues: 174 loop : 0.47 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 298 HIS 0.004 0.001 HIS R 109 PHE 0.012 0.001 PHE R 63 TYR 0.011 0.001 TYR A 339 ARG 0.010 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7622 (tp40) cc_final: 0.7411 (tp40) REVERT: A 208 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6518 (m-80) REVERT: B 69 LEU cc_start: 0.8922 (mt) cc_final: 0.8678 (mm) REVERT: B 153 ASP cc_start: 0.7571 (p0) cc_final: 0.7364 (p0) REVERT: B 258 ASP cc_start: 0.7452 (t0) cc_final: 0.7029 (t0) REVERT: B 333 ASP cc_start: 0.8501 (p0) cc_final: 0.8107 (p0) REVERT: R 182 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.5694 (p90) outliers start: 8 outliers final: 6 residues processed: 135 average time/residue: 0.5694 time to fit residues: 98.0391 Evaluate side-chains 134 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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: 0.7545 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7685 Z= 0.187 Angle : 0.470 5.259 10421 Z= 0.252 Chirality : 0.039 0.137 1187 Planarity : 0.004 0.062 1294 Dihedral : 5.340 48.236 1300 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.37 % Allowed : 11.11 % Favored : 87.52 % 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: 1.91 (0.29), residues: 913 helix: 2.65 (0.25), residues: 411 sheet: -0.20 (0.40), residues: 175 loop : 0.42 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 298 HIS 0.005 0.001 HIS R 109 PHE 0.014 0.001 PHE R 275 TYR 0.012 0.001 TYR A 339 ARG 0.011 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7601 (tp40) cc_final: 0.7399 (tp40) REVERT: B 69 LEU cc_start: 0.8917 (mt) cc_final: 0.8672 (mm) REVERT: B 153 ASP cc_start: 0.7582 (p0) cc_final: 0.7375 (p0) REVERT: B 258 ASP cc_start: 0.7476 (t0) cc_final: 0.6981 (t0) REVERT: R 139 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7310 (mp) REVERT: R 182 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.5775 (p90) outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 0.5662 time to fit residues: 95.1837 Evaluate side-chains 133 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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: 0.7550 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7685 Z= 0.197 Angle : 0.477 5.330 10421 Z= 0.256 Chirality : 0.039 0.137 1187 Planarity : 0.004 0.057 1294 Dihedral : 5.400 49.646 1300 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.00 % Allowed : 11.86 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.85 (0.29), residues: 913 helix: 2.60 (0.25), residues: 411 sheet: -0.30 (0.39), residues: 180 loop : 0.45 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS R 109 PHE 0.013 0.001 PHE R 275 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7650 (tp40) cc_final: 0.7443 (tp40) REVERT: B 69 LEU cc_start: 0.8916 (mt) cc_final: 0.8674 (mm) REVERT: B 153 ASP cc_start: 0.7584 (p0) cc_final: 0.7357 (p0) REVERT: B 258 ASP cc_start: 0.7481 (t0) cc_final: 0.7007 (t0) REVERT: R 139 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7295 (mp) REVERT: R 182 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.5639 (p90) outliers start: 8 outliers final: 6 residues processed: 131 average time/residue: 0.5802 time to fit residues: 96.8963 Evaluate side-chains 132 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7685 Z= 0.224 Angle : 0.497 5.661 10421 Z= 0.268 Chirality : 0.040 0.139 1187 Planarity : 0.004 0.042 1294 Dihedral : 5.543 51.471 1300 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.00 % Allowed : 12.23 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.77 (0.29), residues: 913 helix: 2.52 (0.25), residues: 411 sheet: -0.26 (0.39), residues: 178 loop : 0.37 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS R 109 PHE 0.013 0.001 PHE R 275 TYR 0.013 0.001 TYR A 339 ARG 0.007 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.8911 (mt) cc_final: 0.8667 (mm) REVERT: B 153 ASP cc_start: 0.7601 (p0) cc_final: 0.7363 (p0) REVERT: B 258 ASP cc_start: 0.7463 (t0) cc_final: 0.6987 (t0) REVERT: R 139 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7293 (mp) REVERT: R 182 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.5819 (p90) outliers start: 8 outliers final: 6 residues processed: 130 average time/residue: 0.5787 time to fit residues: 95.7592 Evaluate side-chains 128 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.155324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118923 restraints weight = 22824.812| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.94 r_work: 0.3120 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7685 Z= 0.150 Angle : 0.457 4.906 10421 Z= 0.245 Chirality : 0.039 0.131 1187 Planarity : 0.004 0.056 1294 Dihedral : 5.199 51.763 1300 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.75 % Allowed : 12.36 % Favored : 86.89 % 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: 1.88 (0.29), residues: 913 helix: 2.65 (0.26), residues: 414 sheet: -0.31 (0.40), residues: 180 loop : 0.43 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 298 HIS 0.004 0.001 HIS R 109 PHE 0.011 0.001 PHE A 212 TYR 0.011 0.001 TYR A 339 ARG 0.007 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3920.80 seconds wall clock time: 70 minutes 48.59 seconds (4248.59 seconds total)