Starting phenix.real_space_refine on Fri Jul 19 02:18:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/07_2024/8tgi_41237_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/07_2024/8tgi_41237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/07_2024/8tgi_41237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/07_2024/8tgi_41237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/07_2024/8tgi_41237_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/07_2024/8tgi_41237_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 3846 2.51 5 N 900 2.21 5 O 983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5786 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2873 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 23, 'TRANS': 361} Chain breaks: 1 Chain: "B" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2858 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 21, 'TRANS': 360} Chain breaks: 2 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.16, per 1000 atoms: 0.72 Number of scatterers: 5786 At special positions: 0 Unit cell: (77.688, 57.104, 114.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 983 8.00 N 900 7.00 C 3846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 954.3 milliseconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1370 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.574A pdb=" N VAL A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.591A pdb=" N TYR A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 144 through 165 removed outlier: 3.843A pdb=" N LEU A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 159 - end of helix removed outlier: 3.936A pdb=" N ASN A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 187 removed outlier: 3.502A pdb=" N PHE A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 219 removed outlier: 4.166A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 254 removed outlier: 4.055A pdb=" N ARG A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 256 through 278 removed outlier: 4.344A pdb=" N PHE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 318 removed outlier: 3.686A pdb=" N LEU A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.783A pdb=" N THR A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.891A pdb=" N LEU A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 removed outlier: 4.012A pdb=" N VAL A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 421 Proline residue: A 412 - end of helix removed outlier: 4.205A pdb=" N GLY A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 455 removed outlier: 3.566A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 5.032A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 473 through 480 removed outlier: 4.231A pdb=" N SER A 480 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 54 removed outlier: 4.205A pdb=" N VAL B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Proline residue: B 43 - end of helix Proline residue: B 46 - end of helix removed outlier: 3.564A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 165 removed outlier: 4.423A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 3.899A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix removed outlier: 4.226A pdb=" N ASN B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 187 removed outlier: 3.862A pdb=" N PHE B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 219 removed outlier: 3.731A pdb=" N LEU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 250 removed outlier: 3.935A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix removed outlier: 3.660A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.544A pdb=" N ILE B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.535A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 331 removed outlier: 4.207A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Proline residue: B 321 - end of helix Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 364 removed outlier: 3.840A pdb=" N SER B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 392 through 422 Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 427 through 455 removed outlier: 3.634A pdb=" N ALA B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.919A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 removed outlier: 4.083A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.571A pdb=" N ARG B 479 " --> pdb=" O TYR B 476 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1296 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: 1.52 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 865 1.31 - 1.43: 1566 1.43 - 1.56: 3398 1.56 - 1.68: 1 1.68 - 1.81: 100 Bond restraints: 5930 Sorted by residual: bond pdb=" C31 YHR B 601 " pdb=" O30 YHR B 601 " ideal model delta sigma weight residual 1.326 1.401 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C17 YHR B 601 " pdb=" O19 YHR B 601 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C35 YHR B 601 " pdb=" O43 YHR B 601 " ideal model delta sigma weight residual 1.343 1.403 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C10 YHR B 601 " pdb=" C11 YHR B 601 " ideal model delta sigma weight residual 1.492 1.433 0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" C13 YHR B 601 " pdb=" N8 YHR B 601 " ideal model delta sigma weight residual 1.459 1.518 -0.059 2.00e-02 2.50e+03 8.73e+00 ... (remaining 5925 not shown) Histogram of bond angle deviations from ideal: 98.72 - 106.17: 201 106.17 - 113.61: 3280 113.61 - 121.06: 3291 121.06 - 128.50: 1266 128.50 - 135.95: 39 Bond angle restraints: 8077 Sorted by residual: angle pdb=" N LEU B 359 " pdb=" CA LEU B 359 " pdb=" C LEU B 359 " ideal model delta sigma weight residual 112.41 120.86 -8.45 1.30e+00 5.92e-01 4.22e+01 angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 131.20 -19.31 3.00e+00 1.11e-01 4.14e+01 angle pdb=" C VAL A 41 " pdb=" N VAL A 42 " pdb=" CA VAL A 42 " ideal model delta sigma weight residual 120.33 123.60 -3.27 8.00e-01 1.56e+00 1.67e+01 angle pdb=" C10 YHR B 601 " pdb=" C11 YHR B 601 " pdb=" C23 YHR B 601 " ideal model delta sigma weight residual 130.82 120.88 9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CA GLU A 320 " pdb=" C GLU A 320 " pdb=" N PRO A 321 " ideal model delta sigma weight residual 118.44 123.66 -5.22 1.59e+00 3.96e-01 1.08e+01 ... (remaining 8072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.92: 3127 23.92 - 47.85: 302 47.85 - 71.77: 43 71.77 - 95.69: 5 95.69 - 119.62: 3 Dihedral angle restraints: 3480 sinusoidal: 1324 harmonic: 2156 Sorted by residual: dihedral pdb=" CA PRO B 43 " pdb=" C PRO B 43 " pdb=" N ILE B 44 " pdb=" CA ILE B 44 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C13 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C6 YHR B 601 " ideal model delta sinusoidal sigma weight residual 57.66 -61.96 119.62 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" C5 YHR B 601 " pdb=" C6 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " ideal model delta sinusoidal sigma weight residual -67.41 -170.02 102.61 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 3477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 859 0.070 - 0.140: 99 0.140 - 0.210: 7 0.210 - 0.280: 2 0.280 - 0.350: 1 Chirality restraints: 968 Sorted by residual: chirality pdb=" C13 YHR B 601 " pdb=" C12 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" N8 YHR B 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.64 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB VAL B 425 " pdb=" CA VAL B 425 " pdb=" CG1 VAL B 425 " pdb=" CG2 VAL B 425 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA LEU B 359 " pdb=" N LEU B 359 " pdb=" C LEU B 359 " pdb=" CB LEU B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 965 not shown) Planarity restraints: 985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 42 " 0.058 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO B 43 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 43 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 43 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 319 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C LEU A 319 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU A 319 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 320 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 168 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO A 169 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.032 5.00e-02 4.00e+02 ... (remaining 982 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 607 2.75 - 3.28: 5992 3.28 - 3.82: 9656 3.82 - 4.36: 10628 4.36 - 4.90: 19132 Nonbonded interactions: 46015 Sorted by model distance: nonbonded pdb=" O TRP B 326 " pdb=" OG1 THR B 330 " model vdw 2.208 2.440 nonbonded pdb=" O ARG A 138 " pdb=" OH TYR A 190 " model vdw 2.227 2.440 nonbonded pdb=" O ILE B 443 " pdb=" OG1 THR B 447 " model vdw 2.250 2.440 nonbonded pdb=" O THR A 464 " pdb=" ND2 ASN A 468 " model vdw 2.298 2.520 nonbonded pdb=" O GLY A 158 " pdb=" OG1 THR A 161 " model vdw 2.302 2.440 ... (remaining 46010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 278 or resid 288 through 482)) selection = (chain 'B' and (resid 20 through 51 or resid 134 through 482)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.200 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 5930 Z= 0.292 Angle : 0.758 19.310 8077 Z= 0.385 Chirality : 0.047 0.350 968 Planarity : 0.007 0.088 985 Dihedral : 18.038 119.617 2110 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.81 % Allowed : 32.14 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.29), residues: 757 helix: 0.99 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -1.65 (0.40), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.001 0.001 HIS A 416 PHE 0.020 0.001 PHE A 48 TYR 0.008 0.001 TYR A 430 ARG 0.004 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.524 Fit side-chains REVERT: A 373 MET cc_start: 0.7791 (mmt) cc_final: 0.5397 (mmt) outliers start: 5 outliers final: 3 residues processed: 133 average time/residue: 0.1249 time to fit residues: 23.4959 Evaluate side-chains 133 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 289 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 0.0020 chunk 19 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.0370 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.0570 chunk 69 optimal weight: 0.5980 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN B 35 ASN B 396 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5930 Z= 0.196 Angle : 0.644 8.523 8077 Z= 0.309 Chirality : 0.043 0.148 968 Planarity : 0.005 0.047 985 Dihedral : 8.418 71.288 878 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.55 % Allowed : 28.57 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.31), residues: 757 helix: 1.67 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -1.15 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.002 0.001 HIS A 167 PHE 0.012 0.001 PHE A 356 TYR 0.009 0.001 TYR A 430 ARG 0.002 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 0.604 Fit side-chains REVERT: A 192 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7464 (mm) REVERT: B 170 MET cc_start: 0.6732 (tpt) cc_final: 0.6475 (tpt) outliers start: 28 outliers final: 10 residues processed: 149 average time/residue: 0.1104 time to fit residues: 23.8611 Evaluate side-chains 145 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 322 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.0000 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 0.0020 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5930 Z= 0.201 Angle : 0.620 8.337 8077 Z= 0.298 Chirality : 0.043 0.207 968 Planarity : 0.005 0.043 985 Dihedral : 6.976 57.126 875 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 5.52 % Allowed : 28.73 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.31), residues: 757 helix: 1.89 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.04 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 366 HIS 0.002 0.001 HIS A 167 PHE 0.010 0.001 PHE B 356 TYR 0.011 0.001 TYR B 166 ARG 0.002 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 192 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7513 (mm) REVERT: A 374 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7827 (mt) REVERT: B 367 LEU cc_start: 0.7975 (tp) cc_final: 0.7701 (tt) REVERT: B 477 TYR cc_start: 0.6740 (m-10) cc_final: 0.6313 (m-80) outliers start: 34 outliers final: 15 residues processed: 149 average time/residue: 0.1201 time to fit residues: 25.9009 Evaluate side-chains 143 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 331 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5930 Z= 0.299 Angle : 0.678 9.826 8077 Z= 0.326 Chirality : 0.046 0.142 968 Planarity : 0.005 0.044 985 Dihedral : 5.967 50.377 875 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.52 % Allowed : 28.90 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.31), residues: 757 helix: 1.75 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -1.35 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 366 HIS 0.003 0.001 HIS A 167 PHE 0.018 0.001 PHE B 457 TYR 0.014 0.002 TYR A 349 ARG 0.003 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 0.599 Fit side-chains REVERT: A 192 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7580 (mm) REVERT: A 374 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7829 (mp) REVERT: A 421 ARG cc_start: 0.7077 (mtp85) cc_final: 0.6765 (mtp180) REVERT: B 21 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7550 (mp10) REVERT: B 367 LEU cc_start: 0.8030 (tp) cc_final: 0.7759 (tt) outliers start: 34 outliers final: 17 residues processed: 150 average time/residue: 0.1244 time to fit residues: 26.5971 Evaluate side-chains 152 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5930 Z= 0.280 Angle : 0.672 12.894 8077 Z= 0.322 Chirality : 0.045 0.138 968 Planarity : 0.005 0.043 985 Dihedral : 5.635 50.441 875 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.03 % Allowed : 30.36 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.31), residues: 757 helix: 1.75 (0.22), residues: 599 sheet: None (None), residues: 0 loop : -1.35 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 366 HIS 0.003 0.001 HIS A 167 PHE 0.013 0.001 PHE B 356 TYR 0.012 0.002 TYR A 349 ARG 0.003 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 0.596 Fit side-chains REVERT: A 192 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7588 (mm) REVERT: B 21 GLN cc_start: 0.7790 (mp10) cc_final: 0.7522 (mp10) REVERT: B 367 LEU cc_start: 0.8035 (tp) cc_final: 0.7767 (tt) outliers start: 31 outliers final: 16 residues processed: 145 average time/residue: 0.1248 time to fit residues: 25.6809 Evaluate side-chains 150 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.0770 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.0060 chunk 73 optimal weight: 0.0980 chunk 61 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 0.0870 chunk 38 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 overall best weight: 0.1132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5930 Z= 0.169 Angle : 0.628 8.900 8077 Z= 0.297 Chirality : 0.042 0.133 968 Planarity : 0.005 0.039 985 Dihedral : 5.323 50.180 875 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.92 % Allowed : 32.47 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.32), residues: 757 helix: 2.03 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -1.04 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.001 0.000 HIS B 422 PHE 0.013 0.001 PHE B 356 TYR 0.009 0.001 TYR A 430 ARG 0.001 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 0.592 Fit side-chains REVERT: A 192 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7533 (mm) REVERT: B 367 LEU cc_start: 0.7993 (tp) cc_final: 0.7751 (tt) REVERT: B 373 MET cc_start: 0.7617 (mtp) cc_final: 0.7207 (ttt) outliers start: 18 outliers final: 10 residues processed: 134 average time/residue: 0.1203 time to fit residues: 23.1456 Evaluate side-chains 137 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 331 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 22 optimal weight: 0.0470 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5930 Z= 0.228 Angle : 0.637 8.037 8077 Z= 0.304 Chirality : 0.043 0.137 968 Planarity : 0.005 0.040 985 Dihedral : 5.316 49.912 875 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.41 % Allowed : 32.79 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.32), residues: 757 helix: 1.98 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS A 167 PHE 0.012 0.001 PHE B 356 TYR 0.010 0.001 TYR A 430 ARG 0.003 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.633 Fit side-chains REVERT: A 149 MET cc_start: 0.8139 (ptp) cc_final: 0.7934 (ptm) REVERT: A 151 LEU cc_start: 0.8388 (tt) cc_final: 0.8105 (mp) REVERT: A 192 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7612 (mm) REVERT: B 367 LEU cc_start: 0.8037 (tp) cc_final: 0.7797 (tt) outliers start: 21 outliers final: 14 residues processed: 133 average time/residue: 0.1186 time to fit residues: 22.7826 Evaluate side-chains 142 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 331 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 57 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.0470 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5930 Z= 0.213 Angle : 0.646 10.403 8077 Z= 0.306 Chirality : 0.043 0.141 968 Planarity : 0.005 0.041 985 Dihedral : 5.239 49.464 875 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.41 % Allowed : 32.63 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.32), residues: 757 helix: 1.96 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -1.27 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.000 HIS A 167 PHE 0.012 0.001 PHE B 356 TYR 0.009 0.001 TYR A 430 ARG 0.003 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.567 Fit side-chains REVERT: A 151 LEU cc_start: 0.8397 (tt) cc_final: 0.8121 (mp) REVERT: A 192 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7625 (mm) REVERT: B 229 MET cc_start: 0.5781 (tpt) cc_final: 0.5534 (mmm) REVERT: B 367 LEU cc_start: 0.8027 (tp) cc_final: 0.7792 (tt) outliers start: 21 outliers final: 15 residues processed: 138 average time/residue: 0.1126 time to fit residues: 22.7577 Evaluate side-chains 144 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 75 optimal weight: 0.1980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5930 Z= 0.217 Angle : 0.660 9.638 8077 Z= 0.312 Chirality : 0.044 0.150 968 Planarity : 0.005 0.041 985 Dihedral : 5.177 49.040 875 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.57 % Allowed : 32.14 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.32), residues: 757 helix: 1.95 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -1.23 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS A 167 PHE 0.013 0.001 PHE B 356 TYR 0.009 0.001 TYR A 430 ARG 0.002 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.618 Fit side-chains REVERT: A 151 LEU cc_start: 0.8397 (tt) cc_final: 0.8141 (mp) REVERT: A 192 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7660 (mm) REVERT: A 200 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6985 (tt0) REVERT: B 21 GLN cc_start: 0.7725 (mp10) cc_final: 0.7474 (mp10) REVERT: B 367 LEU cc_start: 0.8030 (tp) cc_final: 0.7791 (tt) outliers start: 22 outliers final: 15 residues processed: 136 average time/residue: 0.1245 time to fit residues: 24.7566 Evaluate side-chains 146 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5930 Z= 0.310 Angle : 0.697 9.563 8077 Z= 0.335 Chirality : 0.047 0.171 968 Planarity : 0.005 0.042 985 Dihedral : 5.336 48.743 875 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.41 % Allowed : 32.14 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.31), residues: 757 helix: 1.81 (0.22), residues: 607 sheet: None (None), residues: 0 loop : -1.12 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 459 HIS 0.003 0.001 HIS A 167 PHE 0.013 0.001 PHE B 356 TYR 0.015 0.002 TYR A 349 ARG 0.004 0.000 ARG A 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.623 Fit side-chains REVERT: A 192 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7754 (mm) REVERT: A 200 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: A 250 MET cc_start: 0.4377 (mmm) cc_final: 0.3993 (mmm) REVERT: B 21 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: B 367 LEU cc_start: 0.8054 (tp) cc_final: 0.7793 (tt) outliers start: 21 outliers final: 14 residues processed: 139 average time/residue: 0.1274 time to fit residues: 25.4466 Evaluate side-chains 150 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** 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 = 0.3816 r_free = 0.3816 target = 0.137203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125734 restraints weight = 8224.200| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.09 r_work: 0.3559 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5930 Z= 0.243 Angle : 0.687 9.852 8077 Z= 0.327 Chirality : 0.045 0.164 968 Planarity : 0.005 0.042 985 Dihedral : 5.211 48.691 875 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.41 % Allowed : 32.79 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.32), residues: 757 helix: 1.81 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -1.05 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 366 HIS 0.002 0.001 HIS A 167 PHE 0.013 0.001 PHE B 356 TYR 0.010 0.001 TYR A 430 ARG 0.003 0.000 ARG A 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1648.51 seconds wall clock time: 29 minutes 46.91 seconds (1786.91 seconds total)