Starting phenix.real_space_refine on Wed Sep 25 06:38:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/09_2024/6ta3_10421.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/09_2024/6ta3_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_10421/09_2024/6ta3_10421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/09_2024/6ta3_10421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/09_2024/6ta3_10421.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/09_2024/6ta3_10421.cif" } resolution = 3.8 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= 0.000 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: 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. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} 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: {'CIS': 2, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 415} 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: {'CIS': 1, 'PTRANS': 10, '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: 8.00, per 1000 atoms: 0.84 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 - 3.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 43 helices and 11 sheets defined 52.7% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.584A pdb=" N GLY B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 69 through 79 removed outlier: 3.932A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 127 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 141 through 159 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) removed outlier: 3.739A pdb=" N TYR B 159 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 196 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 216 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.618A pdb=" N VAL B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.514A pdb=" N LEU B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) 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 299 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.539A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 392 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.782A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.597A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.813A pdb=" N GLN A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 129 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 143 through 162 Processing helix chain 'A' and resid 181 through 198 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 205 through 218 Processing helix chain 'A' and resid 223 through 244 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.677A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 381 through 402 removed outlier: 3.890A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.795A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 Processing helix chain 'K' and resid 29 through 36 Processing helix chain 'K' and resid 77 through 96 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 110 through 117 removed outlier: 3.549A pdb=" N GLY K 117 " --> pdb=" O PHE K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 151 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 206 through 222 removed outlier: 4.247A pdb=" N VAL K 210 " --> pdb=" O ASN K 206 " (cutoff:3.500A) 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 271 through 276 Processing helix chain 'K' and resid 278 through 305 Processing helix chain 'K' and resid 310 through 313 Processing helix chain 'K' and resid 314 through 320 Processing helix chain 'K' and resid 321 through 324 Processing helix chain 'K' and resid 342 through 359 removed outlier: 3.549A pdb=" N THR K 346 " --> pdb=" O ASN K 342 " (cutoff:3.500A) 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) removed outlier: 3.791A pdb=" N ILE K 359 " --> pdb=" O ARG K 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 65 removed outlier: 5.873A pdb=" N VAL B 5 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THR B 136 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE B 7 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N SER B 138 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA3, 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=AA4, first strand: chain 'B' and resid 314 through 317 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 67 removed outlier: 5.661A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA8, 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: 6.488A pdb=" N ASN K 98 " --> pdb=" O ARG K 329 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER K 331 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR K 100 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE K 333 " --> pdb=" O THR K 100 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE K 102 " --> pdb=" O ILE K 333 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR K 335 " --> pdb=" O PHE K 102 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR K 104 " --> pdb=" O THR K 335 " (cutoff:3.500A) Processing sheet with id=AA9, 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: 6.488A pdb=" N ASN K 98 " --> pdb=" O ARG K 329 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER K 331 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR K 100 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE K 333 " --> pdb=" O THR K 100 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE K 102 " --> pdb=" O ILE K 333 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR K 335 " --> pdb=" O PHE K 102 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR K 104 " --> pdb=" O THR K 335 " (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=AB1, first strand: chain 'K' and resid 42 through 44 Processing sheet with id=AB2, first strand: chain 'K' and resid 183 through 187 removed outlier: 4.264A pdb=" N GLN K 183 " --> pdb=" O LYS K 197 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY K 193 " --> pdb=" O ASP K 187 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1551 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: 3.01 Time building geometry restraints manager: 3.66 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: 0.00 - 6.76: 12991 6.76 - 13.52: 125 13.52 - 20.28: 6 20.28 - 27.04: 3 27.04 - 33.80: 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: 5060 18.36 - 36.72: 507 36.72 - 55.08: 182 55.08 - 73.44: 86 73.44 - 91.80: 15 Dihedral angle restraints: 5850 sinusoidal: 2385 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 5847 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: 11913 3.07 - 3.98: 31523 3.98 - 4.90: 53982 Warning: very small nonbonded interaction distances. Nonbonded interactions: 97549 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 97544 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 group one per residue 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: 8.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5093 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= 1.551 Angle : 2.453 33.803 13128 Z= 1.751 Chirality : 0.078 0.913 1461 Planarity : 0.013 0.190 1703 Dihedral : 18.955 91.805 3624 Min Nonbonded Distance : 0.317 Molprobity Statistics. All-atom Clashscore : 210.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 16.02 % Allowed : 16.99 % Favored : 66.99 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP B 344 HIS 0.004 0.000 HIS K 354 PHE 0.033 0.002 PHE K 113 TYR 0.369 0.011 TYR A 399 ARG 0.086 0.002 ARG A 402 *********************** 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 : 1.089 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 REVERT: B 122 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7780 (mttt) REVERT: B 210 ILE cc_start: 0.8044 (mt) cc_final: 0.7747 (mm) REVERT: B 293 MET cc_start: 0.6417 (mtp) cc_final: 0.6210 (mtp) REVERT: B 336 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7157 (mttt) REVERT: B 359 ARG cc_start: 0.6333 (mtt180) cc_final: 0.4900 (mtt180) REVERT: A 22 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: A 164 LYS cc_start: 0.4698 (OUTLIER) cc_final: 0.3022 (mmtp) REVERT: A 212 ILE cc_start: 0.8030 (mm) cc_final: 0.7747 (mm) REVERT: A 220 GLU cc_start: 0.3323 (OUTLIER) cc_final: 0.2577 (pp20) REVERT: A 266 HIS cc_start: 0.6925 (m90) cc_final: 0.6330 (m90) REVERT: A 303 VAL cc_start: 0.8192 (p) cc_final: 0.7169 (p) REVERT: A 396 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7716 (t0) outliers start: 165 outliers final: 67 residues processed: 337 average time/residue: 0.3053 time to fit residues: 130.5985 Evaluate side-chains 182 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 109 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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 ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN ** A 61 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN K 150 ASN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5248 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 9681 Z= 0.473 Angle : 1.073 16.388 13128 Z= 0.570 Chirality : 0.056 0.340 1461 Planarity : 0.010 0.167 1703 Dihedral : 15.556 88.637 1588 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 50.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 11.17 % Allowed : 21.75 % Favored : 67.09 % 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: 0.04 (0.22), residues: 1191 helix: 0.15 (0.19), residues: 577 sheet: 1.17 (0.36), residues: 191 loop : -0.50 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 21 HIS 0.013 0.003 HIS A 393 PHE 0.042 0.004 PHE A 87 TYR 0.149 0.005 TYR A 224 ARG 0.017 0.001 ARG B 251 *********************** 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 281 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 166 time to evaluate : 1.035 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: B 3 GLU cc_start: 0.5840 (OUTLIER) cc_final: 0.5467 (mm-30) REVERT: B 14 ASN cc_start: 0.7515 (m-40) cc_final: 0.7098 (m-40) REVERT: B 22 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6751 (pp20) REVERT: B 23 VAL cc_start: 0.8607 (p) cc_final: 0.8077 (m) REVERT: B 31 ASP cc_start: 0.3227 (OUTLIER) cc_final: 0.2932 (t0) REVERT: B 91 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7896 (p) REVERT: B 122 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.7886 (mtmt) REVERT: B 147 MET cc_start: 0.7114 (pmm) cc_final: 0.6737 (pmm) REVERT: B 154 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8682 (ttpp) REVERT: B 155 ILE cc_start: 0.7307 (pt) cc_final: 0.6901 (tp) REVERT: B 158 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5626 (mp0) REVERT: B 280 GLN cc_start: 0.6607 (pt0) cc_final: 0.6360 (pt0) REVERT: B 293 MET cc_start: 0.7397 (mtp) cc_final: 0.7191 (ptt) REVERT: B 336 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8108 (mttt) REVERT: A 52 PHE cc_start: 0.6567 (m-10) cc_final: 0.6024 (m-10) REVERT: A 164 LYS cc_start: 0.4953 (OUTLIER) cc_final: 0.4416 (tppt) REVERT: A 204 VAL cc_start: 0.3674 (OUTLIER) cc_final: 0.3420 (p) REVERT: A 212 ILE cc_start: 0.8263 (mm) cc_final: 0.8002 (pt) REVERT: A 220 GLU cc_start: 0.5343 (OUTLIER) cc_final: 0.5104 (pp20) REVERT: A 242 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4831 (tm) REVERT: A 338 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7663 (tppp) REVERT: A 371 VAL cc_start: 0.4324 (OUTLIER) cc_final: 0.3983 (t) REVERT: A 373 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.5145 (mtm180) outliers start: 115 outliers final: 49 residues processed: 252 average time/residue: 0.2795 time to fit residues: 91.0492 Evaluate side-chains 181 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 118 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 302 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.0000 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.0010 chunk 29 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 0.0050 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN A 233 GLN A 283 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 ASN ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5259 moved from start: 0.6931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9681 Z= 0.315 Angle : 0.903 16.663 13128 Z= 0.463 Chirality : 0.050 0.293 1461 Planarity : 0.007 0.077 1703 Dihedral : 13.244 91.307 1492 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 35.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 10.19 % Allowed : 22.62 % Favored : 67.18 % 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: -0.22 (0.22), residues: 1191 helix: 0.06 (0.19), residues: 570 sheet: 0.72 (0.36), residues: 198 loop : -0.67 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 101 HIS 0.017 0.003 HIS A 192 PHE 0.028 0.003 PHE A 267 TYR 0.148 0.003 TYR A 224 ARG 0.013 0.001 ARG A 156 *********************** 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 248 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 143 time to evaluate : 1.148 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: B 3 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.5297 (mm-30) REVERT: B 14 ASN cc_start: 0.6818 (OUTLIER) cc_final: 0.6601 (m-40) REVERT: B 114 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8074 (t0) REVERT: B 122 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7998 (mtmt) REVERT: B 155 ILE cc_start: 0.7731 (pt) cc_final: 0.7466 (mm) REVERT: B 289 LEU cc_start: 0.7507 (mp) cc_final: 0.7268 (mp) REVERT: B 336 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8092 (mttt) REVERT: B 376 GLU cc_start: 0.4660 (OUTLIER) cc_final: 0.3934 (mp0) REVERT: A 52 PHE cc_start: 0.6543 (m-10) cc_final: 0.6067 (m-10) REVERT: A 209 ILE cc_start: 0.7012 (mt) cc_final: 0.6717 (mt) REVERT: A 212 ILE cc_start: 0.8158 (mm) cc_final: 0.7784 (mm) REVERT: A 220 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.4901 (pp20) REVERT: A 242 LEU cc_start: 0.4800 (OUTLIER) cc_final: 0.4399 (tm) REVERT: A 267 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.4976 (p90) REVERT: A 432 TYR cc_start: 0.6446 (OUTLIER) cc_final: 0.5782 (t80) outliers start: 105 outliers final: 44 residues processed: 220 average time/residue: 0.2631 time to fit residues: 76.4026 Evaluate side-chains 170 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 116 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.6980 chunk 80 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 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 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5367 moved from start: 0.7892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9681 Z= 0.299 Angle : 0.830 16.733 13128 Z= 0.429 Chirality : 0.049 0.508 1461 Planarity : 0.007 0.076 1703 Dihedral : 12.046 95.645 1446 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 35.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 6.89 % Allowed : 25.05 % Favored : 68.06 % 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: 0.00 (0.19), residues: 584 sheet: 0.56 (0.37), residues: 198 loop : -0.78 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 21 HIS 0.014 0.002 HIS A 192 PHE 0.025 0.002 PHE K 68 TYR 0.142 0.003 TYR A 224 ARG 0.010 0.001 ARG K 33 *********************** 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 191 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 120 time to evaluate : 1.063 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: B 114 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.8013 (t0) REVERT: B 122 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8028 (mtmt) REVERT: B 331 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8350 (pp) REVERT: B 336 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7842 (mttt) REVERT: B 379 LYS cc_start: 0.8239 (pttp) cc_final: 0.7743 (pttp) REVERT: A 52 PHE cc_start: 0.6110 (m-10) cc_final: 0.5555 (m-10) REVERT: A 203 MET cc_start: 0.4670 (OUTLIER) cc_final: 0.4337 (mpp) REVERT: A 212 ILE cc_start: 0.8269 (mm) cc_final: 0.7952 (mm) REVERT: A 267 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5290 (p90) REVERT: A 432 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.5793 (t80) outliers start: 71 outliers final: 40 residues processed: 174 average time/residue: 0.2417 time to fit residues: 57.5826 Evaluate side-chains 157 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 110 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 28 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5415 moved from start: 0.8608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9681 Z= 0.271 Angle : 0.800 16.270 13128 Z= 0.409 Chirality : 0.046 0.239 1461 Planarity : 0.006 0.086 1703 Dihedral : 11.499 94.535 1435 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 31.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 6.99 % Allowed : 25.63 % Favored : 67.38 % 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: -0.23 (0.23), residues: 1191 helix: 0.21 (0.20), residues: 583 sheet: 0.57 (0.38), residues: 188 loop : -0.85 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 21 HIS 0.007 0.001 HIS B 105 PHE 0.027 0.002 PHE B 294 TYR 0.139 0.003 TYR A 224 ARG 0.009 0.001 ARG K 33 *********************** 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 192 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 120 time to evaluate : 1.140 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: B 122 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8064 (mtmt) REVERT: B 257 MET cc_start: 0.8450 (tpp) cc_final: 0.8244 (tpt) REVERT: B 336 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7965 (mttt) REVERT: B 379 LYS cc_start: 0.8484 (pttp) cc_final: 0.8249 (pttp) REVERT: A 52 PHE cc_start: 0.6313 (m-10) cc_final: 0.5872 (m-10) REVERT: A 132 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6573 (mp) REVERT: A 212 ILE cc_start: 0.8342 (mm) cc_final: 0.7997 (mm) REVERT: A 242 LEU cc_start: 0.4643 (OUTLIER) cc_final: 0.4366 (tm) REVERT: A 267 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.5091 (p90) REVERT: A 313 MET cc_start: 0.5085 (mtp) cc_final: 0.4767 (mtt) REVERT: A 432 TYR cc_start: 0.6424 (OUTLIER) cc_final: 0.5800 (t80) outliers start: 72 outliers final: 45 residues processed: 169 average time/residue: 0.2316 time to fit residues: 53.7631 Evaluate side-chains 157 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 106 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 114 optimal weight: 0.0370 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 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 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 HIS ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 0.9121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9681 Z= 0.262 Angle : 0.781 16.123 13128 Z= 0.397 Chirality : 0.046 0.350 1461 Planarity : 0.006 0.089 1703 Dihedral : 11.340 96.120 1431 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 6.50 % Allowed : 26.80 % Favored : 66.70 % 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: -0.21 (0.23), residues: 1191 helix: 0.31 (0.20), residues: 571 sheet: 0.50 (0.36), residues: 193 loop : -0.93 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 21 HIS 0.011 0.002 HIS B 28 PHE 0.021 0.002 PHE A 267 TYR 0.139 0.003 TYR A 224 ARG 0.009 0.001 ARG K 33 *********************** 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 196 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 129 time to evaluate : 1.025 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: B 122 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8133 (mtmt) REVERT: B 299 MET cc_start: 0.7964 (tpp) cc_final: 0.7755 (tpp) REVERT: B 336 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7860 (mtmt) REVERT: A 52 PHE cc_start: 0.6293 (m-10) cc_final: 0.5918 (m-10) REVERT: A 114 ILE cc_start: 0.7948 (tp) cc_final: 0.7697 (mm) REVERT: A 212 ILE cc_start: 0.8301 (mm) cc_final: 0.8067 (pt) REVERT: A 242 LEU cc_start: 0.4712 (OUTLIER) cc_final: 0.4467 (tm) REVERT: A 267 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.5557 (p90) REVERT: A 313 MET cc_start: 0.5157 (mtp) cc_final: 0.4832 (mtt) REVERT: A 432 TYR cc_start: 0.6505 (OUTLIER) cc_final: 0.5858 (t80) outliers start: 67 outliers final: 46 residues processed: 174 average time/residue: 0.2340 time to fit residues: 55.3558 Evaluate side-chains 165 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 114 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 317 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 113 optimal weight: 0.0970 chunk 71 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5494 moved from start: 0.9616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9681 Z= 0.260 Angle : 0.782 16.098 13128 Z= 0.394 Chirality : 0.045 0.269 1461 Planarity : 0.006 0.091 1703 Dihedral : 11.144 94.018 1431 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 27.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.83 % Allowed : 28.54 % Favored : 65.63 % 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: 0.35 (0.20), residues: 579 sheet: 0.44 (0.37), residues: 187 loop : -0.88 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 21 HIS 0.009 0.002 HIS B 105 PHE 0.034 0.002 PHE B 378 TYR 0.137 0.003 TYR A 224 ARG 0.013 0.001 ARG K 83 *********************** 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 176 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 116 time to evaluate : 0.896 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: B 122 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8212 (mtmt) REVERT: B 329 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8372 (tm-30) REVERT: B 330 MET cc_start: 0.6853 (ptt) cc_final: 0.6587 (ptt) REVERT: B 378 PHE cc_start: 0.8084 (m-10) cc_final: 0.7816 (m-10) REVERT: A 52 PHE cc_start: 0.6050 (m-10) cc_final: 0.5578 (m-10) REVERT: A 149 PHE cc_start: 0.6968 (t80) cc_final: 0.6703 (m-80) REVERT: A 154 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.8006 (mmt) REVERT: A 212 ILE cc_start: 0.8401 (mm) cc_final: 0.8085 (mm) REVERT: A 267 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.5578 (p90) REVERT: A 313 MET cc_start: 0.5290 (mtp) cc_final: 0.4948 (mtt) REVERT: A 432 TYR cc_start: 0.6493 (OUTLIER) cc_final: 0.5852 (t80) outliers start: 60 outliers final: 41 residues processed: 160 average time/residue: 0.2463 time to fit residues: 53.6376 Evaluate side-chains 153 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 108 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 306 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 34 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5460 moved from start: 0.9954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9681 Z= 0.236 Angle : 0.779 16.106 13128 Z= 0.391 Chirality : 0.046 0.323 1461 Planarity : 0.006 0.090 1703 Dihedral : 10.768 95.779 1423 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.05 % Allowed : 28.93 % Favored : 66.02 % 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: -0.16 (0.23), residues: 1191 helix: 0.42 (0.21), residues: 575 sheet: 0.40 (0.37), residues: 184 loop : -0.93 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 407 HIS 0.010 0.001 HIS B 190 PHE 0.022 0.002 PHE B 378 TYR 0.134 0.002 TYR A 224 ARG 0.007 0.001 ARG K 33 *********************** 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 177 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 125 time to evaluate : 1.134 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: B 122 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8150 (mtmt) REVERT: B 329 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8363 (tm-30) REVERT: B 330 MET cc_start: 0.6839 (ptt) cc_final: 0.6508 (ptt) REVERT: B 378 PHE cc_start: 0.8124 (m-10) cc_final: 0.7906 (m-10) REVERT: B 379 LYS cc_start: 0.8687 (pttp) cc_final: 0.8191 (tppt) REVERT: A 52 PHE cc_start: 0.6056 (m-10) cc_final: 0.5770 (m-10) REVERT: A 149 PHE cc_start: 0.6936 (t80) cc_final: 0.6670 (m-80) REVERT: A 212 ILE cc_start: 0.8436 (mm) cc_final: 0.8128 (mm) REVERT: A 267 PHE cc_start: 0.6365 (OUTLIER) cc_final: 0.5580 (p90) REVERT: A 302 MET cc_start: 0.7410 (tpp) cc_final: 0.7039 (tpt) REVERT: A 313 MET cc_start: 0.5393 (mtp) cc_final: 0.5003 (mtt) REVERT: A 432 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.5850 (t80) outliers start: 52 outliers final: 37 residues processed: 165 average time/residue: 0.2388 time to fit residues: 53.6227 Evaluate side-chains 149 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 109 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 8 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 ASN ** K 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5548 moved from start: 1.0198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9681 Z= 0.285 Angle : 0.817 15.904 13128 Z= 0.415 Chirality : 0.046 0.262 1461 Planarity : 0.006 0.092 1703 Dihedral : 10.298 89.923 1418 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 26.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.56 % Allowed : 29.61 % Favored : 65.83 % 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: -0.21 (0.23), residues: 1191 helix: 0.44 (0.21), residues: 580 sheet: 0.24 (0.38), residues: 178 loop : -0.98 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 21 HIS 0.015 0.002 HIS K 354 PHE 0.029 0.002 PHE B 378 TYR 0.134 0.003 TYR A 224 ARG 0.028 0.001 ARG A 221 *********************** 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 161 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 114 time to evaluate : 1.060 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: B 122 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8252 (mtmt) REVERT: B 329 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8289 (tm-30) REVERT: B 330 MET cc_start: 0.6770 (ptt) cc_final: 0.6377 (ptt) REVERT: A 52 PHE cc_start: 0.6027 (m-10) cc_final: 0.5628 (m-10) REVERT: A 149 PHE cc_start: 0.7133 (t80) cc_final: 0.6839 (m-80) REVERT: A 212 ILE cc_start: 0.8466 (mm) cc_final: 0.8161 (mm) REVERT: A 267 PHE cc_start: 0.6404 (OUTLIER) cc_final: 0.5689 (p90) REVERT: A 302 MET cc_start: 0.7544 (tpp) cc_final: 0.7144 (tpt) REVERT: A 313 MET cc_start: 0.5468 (mtp) cc_final: 0.5091 (mtt) REVERT: A 432 TYR cc_start: 0.6449 (OUTLIER) cc_final: 0.5825 (t80) outliers start: 47 outliers final: 38 residues processed: 147 average time/residue: 0.2488 time to fit residues: 49.7555 Evaluate side-chains 152 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 111 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 0.0070 chunk 117 optimal weight: 0.0870 chunk 108 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 0.0570 overall best weight: 0.3294 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5489 moved from start: 1.0431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9681 Z= 0.241 Angle : 0.804 16.122 13128 Z= 0.402 Chirality : 0.046 0.244 1461 Planarity : 0.006 0.091 1703 Dihedral : 9.964 88.657 1415 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.98 % Allowed : 30.00 % Favored : 66.02 % 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: -0.22 (0.23), residues: 1191 helix: 0.43 (0.21), residues: 583 sheet: 0.22 (0.37), residues: 182 loop : -1.00 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 21 HIS 0.015 0.002 HIS K 354 PHE 0.024 0.002 PHE K 72 TYR 0.133 0.002 TYR A 224 ARG 0.013 0.001 ARG B 380 ********************** 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 157 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 1.079 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: B 122 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8290 (mtmt) REVERT: B 329 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8340 (tm-30) REVERT: B 330 MET cc_start: 0.6703 (ptt) cc_final: 0.6304 (ptt) REVERT: A 52 PHE cc_start: 0.5892 (m-10) cc_final: 0.5507 (m-10) REVERT: A 71 GLU cc_start: 0.5033 (pt0) cc_final: 0.4795 (pt0) REVERT: A 149 PHE cc_start: 0.7053 (t80) cc_final: 0.6827 (m-80) REVERT: A 212 ILE cc_start: 0.8408 (mm) cc_final: 0.8103 (mm) REVERT: A 267 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.5553 (p90) REVERT: A 302 MET cc_start: 0.7502 (tpp) cc_final: 0.7250 (mmm) REVERT: A 313 MET cc_start: 0.5539 (mtp) cc_final: 0.5132 (mtt) REVERT: A 432 TYR cc_start: 0.6386 (OUTLIER) cc_final: 0.5833 (t80) outliers start: 41 outliers final: 33 residues processed: 147 average time/residue: 0.2500 time to fit residues: 49.6969 Evaluate side-chains 145 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 109 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.0870 chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.0370 chunk 82 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 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 = 0.4168 r_free = 0.4168 target = 0.083694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.068829 restraints weight = 44979.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.070846 restraints weight = 25595.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.072185 restraints weight = 17034.511| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 1.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9681 Z= 0.254 Angle : 0.814 16.071 13128 Z= 0.409 Chirality : 0.048 0.325 1461 Planarity : 0.006 0.090 1703 Dihedral : 9.731 89.070 1409 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 25.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.79 % Allowed : 30.00 % Favored : 66.21 % 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: 0.42 (0.21), residues: 574 sheet: 0.18 (0.36), residues: 184 loop : -1.01 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 21 HIS 0.015 0.002 HIS K 354 PHE 0.020 0.002 PHE A 267 TYR 0.133 0.002 TYR A 224 ARG 0.007 0.001 ARG K 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2562.37 seconds wall clock time: 47 minutes 20.07 seconds (2840.07 seconds total)