Starting phenix.real_space_refine on Sun Apr 27 13:29:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgh_41236/04_2025/8tgh_41236_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgh_41236/04_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_41236/04_2025/8tgh_41236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgh_41236/04_2025/8tgh_41236.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgh_41236/04_2025/8tgh_41236_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgh_41236/04_2025/8tgh_41236_trim.cif" } resolution = 3.5 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= 0.022 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.65, per 1000 atoms: 0.80 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: 1.56 Conformation dependent library (CDL) restraints added in 946.0 milliseconds 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: 0.48 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: 1.60 Time building geometry restraints manager: 1.81 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: 3.860 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.420 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.770 ------------------------------------------------------------------------------- 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 (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: 0.62 (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 TRP 0.008 0.001 TRP A 336 HIS 0.001 0.001 HIS A 167 PHE 0.033 0.002 PHE B 131 TYR 0.029 0.002 TYR B 190 ARG 0.006 0.001 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.17348 ( 441) hydrogen bonds : angle 5.76716 ( 1296) covalent geometry : bond 0.00658 ( 5922) covalent geometry : angle 0.81194 ( 8066) *********************** 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 : 1.275 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 128 average time/residue: 0.1849 time to fit residues: 35.6825 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 : 1.031 ------------------------------------------------------------------------------- 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 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.0020 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.099702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.090499 restraints weight = 8199.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.093390 restraints weight = 3753.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.095221 restraints weight = 2069.290| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1043 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= 0.168 Angle : 0.647 8.784 8066 Z= 0.323 Chirality : 0.043 0.146 969 Planarity : 0.007 0.077 983 Dihedral : 6.465 67.096 874 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.90 % Allowed : 26.18 % Favored : 69.92 % 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: 1.66 (0.30), residues: 757 helix: 1.71 (0.22), residues: 595 sheet: None (None), residues: 0 loop : -1.17 (0.41), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS A 223 PHE 0.017 0.001 PHE B 356 TYR 0.013 0.001 TYR A 430 ARG 0.003 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.05653 ( 441) hydrogen bonds : angle 4.38604 ( 1296) covalent geometry : bond 0.00383 ( 5922) covalent geometry : angle 0.64700 ( 8066) *********************** 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 163 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.687 Fit side-chains REVERT: A 200 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: B 149 MET cc_start: 0.7089 (tpp) cc_final: 0.6644 (tpp) REVERT: B 153 VAL cc_start: 0.7820 (p) cc_final: 0.7562 (t) REVERT: B 168 ILE cc_start: 0.8421 (mp) cc_final: 0.8163 (mt) outliers start: 24 outliers final: 8 residues processed: 157 average time/residue: 0.1527 time to fit residues: 35.3383 Evaluate side-chains 144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLN 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 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 35 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.098880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.089600 restraints weight = 8269.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.092479 restraints weight = 3785.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.094292 restraints weight = 2106.991| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5922 Z= 0.186 Angle : 0.641 8.371 8066 Z= 0.315 Chirality : 0.044 0.159 969 Planarity : 0.006 0.061 983 Dihedral : 5.713 58.436 872 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.76 % Allowed : 26.83 % 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 (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: 1.73 (0.31), residues: 757 helix: 1.83 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.40 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS B 223 PHE 0.019 0.001 PHE A 184 TYR 0.013 0.001 TYR A 476 ARG 0.003 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.05653 ( 441) hydrogen bonds : angle 4.29875 ( 1296) covalent geometry : bond 0.00445 ( 5922) covalent geometry : angle 0.64090 ( 8066) *********************** 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 154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.636 Fit side-chains REVERT: A 38 PHE cc_start: 0.8449 (t80) cc_final: 0.8228 (t80) REVERT: B 149 MET cc_start: 0.7090 (tpp) cc_final: 0.6720 (tpp) REVERT: B 153 VAL cc_start: 0.7829 (p) cc_final: 0.7563 (t) REVERT: B 168 ILE cc_start: 0.8404 (mp) cc_final: 0.8148 (mt) outliers start: 17 outliers final: 15 residues processed: 146 average time/residue: 0.1195 time to fit residues: 25.4969 Evaluate side-chains 151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.0670 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.099317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.089941 restraints weight = 8369.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.092813 restraints weight = 3808.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.094644 restraints weight = 2115.188| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5922 Z= 0.165 Angle : 0.624 7.792 8066 Z= 0.307 Chirality : 0.043 0.153 969 Planarity : 0.006 0.055 983 Dihedral : 5.364 51.742 872 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.41 % Allowed : 26.83 % Favored : 69.76 % 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: 1.95 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.44 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS B 223 PHE 0.022 0.001 PHE B 356 TYR 0.013 0.001 TYR B 349 ARG 0.003 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 441) hydrogen bonds : angle 4.23185 ( 1296) covalent geometry : bond 0.00388 ( 5922) covalent geometry : angle 0.62398 ( 8066) *********************** 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 156 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.615 Fit side-chains REVERT: A 38 PHE cc_start: 0.8441 (t80) cc_final: 0.8202 (t80) REVERT: B 40 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7362 (t) REVERT: B 149 MET cc_start: 0.7120 (tpp) cc_final: 0.6739 (tpp) REVERT: B 153 VAL cc_start: 0.7766 (p) cc_final: 0.7509 (t) REVERT: B 168 ILE cc_start: 0.8316 (mp) cc_final: 0.8067 (mt) outliers start: 21 outliers final: 17 residues processed: 148 average time/residue: 0.1130 time to fit residues: 24.7061 Evaluate side-chains 153 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 40 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 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 = 0.3201 r_free = 0.3201 target = 0.098564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.089260 restraints weight = 8247.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.092080 restraints weight = 3808.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.093926 restraints weight = 2130.004| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1411 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 : 0.636 7.771 8066 Z= 0.314 Chirality : 0.044 0.156 969 Planarity : 0.006 0.056 983 Dihedral : 5.058 46.810 872 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.07 % Allowed : 26.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.31), residues: 757 helix: 1.94 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.40 (0.41), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS B 223 PHE 0.020 0.001 PHE B 356 TYR 0.013 0.002 TYR B 471 ARG 0.003 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.05595 ( 441) hydrogen bonds : angle 4.23606 ( 1296) covalent geometry : bond 0.00468 ( 5922) covalent geometry : angle 0.63578 ( 8066) *********************** 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 159 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.604 Fit side-chains REVERT: A 38 PHE cc_start: 0.8437 (t80) cc_final: 0.8202 (t80) REVERT: A 240 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 40 VAL cc_start: 0.7812 (OUTLIER) cc_final: 0.7430 (t) REVERT: B 149 MET cc_start: 0.7063 (tpp) cc_final: 0.6694 (tpp) REVERT: B 153 VAL cc_start: 0.7817 (p) cc_final: 0.7549 (t) REVERT: B 168 ILE cc_start: 0.8350 (mp) cc_final: 0.8085 (mt) outliers start: 25 outliers final: 19 residues processed: 150 average time/residue: 0.1257 time to fit residues: 27.1733 Evaluate side-chains 152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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 40 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 0 optimal weight: 0.9990 chunk 66 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.099327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.089789 restraints weight = 8317.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.092716 restraints weight = 3738.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.094572 restraints weight = 2058.983| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1467 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= 0.157 Angle : 0.613 7.298 8066 Z= 0.303 Chirality : 0.042 0.151 969 Planarity : 0.006 0.055 983 Dihedral : 4.939 43.996 872 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.55 % Allowed : 26.34 % 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 (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: 1.96 (0.31), residues: 757 helix: 2.01 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.37 (0.42), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 336 HIS 0.001 0.000 HIS B 223 PHE 0.020 0.001 PHE B 356 TYR 0.013 0.001 TYR B 349 ARG 0.001 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.05219 ( 441) hydrogen bonds : angle 4.15690 ( 1296) covalent geometry : bond 0.00367 ( 5922) covalent geometry : angle 0.61276 ( 8066) *********************** 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 158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.434 Fit side-chains REVERT: A 38 PHE cc_start: 0.8429 (t80) cc_final: 0.8194 (t80) REVERT: A 177 MET cc_start: 0.7577 (ttp) cc_final: 0.7348 (ttp) REVERT: A 240 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8306 (mp) REVERT: B 40 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7431 (t) REVERT: B 149 MET cc_start: 0.7031 (tpp) cc_final: 0.6658 (tpp) REVERT: B 153 VAL cc_start: 0.7838 (p) cc_final: 0.7560 (t) REVERT: B 168 ILE cc_start: 0.8326 (mp) cc_final: 0.8064 (mt) outliers start: 28 outliers final: 20 residues processed: 149 average time/residue: 0.1294 time to fit residues: 28.3266 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 : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 40 VAL 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 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: 0.5980 chunk 4 optimal weight: 0.3980 chunk 70 optimal weight: 0.0370 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.099621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.089902 restraints weight = 8383.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.092866 restraints weight = 3773.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.094770 restraints weight = 2072.937| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1572 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= 0.155 Angle : 0.612 7.068 8066 Z= 0.302 Chirality : 0.042 0.154 969 Planarity : 0.006 0.055 983 Dihedral : 4.886 44.685 872 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.72 % Allowed : 26.18 % 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 (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: 2.04 (0.31), residues: 757 helix: 2.05 (0.22), residues: 593 sheet: None (None), residues: 0 loop : -1.34 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 336 HIS 0.001 0.000 HIS B 223 PHE 0.021 0.001 PHE B 356 TYR 0.022 0.002 TYR B 349 ARG 0.001 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 441) hydrogen bonds : angle 4.12623 ( 1296) covalent geometry : bond 0.00362 ( 5922) covalent geometry : angle 0.61163 ( 8066) *********************** 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 158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.647 Fit side-chains REVERT: A 240 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8272 (mp) REVERT: B 40 VAL cc_start: 0.7819 (OUTLIER) cc_final: 0.7475 (t) REVERT: B 149 MET cc_start: 0.7024 (tpp) cc_final: 0.6657 (tpp) REVERT: B 153 VAL cc_start: 0.7865 (p) cc_final: 0.7589 (t) REVERT: B 168 ILE cc_start: 0.8303 (mp) cc_final: 0.8041 (mt) REVERT: B 479 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6467 (ptt-90) outliers start: 29 outliers final: 22 residues processed: 148 average time/residue: 0.1274 time to fit residues: 27.1217 Evaluate side-chains 150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 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 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 14 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.100379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.090870 restraints weight = 8286.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.093796 restraints weight = 3703.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.095703 restraints weight = 2031.660| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1610 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= 0.145 Angle : 0.611 6.729 8066 Z= 0.302 Chirality : 0.042 0.157 969 Planarity : 0.006 0.055 983 Dihedral : 4.866 44.345 872 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.55 % Allowed : 26.02 % 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 (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: 2.12 (0.31), residues: 757 helix: 2.12 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -1.33 (0.44), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 336 HIS 0.001 0.000 HIS A 422 PHE 0.021 0.001 PHE B 356 TYR 0.019 0.001 TYR B 349 ARG 0.001 0.000 ARG B 421 Details of bonding type rmsd hydrogen bonds : bond 0.04927 ( 441) hydrogen bonds : angle 4.08871 ( 1296) covalent geometry : bond 0.00333 ( 5922) covalent geometry : angle 0.61133 ( 8066) *********************** 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 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.610 Fit side-chains REVERT: A 240 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8272 (mp) REVERT: B 40 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7488 (t) REVERT: B 149 MET cc_start: 0.7011 (tpp) cc_final: 0.6643 (tpp) REVERT: B 153 VAL cc_start: 0.7865 (p) cc_final: 0.7587 (t) REVERT: B 168 ILE cc_start: 0.8283 (mp) cc_final: 0.8008 (mt) outliers start: 28 outliers final: 22 residues processed: 138 average time/residue: 0.1144 time to fit residues: 23.0331 Evaluate side-chains 144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 171 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 53 optimal weight: 0.0980 chunk 70 optimal weight: 0.0770 chunk 3 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.2336 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.101732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092216 restraints weight = 8347.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095113 restraints weight = 3760.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096990 restraints weight = 2093.215| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5922 Z= 0.129 Angle : 0.599 6.441 8066 Z= 0.296 Chirality : 0.041 0.148 969 Planarity : 0.005 0.054 983 Dihedral : 4.849 44.174 872 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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 (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: 2.22 (0.31), residues: 757 helix: 2.18 (0.22), residues: 593 sheet: None (None), residues: 0 loop : -1.29 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 336 HIS 0.001 0.000 HIS A 422 PHE 0.020 0.001 PHE B 131 TYR 0.019 0.001 TYR B 349 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 441) hydrogen bonds : angle 4.02499 ( 1296) covalent geometry : bond 0.00280 ( 5922) covalent geometry : angle 0.59940 ( 8066) *********************** 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 149 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.614 Fit side-chains REVERT: A 229 MET cc_start: 0.7451 (mtt) cc_final: 0.7172 (mtt) REVERT: A 240 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8280 (mp) REVERT: B 40 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7482 (t) REVERT: B 149 MET cc_start: 0.6996 (tpp) cc_final: 0.6622 (tpp) REVERT: B 153 VAL cc_start: 0.7899 (p) cc_final: 0.7638 (t) REVERT: B 168 ILE cc_start: 0.8238 (mp) cc_final: 0.7968 (mt) outliers start: 26 outliers final: 21 residues processed: 140 average time/residue: 0.1142 time to fit residues: 23.2894 Evaluate side-chains 145 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 171 PHE 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 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 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 = 0.3230 r_free = 0.3230 target = 0.100310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.090805 restraints weight = 8332.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.093775 restraints weight = 3741.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.095672 restraints weight = 2051.542| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1731 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= 0.162 Angle : 0.624 6.725 8066 Z= 0.306 Chirality : 0.043 0.161 969 Planarity : 0.006 0.054 983 Dihedral : 4.826 45.068 872 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.74 % Allowed : 27.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.31), residues: 757 helix: 2.12 (0.22), residues: 593 sheet: None (None), residues: 0 loop : -1.32 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS B 416 PHE 0.025 0.001 PHE A 246 TYR 0.017 0.001 TYR B 349 ARG 0.001 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 441) hydrogen bonds : angle 4.05034 ( 1296) covalent geometry : bond 0.00385 ( 5922) covalent geometry : angle 0.62392 ( 8066) ********************** 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 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.600 Fit side-chains REVERT: A 240 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8253 (mp) REVERT: B 40 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7499 (t) REVERT: B 149 MET cc_start: 0.7019 (tpp) cc_final: 0.6652 (tpp) REVERT: B 153 VAL cc_start: 0.7882 (p) cc_final: 0.7604 (t) REVERT: B 168 ILE cc_start: 0.8258 (mp) cc_final: 0.7974 (mt) outliers start: 23 outliers final: 20 residues processed: 137 average time/residue: 0.1128 time to fit residues: 22.9997 Evaluate side-chains 142 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 214 MET 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 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 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 47 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 75 optimal weight: 0.2980 chunk 28 optimal weight: 0.0040 overall best weight: 0.2992 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.101506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.091940 restraints weight = 8380.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.094930 restraints weight = 3749.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.096835 restraints weight = 2050.929| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5922 Z= 0.133 Angle : 0.623 7.883 8066 Z= 0.304 Chirality : 0.042 0.164 969 Planarity : 0.005 0.054 983 Dihedral : 4.846 45.238 872 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.58 % Allowed : 27.80 % Favored : 68.62 % 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: 2.20 (0.31), residues: 757 helix: 2.17 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -1.28 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 336 HIS 0.001 0.000 HIS A 422 PHE 0.023 0.001 PHE B 356 TYR 0.017 0.001 TYR B 349 ARG 0.001 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 441) hydrogen bonds : angle 4.00699 ( 1296) covalent geometry : bond 0.00298 ( 5922) covalent geometry : angle 0.62343 ( 8066) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.32 seconds wall clock time: 42 minutes 42.35 seconds (2562.35 seconds total)