Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 21:49:28 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2021/6ta3_10421_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2021/6ta3_10421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2021/6ta3_10421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2021/6ta3_10421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2021/6ta3_10421_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2021/6ta3_10421_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 9491 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3372 Classifications: {'peptide': 429} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 408, 'PCIS': 1} Chain: "A" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3425 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'CIS': 2, 'TRANS': 415, 'PCIS': 1} Chain: "K" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2607 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'CIS': 1, 'TRANS': 322} Chain breaks: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'MZK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.65, per 1000 atoms: 0.60 Number of scatterers: 9491 At special positions: 0 Unit cell: (70.85, 103.55, 111.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1833 8.00 N 1637 7.00 C 5952 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 Amimo 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 1.4 seconds 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 12 sheets defined 46.1% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.857A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 101 through 126 removed outlier: 4.282A pdb=" N ALA B 110 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 158 removed outlier: 3.567A pdb=" N LEU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 removed outlier: 4.045A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 222 through 241 removed outlier: 3.618A pdb=" N VAL B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 286 through 294 removed outlier: 4.281A pdb=" N THR B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 323 through 336 removed outlier: 3.539A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 405 through 427 removed outlier: 3.782A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.516A pdb=" N LEU A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 86' Processing helix chain 'A' and resid 103 through 128 removed outlier: 4.339A pdb=" N GLU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 Processing helix chain 'A' and resid 181 through 197 removed outlier: 4.027A pdb=" N TYR A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 243 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.956A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'K' and resid 30 through 35 Processing helix chain 'K' and resid 78 through 95 removed outlier: 3.695A pdb=" N CYS K 87 " --> pdb=" O ARG K 83 " (cutoff:3.500A) Proline residue: K 88 - end of helix removed outlier: 3.503A pdb=" N GLU K 92 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 116 Processing helix chain 'K' and resid 136 through 150 removed outlier: 3.601A pdb=" N LEU K 140 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS K 141 " --> pdb=" O PRO K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 221 removed outlier: 3.621A pdb=" N ALA K 219 " --> pdb=" O GLU K 215 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS K 220 " --> pdb=" O LYS K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 275 No H-bonds generated for 'chain 'K' and resid 272 through 275' Processing helix chain 'K' and resid 279 through 304 Processing helix chain 'K' and resid 311 through 313 No H-bonds generated for 'chain 'K' and resid 311 through 313' Processing helix chain 'K' and resid 315 through 319 Processing helix chain 'K' and resid 321 through 323 No H-bonds generated for 'chain 'K' and resid 321 through 323' Processing helix chain 'K' and resid 343 through 358 removed outlier: 3.542A pdb=" N LYS K 357 " --> pdb=" O ALA K 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN K 358 " --> pdb=" O HIS K 354 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 63 through 65 removed outlier: 7.223A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU B 198 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N SER B 168 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR B 200 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 170 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 202 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'B' and resid 267 through 270 removed outlier: 3.527A pdb=" N GLY B 369 " --> pdb=" O MET B 267 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 314 through 317 removed outlier: 6.073A pdb=" N LYS B 350 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHE B 317 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA B 352 " --> pdb=" O PHE B 317 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 6 through 8 Processing sheet with id= F, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= G, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.841A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= I, first strand: chain 'K' and resid 70 through 72 removed outlier: 3.669A pdb=" N MET K 70 " --> pdb=" O VAL K 21 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N CYS K 99 " --> pdb=" O ILE K 258 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS K 260 " --> pdb=" O CYS K 99 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE K 101 " --> pdb=" O LYS K 260 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN K 262 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA K 103 " --> pdb=" O ASN K 262 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL K 264 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N GLY K 105 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL K 158 " --> pdb=" O ILE K 202 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE K 202 " --> pdb=" O VAL K 158 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 42 through 44 Processing sheet with id= K, first strand: chain 'K' and resid 161 through 164 Processing sheet with id= L, first strand: chain 'K' and resid 183 through 186 removed outlier: 4.264A pdb=" N GLN K 183 " --> pdb=" O LYS K 197 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1260 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: 2.96 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.91: 1 0.91 - 1.14: 3 1.14 - 1.36: 3087 1.36 - 1.59: 6495 1.59 - 1.82: 95 Bond restraints: 9681 Sorted by residual: bond pdb=" CB SER K 84 " pdb=" OG SER K 84 " ideal model delta sigma weight residual 1.417 0.678 0.739 2.00e-02 2.50e+03 1.37e+03 bond pdb=" CB GLU K 254 " pdb=" CG GLU K 254 " ideal model delta sigma weight residual 1.520 1.061 0.459 3.00e-02 1.11e+03 2.35e+02 bond pdb=" C3A G2P A 501 " pdb=" PB G2P A 501 " ideal model delta sigma weight residual 1.850 1.591 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C THR K 306 " pdb=" O THR K 306 " ideal model delta sigma weight residual 1.234 1.083 0.151 1.26e-02 6.30e+03 1.43e+02 bond pdb=" C3A G2P A 501 " pdb=" PA G2P A 501 " ideal model delta sigma weight residual 1.818 1.592 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 9676 not shown) Histogram of bond angle deviations from ideal: 90.86 - 102.48: 46 102.48 - 114.09: 5889 114.09 - 125.71: 7091 125.71 - 137.32: 99 137.32 - 148.93: 3 Bond angle restraints: 13128 Sorted by residual: angle pdb=" CA GLY B 10 " pdb=" C GLY B 10 " pdb=" N GLN B 11 " ideal model delta sigma weight residual 115.13 148.93 -33.80 1.05e+00 9.07e-01 1.04e+03 angle pdb=" O GLY B 10 " pdb=" C GLY B 10 " pdb=" N GLN B 11 " ideal model delta sigma weight residual 122.56 90.86 31.70 1.15e+00 7.56e-01 7.60e+02 angle pdb=" CA SER K 84 " pdb=" CB SER K 84 " pdb=" OG SER K 84 " ideal model delta sigma weight residual 111.10 139.29 -28.19 2.00e+00 2.50e-01 1.99e+02 angle pdb=" CA GLU K 254 " pdb=" CB GLU K 254 " pdb=" CG GLU K 254 " ideal model delta sigma weight residual 114.10 139.62 -25.52 2.00e+00 2.50e-01 1.63e+02 angle pdb=" N ASN K 289 " pdb=" CA ASN K 289 " pdb=" C ASN K 289 " ideal model delta sigma weight residual 111.07 99.23 11.84 1.07e+00 8.73e-01 1.22e+02 ... (remaining 13123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.36: 5025 18.36 - 36.72: 493 36.72 - 55.08: 178 55.08 - 73.44: 80 73.44 - 91.80: 14 Dihedral angle restraints: 5790 sinusoidal: 2325 harmonic: 3465 Sorted by residual: dihedral pdb=" CA GLY K 110 " pdb=" C GLY K 110 " pdb=" N LYS K 111 " pdb=" CA LYS K 111 " ideal model delta harmonic sigma weight residual 180.00 137.42 42.58 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA GLN B 15 " pdb=" C GLN B 15 " pdb=" N ILE B 16 " pdb=" CA ILE B 16 " ideal model delta harmonic sigma weight residual -180.00 -146.07 -33.93 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" N THR B 143 " pdb=" C THR B 143 " pdb=" CA THR B 143 " pdb=" CB THR B 143 " ideal model delta harmonic sigma weight residual 123.40 138.49 -15.09 0 2.50e+00 1.60e-01 3.64e+01 ... (remaining 5787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 1413 0.183 - 0.365: 43 0.365 - 0.548: 3 0.548 - 0.731: 1 0.731 - 0.913: 1 Chirality restraints: 1461 Sorted by residual: chirality pdb=" CG LEU K 266 " pdb=" CB LEU K 266 " pdb=" CD1 LEU K 266 " pdb=" CD2 LEU K 266 " both_signs ideal model delta sigma weight residual False -2.59 -1.68 -0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" CA THR B 143 " pdb=" N THR B 143 " pdb=" C THR B 143 " pdb=" CB THR B 143 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA PRO K 137 " pdb=" N PRO K 137 " pdb=" C PRO K 137 " pdb=" CB PRO K 137 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.48 2.00e-01 2.50e+01 5.87e+00 ... (remaining 1458 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 399 " -0.268 2.00e-02 2.50e+03 1.90e-01 7.21e+02 pdb=" CG TYR A 399 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 399 " 0.091 2.00e-02 2.50e+03 pdb=" CD2 TYR A 399 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR A 399 " 0.170 2.00e-02 2.50e+03 pdb=" CE2 TYR A 399 " 0.155 2.00e-02 2.50e+03 pdb=" CZ TYR A 399 " 0.109 2.00e-02 2.50e+03 pdb=" OH TYR A 399 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 345 " -0.043 2.00e-02 2.50e+03 9.65e-02 9.30e+01 pdb=" CD GLU K 345 " 0.167 2.00e-02 2.50e+03 pdb=" OE1 GLU K 345 " -0.063 2.00e-02 2.50e+03 pdb=" OE2 GLU K 345 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 104 " -0.128 2.00e-02 2.50e+03 6.80e-02 9.24e+01 pdb=" CG TYR K 104 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR K 104 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR K 104 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR K 104 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR K 104 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR K 104 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR K 104 " -0.085 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 0.32 - 1.23: 18 1.23 - 2.15: 113 2.15 - 3.07: 11961 3.07 - 3.98: 31684 3.98 - 4.90: 54033 Warning: very small nonbonded interaction distances. Nonbonded interactions: 97809 Sorted by model distance: nonbonded pdb=" NE ARG B 251 " pdb=" CB ALA A 100 " model vdw 0.317 3.540 nonbonded pdb=" OD1 ASN B 99 " pdb=" PG G2P B 501 " model vdw 0.439 2.720 nonbonded pdb=" O PRO B 259 " pdb=" CD1 PHE A 404 " model vdw 0.578 3.340 nonbonded pdb=" NZ LYS B 350 " pdb=" CA THR A 179 " model vdw 0.589 3.550 nonbonded pdb=" NZ LYS B 324 " pdb=" CB ARG A 221 " model vdw 0.616 3.520 ... (remaining 97804 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5952 2.51 5 N 1637 2.21 5 O 1833 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Write .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: 7.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 25.740 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.110 Process input model: 32.460 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.420 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 68.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4906 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 : 0.024 0.739 9681 Z= 1.645 Angle : 2.453 33.803 13128 Z= 1.751 Chirality : 0.078 0.913 1461 Planarity : 0.013 0.190 1703 Dihedral : 18.763 91.805 3564 Min Nonbonded Distance : 0.317 Molprobity Statistics. All-atom Clashscore : 210.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 16.02 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.86 (0.22), residues: 1191 helix: 2.57 (0.20), residues: 558 sheet: 1.18 (0.37), residues: 171 loop : -0.45 (0.23), residues: 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 208 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 67 residues processed: 337 average time/residue: 0.2866 time to fit residues: 123.4187 Evaluate side-chains 172 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 105 time to evaluate : 1.174 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 6 residues processed: 67 average time/residue: 0.2307 time to fit residues: 22.0851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.0570 chunk 107 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN B 424 GLN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS A 176 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN A 233 GLN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4988 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.095 9681 Z= 0.429 Angle : 1.070 16.188 13128 Z= 0.560 Chirality : 0.059 0.480 1461 Planarity : 0.011 0.229 1703 Dihedral : 8.501 88.279 1321 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 51.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 7.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.10 (0.22), residues: 1191 helix: 0.02 (0.19), residues: 554 sheet: 1.28 (0.36), residues: 194 loop : -0.65 (0.27), residues: 443 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 169 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 28 residues processed: 220 average time/residue: 0.2256 time to fit residues: 68.2372 Evaluate side-chains 152 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 1.157 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 3 residues processed: 28 average time/residue: 0.1563 time to fit residues: 8.0989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 GLN ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5159 moved from start: 0.7094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 9681 Z= 0.352 Angle : 0.903 17.214 13128 Z= 0.463 Chirality : 0.051 0.396 1461 Planarity : 0.008 0.111 1703 Dihedral : 7.721 87.187 1321 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 42.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 4.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.31 (0.23), residues: 1191 helix: -0.09 (0.20), residues: 554 sheet: 0.71 (0.36), residues: 196 loop : -0.59 (0.28), residues: 441 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 138 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 21 residues processed: 172 average time/residue: 0.2369 time to fit residues: 56.4736 Evaluate side-chains 137 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.047 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 2 residues processed: 21 average time/residue: 0.1318 time to fit residues: 6.1361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.0470 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5147 moved from start: 0.7861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 9681 Z= 0.269 Angle : 0.827 18.309 13128 Z= 0.415 Chirality : 0.046 0.273 1461 Planarity : 0.007 0.081 1703 Dihedral : 7.310 84.157 1321 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 35.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 4.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.23), residues: 1191 helix: 0.03 (0.20), residues: 546 sheet: 0.53 (0.36), residues: 200 loop : -0.77 (0.27), residues: 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 128 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 15 residues processed: 161 average time/residue: 0.2206 time to fit residues: 49.8836 Evaluate side-chains 127 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.208 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 15 average time/residue: 0.1555 time to fit residues: 5.1669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5225 moved from start: 0.8540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9681 Z= 0.265 Angle : 0.789 17.406 13128 Z= 0.397 Chirality : 0.046 0.324 1461 Planarity : 0.007 0.085 1703 Dihedral : 7.060 78.826 1321 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 32.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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 (0.23), residues: 1191 helix: 0.07 (0.21), residues: 551 sheet: 0.60 (0.37), residues: 198 loop : -0.86 (0.27), residues: 442 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 137 average time/residue: 0.2119 time to fit residues: 41.3087 Evaluate side-chains 116 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.181 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.1059 time to fit residues: 4.1053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 ASN ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 moved from start: 0.9095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9681 Z= 0.295 Angle : 0.833 17.516 13128 Z= 0.422 Chirality : 0.045 0.272 1461 Planarity : 0.007 0.100 1703 Dihedral : 6.952 70.133 1321 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 31.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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: -0.26 (0.23), residues: 1191 helix: 0.19 (0.21), residues: 552 sheet: 0.48 (0.37), residues: 201 loop : -0.80 (0.29), residues: 438 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 131 average time/residue: 0.2027 time to fit residues: 38.3416 Evaluate side-chains 114 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.136 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.1071 time to fit residues: 3.6215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.0050 chunk 52 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 ASN ** K 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 moved from start: 0.9465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.245 9681 Z= 0.279 Angle : 0.837 23.683 13128 Z= 0.429 Chirality : 0.044 0.309 1461 Planarity : 0.006 0.124 1703 Dihedral : 6.794 66.748 1321 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 30.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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: -0.26 (0.23), residues: 1191 helix: 0.27 (0.21), residues: 553 sheet: 0.50 (0.38), residues: 194 loop : -0.91 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 138 average time/residue: 0.2336 time to fit residues: 44.8224 Evaluate side-chains 112 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1008 time to fit residues: 3.1706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5357 moved from start: 0.9857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 9681 Z= 0.274 Angle : 0.845 16.224 13128 Z= 0.429 Chirality : 0.045 0.234 1461 Planarity : 0.006 0.091 1703 Dihedral : 6.829 64.178 1321 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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: -0.18 (0.23), residues: 1191 helix: 0.37 (0.21), residues: 548 sheet: 0.56 (0.37), residues: 196 loop : -0.93 (0.28), residues: 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 120 average time/residue: 0.2261 time to fit residues: 38.5241 Evaluate side-chains 109 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1109 time to fit residues: 2.7133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 0.0570 chunk 83 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 112 optimal weight: 0.0670 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 256 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5290 moved from start: 1.0150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.435 9681 Z= 0.282 Angle : 0.875 25.330 13128 Z= 0.446 Chirality : 0.046 0.333 1461 Planarity : 0.007 0.157 1703 Dihedral : 6.790 63.050 1321 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 26.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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: -0.17 (0.23), residues: 1191 helix: 0.30 (0.21), residues: 567 sheet: 0.72 (0.37), residues: 196 loop : -0.94 (0.28), residues: 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 119 average time/residue: 0.2257 time to fit residues: 38.3924 Evaluate side-chains 106 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1221 time to fit residues: 2.4707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** K 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5303 moved from start: 1.0195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.491 9681 Z= 0.441 Angle : 1.145 73.842 13128 Z= 0.540 Chirality : 0.050 0.546 1461 Planarity : 0.006 0.098 1703 Dihedral : 6.854 63.022 1321 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 31.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 2.00 % 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: -0.17 (0.23), residues: 1191 helix: 0.32 (0.21), residues: 567 sheet: 0.68 (0.37), residues: 196 loop : -0.94 (0.28), residues: 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 109 average time/residue: 0.2303 time to fit residues: 35.6621 Evaluate side-chains 106 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1030 time to fit residues: 3.0914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.0020 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 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 = 0.4197 r_free = 0.4197 target = 0.084936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.070404 restraints weight = 44426.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.072480 restraints weight = 25212.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.073831 restraints weight = 16652.547| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 1.0202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.491 9681 Z= 0.441 Angle : 1.145 73.842 13128 Z= 0.540 Chirality : 0.050 0.546 1461 Planarity : 0.006 0.098 1703 Dihedral : 6.854 63.022 1321 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 33.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 2.00 % 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: -0.17 (0.23), residues: 1191 helix: 0.32 (0.21), residues: 567 sheet: 0.68 (0.37), residues: 196 loop : -0.94 (0.28), residues: 428 =============================================================================== Job complete usr+sys time: 2351.01 seconds wall clock time: 45 minutes 3.14 seconds (2703.14 seconds total)