Starting phenix.real_space_refine on Fri Aug 22 16:22:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgh_41236/08_2025/8tgh_41236_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgh_41236/08_2025/8tgh_41236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tgh_41236/08_2025/8tgh_41236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgh_41236/08_2025/8tgh_41236.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgh_41236/08_2025/8tgh_41236_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgh_41236/08_2025/8tgh_41236_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 3843 2.51 5 N 900 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5778 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2860 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2864 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 21, 'TRANS': 361} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'1WE': 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: 1.41, per 1000 atoms: 0.24 Number of scatterers: 5778 At special positions: 0 Unit cell: (77.688, 62.416, 114.872, 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 978 8.00 N 900 7.00 C 3843 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=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 365.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 1WE A 601 " Number of C-beta restraints generated: 1370 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 19 through 51 removed outlier: 3.868A pdb=" N VAL A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Proline residue: A 43 - end of helix Proline residue: A 46 - end of helix removed outlier: 3.828A pdb=" N TYR A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.506A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 157 through 165 removed outlier: 4.041A pdb=" N ASN A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 189 through 219 removed outlier: 3.766A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 254 removed outlier: 4.524A 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 257 through 278 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.793A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 331 removed outlier: 3.715A pdb=" N LEU A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 336 through 342 removed outlier: 4.162A pdb=" N LEU A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 removed outlier: 3.540A pdb=" N SER A 346 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.142A 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: 4.107A pdb=" N GLY A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 456 removed outlier: 3.622A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 4.941A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.160A 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 479 removed outlier: 3.524A pdb=" N TYR A 477 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 removed outlier: 4.098A pdb=" N VAL B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.768A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 165 removed outlier: 4.120A pdb=" N GLU B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 4.407A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 166 through 187 removed outlier: 3.540A pdb=" N GLY B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 219 removed outlier: 3.864A pdb=" N LEU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 242 removed outlier: 3.882A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.838A pdb=" N GLY B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.825A pdb=" N CYS B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 299 through 318 removed outlier: 3.797A pdb=" N ALA B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 331 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: 3.514A pdb=" N SER B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.542A pdb=" N CYS B 368 " --> pdb=" O GLY B 364 " (cutoff:3.500A) 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 removed outlier: 3.617A pdb=" N ALA B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 427 through 455 removed outlier: 3.552A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.879A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 removed outlier: 3.692A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 441 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: 0.67 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 861 1.28 - 1.41: 1471 1.41 - 1.54: 3480 1.54 - 1.68: 10 1.68 - 1.81: 100 Bond restraints: 5922 Sorted by residual: bond pdb=" C ALA B 244 " pdb=" O ALA B 244 " ideal model delta sigma weight residual 1.244 1.157 0.087 1.00e-02 1.00e+04 7.62e+01 bond pdb=" C LEU B 238 " pdb=" O LEU B 238 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.17e-02 7.31e+03 4.13e+01 bond pdb=" C PRO B 245 " pdb=" O PRO B 245 " ideal model delta sigma weight residual 1.236 1.144 0.092 1.76e-02 3.23e+03 2.71e+01 bond pdb=" C GLY B 243 " pdb=" O GLY B 243 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.35e-02 5.49e+03 2.62e+01 bond pdb=" C VAL B 242 " pdb=" O VAL B 242 " ideal model delta sigma weight residual 1.230 1.161 0.069 1.57e-02 4.06e+03 1.92e+01 ... (remaining 5917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 7998 3.69 - 7.37: 61 7.37 - 11.06: 6 11.06 - 14.74: 0 14.74 - 18.43: 1 Bond angle restraints: 8066 Sorted by residual: angle pdb=" CA ALA B 244 " pdb=" C ALA B 244 " pdb=" O ALA B 244 " ideal model delta sigma weight residual 118.79 110.51 8.28 9.60e-01 1.09e+00 7.45e+01 angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 130.32 -18.43 3.00e+00 1.11e-01 3.77e+01 angle pdb=" N GLY A 243 " pdb=" CA GLY A 243 " pdb=" C GLY A 243 " ideal model delta sigma weight residual 112.50 119.23 -6.73 1.16e+00 7.43e-01 3.36e+01 angle pdb=" C VAL B 242 " pdb=" CA VAL B 242 " pdb=" CB VAL B 242 " ideal model delta sigma weight residual 112.19 106.43 5.76 1.15e+00 7.56e-01 2.51e+01 angle pdb=" CA LEU B 241 " pdb=" C LEU B 241 " pdb=" O LEU B 241 " ideal model delta sigma weight residual 120.82 116.34 4.48 1.05e+00 9.07e-01 1.82e+01 ... (remaining 8061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 3124 23.14 - 46.28: 314 46.28 - 69.42: 28 69.42 - 92.56: 9 92.56 - 115.70: 1 Dihedral angle restraints: 3476 sinusoidal: 1320 harmonic: 2156 Sorted by residual: dihedral pdb=" CA VAL B 358 " pdb=" C VAL B 358 " pdb=" N LEU B 359 " pdb=" CA LEU B 359 " ideal model delta harmonic sigma weight residual 180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO A 43 " pdb=" C PRO A 43 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+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 -58.04 115.70 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 3473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 877 0.078 - 0.156: 85 0.156 - 0.234: 5 0.234 - 0.312: 0 0.312 - 0.389: 2 Chirality restraints: 969 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 -2.68 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CG LEU A 381 " pdb=" CB LEU A 381 " pdb=" CD1 LEU A 381 " pdb=" CD2 LEU A 381 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA VAL B 242 " pdb=" N VAL B 242 " pdb=" C VAL B 242 " pdb=" CB VAL B 242 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 966 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 42 " 0.088 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO A 43 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 244 " -0.022 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C ALA B 244 " 0.078 2.00e-02 2.50e+03 pdb=" O ALA B 244 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO B 245 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 472 " -0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO A 473 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.047 5.00e-02 4.00e+02 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1562 2.80 - 3.32: 5507 3.32 - 3.85: 9391 3.85 - 4.37: 10124 4.37 - 4.90: 18688 Nonbonded interactions: 45272 Sorted by model distance: nonbonded pdb=" O MET A 183 " pdb=" OG SER A 187 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU B 135 " pdb=" NH1 ARG B 138 " model vdw 2.285 3.120 nonbonded pdb=" OD1 ASP A 299 " pdb=" NH1 ARG A 421 " model vdw 2.291 3.120 nonbonded pdb=" OD2 ASP A 299 " pdb=" NE2 HIS A 422 " model vdw 2.299 3.120 nonbonded pdb=" OD1 ASN A 313 " pdb=" N 1WE A 601 " model vdw 2.309 3.120 ... (remaining 45267 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 278 or resid 289 through 482)) selection = (chain 'B' and (resid 19 through 51 or resid 136 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 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: 6.540 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.210 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.007 0.092 5922 Z= 0.354 Angle : 0.812 18.427 8066 Z= 0.452 Chirality : 0.049 0.389 969 Planarity : 0.010 0.131 983 Dihedral : 17.208 115.698 2106 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.98 % Allowed : 29.92 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.29), residues: 757 helix: 0.97 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -1.28 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 479 TYR 0.029 0.002 TYR B 190 PHE 0.033 0.002 PHE B 131 TRP 0.008 0.001 TRP A 336 HIS 0.001 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00658 ( 5922) covalent geometry : angle 0.81194 ( 8066) hydrogen bonds : bond 0.17348 ( 441) hydrogen bonds : angle 5.76716 ( 1296) *********************** 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 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.128 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 128 average time/residue: 0.0410 time to fit residues: 7.8588 Evaluate side-chains 124 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 274 GLN B 313 ASN B 329 GLN B 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.090756 restraints weight = 8276.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.093661 restraints weight = 3785.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095481 restraints weight = 2092.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.096684 restraints weight = 1314.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.097427 restraints weight = 894.856| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5922 Z= 0.157 Angle : 0.641 8.668 8066 Z= 0.320 Chirality : 0.043 0.143 969 Planarity : 0.007 0.077 983 Dihedral : 6.536 68.639 874 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.07 % Allowed : 26.34 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.30), residues: 757 helix: 1.76 (0.22), residues: 595 sheet: None (None), residues: 0 loop : -1.17 (0.41), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 479 TYR 0.013 0.001 TYR A 430 PHE 0.017 0.001 PHE B 356 TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5922) covalent geometry : angle 0.64136 ( 8066) hydrogen bonds : bond 0.05623 ( 441) hydrogen bonds : angle 4.40285 ( 1296) *********************** 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 166 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.200 Fit side-chains REVERT: A 200 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: B 149 MET cc_start: 0.7117 (tpp) cc_final: 0.6637 (tpp) REVERT: B 153 VAL cc_start: 0.7752 (p) cc_final: 0.7516 (t) REVERT: B 160 LEU cc_start: 0.8347 (tp) cc_final: 0.8023 (tt) REVERT: B 168 ILE cc_start: 0.8426 (mp) cc_final: 0.8180 (mt) outliers start: 25 outliers final: 10 residues processed: 158 average time/residue: 0.0439 time to fit residues: 10.4949 Evaluate side-chains 147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.090213 restraints weight = 8269.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.093108 restraints weight = 3784.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.094942 restraints weight = 2104.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.096133 restraints weight = 1332.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.096924 restraints weight = 918.031| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5922 Z= 0.164 Angle : 0.627 8.209 8066 Z= 0.309 Chirality : 0.043 0.143 969 Planarity : 0.006 0.061 983 Dihedral : 5.746 59.848 872 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.25 % Allowed : 26.67 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.31), residues: 757 helix: 1.91 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.37 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 479 TYR 0.012 0.001 TYR A 476 PHE 0.018 0.001 PHE B 131 TRP 0.006 0.001 TRP B 336 HIS 0.001 0.000 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 5922) covalent geometry : angle 0.62733 ( 8066) hydrogen bonds : bond 0.05414 ( 441) hydrogen bonds : angle 4.25720 ( 1296) *********************** 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 153 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.250 Fit side-chains REVERT: B 149 MET cc_start: 0.7112 (tpp) cc_final: 0.6750 (tpp) REVERT: B 153 VAL cc_start: 0.7759 (p) cc_final: 0.7510 (t) REVERT: B 168 ILE cc_start: 0.8368 (mp) cc_final: 0.8117 (mt) outliers start: 20 outliers final: 15 residues processed: 144 average time/residue: 0.0504 time to fit residues: 10.8979 Evaluate side-chains 147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.089454 restraints weight = 8262.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.092288 restraints weight = 3768.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.094112 restraints weight = 2109.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095313 restraints weight = 1338.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.096118 restraints weight = 923.172| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5922 Z= 0.194 Angle : 0.640 7.879 8066 Z= 0.315 Chirality : 0.044 0.159 969 Planarity : 0.006 0.056 983 Dihedral : 5.339 53.067 872 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.09 % Allowed : 26.67 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.31), residues: 757 helix: 1.93 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.43 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 479 TYR 0.013 0.001 TYR A 476 PHE 0.022 0.002 PHE B 356 TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 5922) covalent geometry : angle 0.64006 ( 8066) hydrogen bonds : bond 0.05630 ( 441) hydrogen bonds : angle 4.25085 ( 1296) *********************** 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 154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.191 Fit side-chains REVERT: B 149 MET cc_start: 0.7093 (tpp) cc_final: 0.6701 (tpp) REVERT: B 153 VAL cc_start: 0.7816 (p) cc_final: 0.7548 (t) REVERT: B 168 ILE cc_start: 0.8395 (mp) cc_final: 0.8130 (mt) outliers start: 19 outliers final: 15 residues processed: 146 average time/residue: 0.0505 time to fit residues: 11.0469 Evaluate side-chains 150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.098560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.089203 restraints weight = 8406.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092073 restraints weight = 3822.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.093924 restraints weight = 2124.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095043 restraints weight = 1335.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.095866 restraints weight = 942.365| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5922 Z= 0.194 Angle : 0.638 7.757 8066 Z= 0.315 Chirality : 0.044 0.160 969 Planarity : 0.006 0.056 983 Dihedral : 5.064 47.503 872 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.58 % Allowed : 26.02 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.31), residues: 757 helix: 1.94 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.42 (0.41), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 479 TYR 0.014 0.002 TYR B 471 PHE 0.022 0.002 PHE B 356 TRP 0.008 0.001 TRP B 336 HIS 0.001 0.000 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 5922) covalent geometry : angle 0.63764 ( 8066) hydrogen bonds : bond 0.05655 ( 441) hydrogen bonds : angle 4.24265 ( 1296) *********************** 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 157 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.230 Fit side-chains REVERT: B 40 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7550 (p) REVERT: B 149 MET cc_start: 0.7062 (tpp) cc_final: 0.6684 (tpp) REVERT: B 153 VAL cc_start: 0.7806 (p) cc_final: 0.7541 (t) REVERT: B 168 ILE cc_start: 0.8370 (mp) cc_final: 0.8101 (mt) outliers start: 22 outliers final: 16 residues processed: 149 average time/residue: 0.0436 time to fit residues: 9.5875 Evaluate side-chains 150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 69 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.088966 restraints weight = 8452.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.091927 restraints weight = 3761.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.093822 restraints weight = 2067.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.095053 restraints weight = 1306.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.095857 restraints weight = 906.357| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5922 Z= 0.173 Angle : 0.625 7.420 8066 Z= 0.310 Chirality : 0.043 0.157 969 Planarity : 0.006 0.056 983 Dihedral : 4.952 44.646 872 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.39 % Allowed : 26.34 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.31), residues: 757 helix: 1.98 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.37 (0.42), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 479 TYR 0.012 0.001 TYR B 349 PHE 0.022 0.001 PHE B 356 TRP 0.008 0.001 TRP B 336 HIS 0.001 0.000 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 5922) covalent geometry : angle 0.62512 ( 8066) hydrogen bonds : bond 0.05441 ( 441) hydrogen bonds : angle 4.19951 ( 1296) *********************** 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 159 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.126 Fit side-chains REVERT: A 177 MET cc_start: 0.7565 (ttp) cc_final: 0.7300 (ttp) REVERT: A 240 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8258 (mp) REVERT: B 40 VAL cc_start: 0.7764 (OUTLIER) cc_final: 0.7553 (p) REVERT: B 149 MET cc_start: 0.7032 (tpp) cc_final: 0.6650 (tpp) REVERT: B 153 VAL cc_start: 0.7837 (p) cc_final: 0.7563 (t) REVERT: B 168 ILE cc_start: 0.8359 (mp) cc_final: 0.8080 (mt) outliers start: 27 outliers final: 19 residues processed: 152 average time/residue: 0.0435 time to fit residues: 9.7055 Evaluate side-chains 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 48 optimal weight: 0.2980 chunk 67 optimal weight: 0.3980 chunk 37 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.089808 restraints weight = 8450.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.092751 restraints weight = 3803.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.094700 restraints weight = 2083.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095954 restraints weight = 1313.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096778 restraints weight = 906.714| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5922 Z= 0.146 Angle : 0.610 7.040 8066 Z= 0.302 Chirality : 0.042 0.152 969 Planarity : 0.006 0.055 983 Dihedral : 4.887 43.948 872 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.23 % Allowed : 26.34 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.31), residues: 757 helix: 2.07 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.39 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 421 TYR 0.014 0.001 TYR B 471 PHE 0.021 0.001 PHE B 356 TRP 0.009 0.001 TRP B 336 HIS 0.001 0.000 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5922) covalent geometry : angle 0.60957 ( 8066) hydrogen bonds : bond 0.05022 ( 441) hydrogen bonds : angle 4.12991 ( 1296) *********************** 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 156 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.143 Fit side-chains REVERT: A 240 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8254 (mp) REVERT: B 149 MET cc_start: 0.7004 (tpp) cc_final: 0.6637 (tpp) REVERT: B 153 VAL cc_start: 0.7868 (p) cc_final: 0.7588 (t) REVERT: B 168 ILE cc_start: 0.8316 (mp) cc_final: 0.8047 (mt) REVERT: B 479 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6478 (ptt-90) outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 0.0415 time to fit residues: 9.0186 Evaluate side-chains 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.098363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.088702 restraints weight = 8392.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.091559 restraints weight = 3824.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.093462 restraints weight = 2127.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.094697 restraints weight = 1353.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.095497 restraints weight = 941.826| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5922 Z= 0.195 Angle : 0.645 7.235 8066 Z= 0.318 Chirality : 0.045 0.163 969 Planarity : 0.006 0.055 983 Dihedral : 4.836 43.730 872 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.90 % Allowed : 27.15 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.31), residues: 757 helix: 1.99 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.42 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 479 TYR 0.012 0.001 TYR A 476 PHE 0.023 0.002 PHE B 356 TRP 0.007 0.001 TRP B 366 HIS 0.001 0.000 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 5922) covalent geometry : angle 0.64453 ( 8066) hydrogen bonds : bond 0.05509 ( 441) hydrogen bonds : angle 4.17544 ( 1296) *********************** 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 151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.213 Fit side-chains REVERT: A 240 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8274 (mp) REVERT: B 149 MET cc_start: 0.7037 (tpp) cc_final: 0.6657 (tpp) REVERT: B 153 VAL cc_start: 0.7842 (p) cc_final: 0.7565 (t) REVERT: B 168 ILE cc_start: 0.8338 (mp) cc_final: 0.8060 (mt) REVERT: B 479 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6657 (ptt-90) outliers start: 24 outliers final: 20 residues processed: 144 average time/residue: 0.0507 time to fit residues: 10.8042 Evaluate side-chains 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.089804 restraints weight = 8405.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.092678 restraints weight = 3816.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.094575 restraints weight = 2120.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095780 restraints weight = 1345.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.096590 restraints weight = 939.012| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5922 Z= 0.164 Angle : 0.628 6.895 8066 Z= 0.309 Chirality : 0.043 0.162 969 Planarity : 0.006 0.055 983 Dihedral : 4.836 43.861 872 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.23 % Allowed : 26.99 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.31), residues: 757 helix: 2.02 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.42 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 479 TYR 0.016 0.002 TYR B 166 PHE 0.024 0.002 PHE B 356 TRP 0.008 0.001 TRP B 336 HIS 0.001 0.000 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 5922) covalent geometry : angle 0.62772 ( 8066) hydrogen bonds : bond 0.05263 ( 441) hydrogen bonds : angle 4.14401 ( 1296) *********************** 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 153 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.200 Fit side-chains REVERT: A 240 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8275 (mp) REVERT: B 149 MET cc_start: 0.7006 (tpp) cc_final: 0.6644 (tpp) REVERT: B 153 VAL cc_start: 0.7864 (p) cc_final: 0.7585 (t) REVERT: B 168 ILE cc_start: 0.8321 (mp) cc_final: 0.8038 (mt) REVERT: B 453 LYS cc_start: 0.7855 (tttp) cc_final: 0.7615 (tttp) REVERT: B 479 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6565 (ptt-90) outliers start: 26 outliers final: 22 residues processed: 144 average time/residue: 0.0502 time to fit residues: 10.6758 Evaluate side-chains 151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 15 optimal weight: 0.0010 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.090222 restraints weight = 8418.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093190 restraints weight = 3768.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.094995 restraints weight = 2076.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096271 restraints weight = 1335.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096995 restraints weight = 918.841| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5922 Z= 0.157 Angle : 0.624 6.748 8066 Z= 0.308 Chirality : 0.043 0.161 969 Planarity : 0.006 0.055 983 Dihedral : 4.808 43.377 872 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.90 % Allowed : 27.15 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.31), residues: 757 helix: 2.04 (0.22), residues: 593 sheet: None (None), residues: 0 loop : -1.39 (0.43), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 421 TYR 0.015 0.001 TYR B 166 PHE 0.024 0.002 PHE B 356 TRP 0.009 0.001 TRP B 336 HIS 0.001 0.000 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5922) covalent geometry : angle 0.62352 ( 8066) hydrogen bonds : bond 0.05141 ( 441) hydrogen bonds : angle 4.10823 ( 1296) ********************** 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 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.219 Fit side-chains REVERT: A 240 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8285 (mp) REVERT: B 149 MET cc_start: 0.7029 (tpp) cc_final: 0.6657 (tpp) REVERT: B 153 VAL cc_start: 0.7848 (p) cc_final: 0.7571 (t) REVERT: B 168 ILE cc_start: 0.8284 (mp) cc_final: 0.8000 (mt) REVERT: B 479 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6580 (ptt-90) outliers start: 24 outliers final: 21 residues processed: 140 average time/residue: 0.0487 time to fit residues: 10.1137 Evaluate side-chains 147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.088323 restraints weight = 8368.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091234 restraints weight = 3793.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.093104 restraints weight = 2076.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.094269 restraints weight = 1303.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.095092 restraints weight = 918.729| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5922 Z= 0.226 Angle : 0.658 7.107 8066 Z= 0.326 Chirality : 0.046 0.170 969 Planarity : 0.006 0.056 983 Dihedral : 4.818 43.140 872 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.74 % Allowed : 26.99 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.31), residues: 757 helix: 1.90 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.47 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.018 0.002 TYR B 471 PHE 0.026 0.002 PHE B 356 TRP 0.008 0.001 TRP B 366 HIS 0.001 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 5922) covalent geometry : angle 0.65822 ( 8066) hydrogen bonds : bond 0.05819 ( 441) hydrogen bonds : angle 4.20701 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1065.18 seconds wall clock time: 19 minutes 3.49 seconds (1143.49 seconds total)