Starting phenix.real_space_refine on Thu Mar 5 06:23:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m33_23641/03_2026/7m33_23641_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m33_23641/03_2026/7m33_23641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m33_23641/03_2026/7m33_23641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m33_23641/03_2026/7m33_23641.map" model { file = "/net/cci-nas-00/data/ceres_data/7m33_23641/03_2026/7m33_23641_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m33_23641/03_2026/7m33_23641_trim.cif" } resolution = 3.55 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= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 6328 2.51 5 N 1657 2.21 5 O 1802 1.98 5 H 9742 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19575 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 8993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 8993 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 19, 'TRANS': 553} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 10452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 10452 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 13, 'TRANS': 650} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'ATP': 1, 'HT1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.18, per 1000 atoms: 0.16 Number of scatterers: 19575 At special positions: 0 Unit cell: (100.605, 151.437, 96.369, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 6 15.00 O 1802 8.00 N 1657 7.00 C 6328 6.00 H 9742 1.00 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: 1.77 Conformation dependent library (CDL) restraints added in 543.4 milliseconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 66.9% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.948A pdb=" N LYS C 6 " --> pdb=" O PHE C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 15 Processing helix chain 'C' and resid 15 through 33 Processing helix chain 'C' and resid 34 through 49 removed outlier: 3.778A pdb=" N LYS C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 103 Processing helix chain 'C' and resid 105 through 112 removed outlier: 4.121A pdb=" N TYR C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 121 Processing helix chain 'C' and resid 122 through 133 removed outlier: 3.528A pdb=" N GLN C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 156 removed outlier: 4.120A pdb=" N PHE C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 167 through 207 removed outlier: 4.161A pdb=" N VAL C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 220 through 233 Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.968A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 268 removed outlier: 3.542A pdb=" N THR C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.528A pdb=" N LEU C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 317 removed outlier: 4.012A pdb=" N MET C 292 " --> pdb=" O MET C 288 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 385 removed outlier: 4.064A pdb=" N ILE C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 428 through 434 Processing helix chain 'C' and resid 442 through 451 Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 476 through 492 Processing helix chain 'C' and resid 501 through 505 removed outlier: 3.815A pdb=" N ALA C 504 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 522 removed outlier: 4.013A pdb=" N ALA C 512 " --> pdb=" O LYS C 508 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS C 522 " --> pdb=" O ARG C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 538 removed outlier: 4.037A pdb=" N HIS C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 562 Processing helix chain 'C' and resid 563 through 574 removed outlier: 3.782A pdb=" N ARG C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C 574 " --> pdb=" O TYR C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.742A pdb=" N LEU D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 45 removed outlier: 3.935A pdb=" N GLY D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 145 through 196 removed outlier: 3.631A pdb=" N VAL D 150 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 162 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE D 165 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 204 removed outlier: 4.226A pdb=" N PHE D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 204 " --> pdb=" O TYR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.918A pdb=" N VAL D 209 " --> pdb=" O PRO D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 230 Processing helix chain 'D' and resid 230 through 249 removed outlier: 3.551A pdb=" N SER D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 257 removed outlier: 3.665A pdb=" N VAL D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 298 removed outlier: 4.289A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 307 through 337 Processing helix chain 'D' and resid 338 through 361 Processing helix chain 'D' and resid 368 through 384 removed outlier: 3.671A pdb=" N ASN D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 411 removed outlier: 4.690A pdb=" N GLU D 397 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 477 removed outlier: 3.540A pdb=" N LEU D 475 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 504 Processing helix chain 'D' and resid 520 through 526 Processing helix chain 'D' and resid 531 through 546 removed outlier: 3.725A pdb=" N ILE D 536 " --> pdb=" O THR D 532 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 541 " --> pdb=" O LYS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 584 removed outlier: 3.554A pdb=" N ARG D 572 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN D 573 " --> pdb=" O SER D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 613 removed outlier: 3.787A pdb=" N VAL D 604 " --> pdb=" O GLU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 630 Processing helix chain 'D' and resid 648 through 654 Processing helix chain 'D' and resid 654 through 665 removed outlier: 4.110A pdb=" N TYR D 658 " --> pdb=" O LEU D 654 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 355 through 361 removed outlier: 4.397A pdb=" N PHE C 359 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C 361 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL C 338 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER C 340 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SER C 394 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL C 342 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU C 392 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 414 through 417 removed outlier: 6.250A pdb=" N GLY C 415 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP C 499 " --> pdb=" O GLY C 415 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 417 " --> pdb=" O ASP C 499 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 552 " --> pdb=" O VAL C 544 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 426 through 427 Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 56 Processing sheet with id=AA5, first strand: chain 'D' and resid 89 through 93 removed outlier: 3.533A pdb=" N PHE D 99 " --> pdb=" O GLU D 131 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 131 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 109 through 113 Processing sheet with id=AA7, first strand: chain 'D' and resid 430 through 433 Processing sheet with id=AA8, first strand: chain 'D' and resid 506 through 508 removed outlier: 6.618A pdb=" N GLY D 507 " --> pdb=" O ILE D 589 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 518 through 519 removed outlier: 4.236A pdb=" N GLY D 518 " --> pdb=" O VAL D 560 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 637 through 638 624 hydrogen bonds defined for protein. 1821 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: 4.62 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9742 1.04 - 1.24: 1338 1.24 - 1.45: 3032 1.45 - 1.65: 5588 1.65 - 1.85: 80 Bond restraints: 19780 Sorted by residual: bond pdb=" C4 ATP D 701 " pdb=" C5 ATP D 701 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.82e+01 bond pdb=" C4 ATP C 801 " pdb=" C5 ATP C 801 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.52e+01 bond pdb=" C5 ATP D 701 " pdb=" C6 ATP D 701 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.47e+01 bond pdb=" C5 ATP C 801 " pdb=" C6 ATP C 801 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C5 ATP C 801 " pdb=" N7 ATP C 801 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.19e+01 ... (remaining 19775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 35528 4.04 - 8.07: 153 8.07 - 12.11: 13 12.11 - 16.15: 3 16.15 - 20.19: 1 Bond angle restraints: 35698 Sorted by residual: angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 119.68 20.19 1.00e+00 1.00e+00 4.08e+02 angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 125.37 14.50 1.00e+00 1.00e+00 2.10e+02 angle pdb=" PA ATP D 701 " pdb=" O3A ATP D 701 " pdb=" PB ATP D 701 " ideal model delta sigma weight residual 136.83 122.52 14.31 1.00e+00 1.00e+00 2.05e+02 angle pdb=" PA ATP C 801 " pdb=" O3A ATP C 801 " pdb=" PB ATP C 801 " ideal model delta sigma weight residual 136.83 123.50 13.33 1.00e+00 1.00e+00 1.78e+02 angle pdb=" C5 ATP C 801 " pdb=" C4 ATP C 801 " pdb=" N3 ATP C 801 " ideal model delta sigma weight residual 126.80 118.76 8.04 1.00e+00 1.00e+00 6.47e+01 ... (remaining 35693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8368 17.79 - 35.58: 595 35.58 - 53.37: 192 53.37 - 71.16: 100 71.16 - 88.95: 15 Dihedral angle restraints: 9270 sinusoidal: 5032 harmonic: 4238 Sorted by residual: dihedral pdb=" CA SER C 340 " pdb=" C SER C 340 " pdb=" N HIS C 341 " pdb=" CA HIS C 341 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA TYR D 439 " pdb=" C TYR D 439 " pdb=" N GLN D 440 " pdb=" CA GLN D 440 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LEU D 335 " pdb=" C LEU D 335 " pdb=" N MET D 336 " pdb=" CA MET D 336 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 9267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1269 0.088 - 0.177: 231 0.177 - 0.265: 34 0.265 - 0.353: 4 0.353 - 0.441: 2 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CG LEU D 340 " pdb=" CB LEU D 340 " pdb=" CD1 LEU D 340 " pdb=" CD2 LEU D 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CG LEU C 137 " pdb=" CB LEU C 137 " pdb=" CD1 LEU C 137 " pdb=" CD2 LEU C 137 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CB VAL D 620 " pdb=" CA VAL D 620 " pdb=" CG1 VAL D 620 " pdb=" CG2 VAL D 620 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1537 not shown) Planarity restraints: 2916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 175 " -0.017 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C GLN D 175 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN D 175 " -0.023 2.00e-02 2.50e+03 pdb=" N MET D 176 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 282 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C ASN C 282 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN C 282 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 283 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 361 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C LEU D 361 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU D 361 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN D 362 " -0.015 2.00e-02 2.50e+03 ... (remaining 2913 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1679 2.23 - 2.83: 43414 2.83 - 3.42: 51606 3.42 - 4.01: 68979 4.01 - 4.60: 108314 Nonbonded interactions: 273992 Sorted by model distance: nonbonded pdb=" OE1 GLU C 537 " pdb=" HH TYR C 566 " model vdw 1.643 2.450 nonbonded pdb=" HG1 THR C 95 " pdb=" OE2 GLU D 316 " model vdw 1.659 2.450 nonbonded pdb=" HZ1 LYS C 250 " pdb=" OE2 GLU D 32 " model vdw 1.677 2.450 nonbonded pdb=" O ALA C 165 " pdb=" HG SER C 256 " model vdw 1.688 2.450 nonbonded pdb=" O VAL C 71 " pdb=" HG SER C 75 " model vdw 1.695 2.450 ... (remaining 273987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.100 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 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 : 0.014 0.129 10038 Z= 0.579 Angle : 1.138 20.187 13607 Z= 0.662 Chirality : 0.071 0.441 1540 Planarity : 0.006 0.064 1713 Dihedral : 14.886 88.954 3681 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.23 % Allowed : 9.70 % Favored : 87.07 % 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 are not related in a simple way. whole: -2.02 (0.21), residues: 1233 helix: -0.54 (0.16), residues: 778 sheet: -1.99 (0.58), residues: 74 loop : -2.71 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG D 345 TYR 0.027 0.003 TYR C 257 PHE 0.036 0.003 PHE D 141 TRP 0.030 0.003 TRP C 78 HIS 0.017 0.002 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.01351 (10038) covalent geometry : angle 1.13780 (13607) hydrogen bonds : bond 0.13080 ( 624) hydrogen bonds : angle 6.35414 ( 1821) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 108 PHE cc_start: 0.7654 (t80) cc_final: 0.7134 (t80) REVERT: C 258 LEU cc_start: 0.8455 (tm) cc_final: 0.8156 (tp) REVERT: C 517 ILE cc_start: 0.8775 (mt) cc_final: 0.8573 (mt) REVERT: C 543 LEU cc_start: 0.8253 (pp) cc_final: 0.7977 (pp) REVERT: D 259 ILE cc_start: 0.5515 (OUTLIER) cc_final: 0.5221 (mt) REVERT: D 588 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8105 (pp) outliers start: 33 outliers final: 4 residues processed: 207 average time/residue: 0.1951 time to fit residues: 57.3775 Evaluate side-chains 117 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 266 TRP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 588 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 HIS C 355 GLN C 520 ASN D 46 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.195627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146369 restraints weight = 34559.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143871 restraints weight = 28332.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147167 restraints weight = 23403.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147355 restraints weight = 13750.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.147897 restraints weight = 13229.420| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 10038 Z= 0.314 Angle : 0.653 9.160 13607 Z= 0.370 Chirality : 0.043 0.161 1540 Planarity : 0.005 0.067 1713 Dihedral : 9.400 86.079 1438 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.18 % Allowed : 13.91 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.22), residues: 1233 helix: 0.19 (0.17), residues: 784 sheet: -2.24 (0.50), residues: 88 loop : -2.35 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 126 TYR 0.012 0.002 TYR C 257 PHE 0.021 0.002 PHE C 77 TRP 0.015 0.002 TRP C 78 HIS 0.006 0.002 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00718 (10038) covalent geometry : angle 0.65335 (13607) hydrogen bonds : bond 0.04888 ( 624) hydrogen bonds : angle 5.34166 ( 1821) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.7710 (tpp) cc_final: 0.7274 (tpp) REVERT: C 258 LEU cc_start: 0.8580 (tm) cc_final: 0.8336 (tp) REVERT: D 162 PHE cc_start: 0.7085 (m-80) cc_final: 0.6855 (m-80) REVERT: D 259 ILE cc_start: 0.5862 (OUTLIER) cc_final: 0.5488 (mt) REVERT: D 501 GLU cc_start: 0.6857 (tt0) cc_final: 0.6576 (tp30) REVERT: D 661 MET cc_start: 0.4367 (OUTLIER) cc_final: 0.3947 (mpp) outliers start: 12 outliers final: 8 residues processed: 133 average time/residue: 0.1835 time to fit residues: 35.7687 Evaluate side-chains 123 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 266 TRP Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.197493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.148689 restraints weight = 34465.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.145691 restraints weight = 29171.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.149300 restraints weight = 22835.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.149463 restraints weight = 13810.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.149729 restraints weight = 13635.244| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10038 Z= 0.157 Angle : 0.524 5.846 13607 Z= 0.291 Chirality : 0.038 0.145 1540 Planarity : 0.004 0.060 1713 Dihedral : 8.953 81.695 1435 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.37 % Allowed : 14.30 % Favored : 84.33 % 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 are not related in a simple way. whole: -0.49 (0.23), residues: 1233 helix: 0.75 (0.18), residues: 785 sheet: -2.14 (0.49), residues: 88 loop : -2.19 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 120 TYR 0.017 0.001 TYR D 495 PHE 0.014 0.001 PHE D 139 TRP 0.015 0.001 TRP C 78 HIS 0.008 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00347 (10038) covalent geometry : angle 0.52414 (13607) hydrogen bonds : bond 0.04144 ( 624) hydrogen bonds : angle 4.95820 ( 1821) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.7720 (tpp) cc_final: 0.7254 (tpp) REVERT: D 162 PHE cc_start: 0.6989 (m-80) cc_final: 0.6731 (m-80) REVERT: D 259 ILE cc_start: 0.5823 (OUTLIER) cc_final: 0.5502 (mt) REVERT: D 299 MET cc_start: 0.8003 (mmm) cc_final: 0.7311 (tmm) REVERT: D 661 MET cc_start: 0.4203 (OUTLIER) cc_final: 0.3795 (mpp) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 0.1587 time to fit residues: 29.6980 Evaluate side-chains 115 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 21 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.195605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.146078 restraints weight = 34540.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144250 restraints weight = 30057.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.147617 restraints weight = 23903.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.147757 restraints weight = 14078.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148145 restraints weight = 13187.675| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10038 Z= 0.200 Angle : 0.528 7.277 13607 Z= 0.294 Chirality : 0.039 0.142 1540 Planarity : 0.004 0.062 1713 Dihedral : 8.595 84.010 1433 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.18 % Allowed : 14.20 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.24), residues: 1233 helix: 0.98 (0.18), residues: 781 sheet: -1.93 (0.50), residues: 88 loop : -2.12 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 120 TYR 0.019 0.002 TYR D 495 PHE 0.020 0.001 PHE D 139 TRP 0.014 0.001 TRP C 78 HIS 0.007 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00446 (10038) covalent geometry : angle 0.52803 (13607) hydrogen bonds : bond 0.03997 ( 624) hydrogen bonds : angle 4.80706 ( 1821) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.7820 (tpp) cc_final: 0.7379 (tpp) REVERT: C 191 GLN cc_start: 0.6755 (tp-100) cc_final: 0.6446 (tp40) REVERT: D 91 TYR cc_start: 0.7561 (m-80) cc_final: 0.7329 (m-80) REVERT: D 162 PHE cc_start: 0.7088 (m-80) cc_final: 0.6779 (m-80) REVERT: D 259 ILE cc_start: 0.6040 (OUTLIER) cc_final: 0.5738 (mt) REVERT: D 661 MET cc_start: 0.4375 (OUTLIER) cc_final: 0.3992 (mpp) outliers start: 12 outliers final: 6 residues processed: 120 average time/residue: 0.1612 time to fit residues: 29.8406 Evaluate side-chains 114 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 73 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 112 optimal weight: 6.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.197445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.148301 restraints weight = 34075.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.146441 restraints weight = 28470.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148994 restraints weight = 24556.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.149446 restraints weight = 14668.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.150134 restraints weight = 13434.723| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10038 Z= 0.120 Angle : 0.480 5.625 13607 Z= 0.265 Chirality : 0.037 0.139 1540 Planarity : 0.004 0.057 1713 Dihedral : 8.244 84.599 1431 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.47 % Allowed : 13.81 % Favored : 84.72 % 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 are not related in a simple way. whole: 0.15 (0.24), residues: 1233 helix: 1.26 (0.18), residues: 784 sheet: -1.84 (0.52), residues: 83 loop : -1.97 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 120 TYR 0.013 0.001 TYR C 15 PHE 0.009 0.001 PHE C 77 TRP 0.014 0.001 TRP C 78 HIS 0.006 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00251 (10038) covalent geometry : angle 0.47987 (13607) hydrogen bonds : bond 0.03704 ( 624) hydrogen bonds : angle 4.59663 ( 1821) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.7826 (tpp) cc_final: 0.7398 (tpp) REVERT: C 191 GLN cc_start: 0.6748 (tp-100) cc_final: 0.6428 (tp40) REVERT: C 545 MET cc_start: 0.5095 (ttm) cc_final: 0.4753 (ttm) REVERT: C 556 HIS cc_start: 0.5940 (p90) cc_final: 0.5424 (p90) REVERT: C 557 GLN cc_start: 0.7868 (pm20) cc_final: 0.7637 (mp10) REVERT: D 91 TYR cc_start: 0.7561 (m-80) cc_final: 0.7294 (m-80) REVERT: D 162 PHE cc_start: 0.6963 (m-80) cc_final: 0.6702 (m-80) REVERT: D 259 ILE cc_start: 0.6004 (OUTLIER) cc_final: 0.5727 (mt) REVERT: D 661 MET cc_start: 0.4387 (OUTLIER) cc_final: 0.3976 (mpp) outliers start: 15 outliers final: 12 residues processed: 121 average time/residue: 0.1686 time to fit residues: 30.6621 Evaluate side-chains 119 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.196474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.147319 restraints weight = 34349.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.144418 restraints weight = 29881.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.147958 restraints weight = 24060.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148226 restraints weight = 14102.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.148741 restraints weight = 13064.716| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10038 Z= 0.135 Angle : 0.478 5.537 13607 Z= 0.264 Chirality : 0.037 0.140 1540 Planarity : 0.004 0.057 1713 Dihedral : 8.034 86.262 1431 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.37 % Allowed : 14.10 % Favored : 84.52 % 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 are not related in a simple way. whole: 0.39 (0.24), residues: 1233 helix: 1.44 (0.18), residues: 784 sheet: -1.79 (0.53), residues: 83 loop : -1.87 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 405 TYR 0.016 0.001 TYR D 495 PHE 0.025 0.001 PHE D 139 TRP 0.014 0.001 TRP C 78 HIS 0.011 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00287 (10038) covalent geometry : angle 0.47816 (13607) hydrogen bonds : bond 0.03634 ( 624) hydrogen bonds : angle 4.46970 ( 1821) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.7814 (tpp) cc_final: 0.7375 (tpp) REVERT: C 545 MET cc_start: 0.5309 (ttm) cc_final: 0.4959 (ttm) REVERT: C 556 HIS cc_start: 0.5897 (p90) cc_final: 0.5351 (p90) REVERT: C 557 GLN cc_start: 0.7818 (pm20) cc_final: 0.7609 (mp10) REVERT: D 91 TYR cc_start: 0.7570 (m-80) cc_final: 0.7354 (m-80) REVERT: D 162 PHE cc_start: 0.7028 (m-80) cc_final: 0.6769 (m-80) REVERT: D 259 ILE cc_start: 0.6075 (OUTLIER) cc_final: 0.5847 (mt) REVERT: D 661 MET cc_start: 0.4310 (OUTLIER) cc_final: 0.3909 (mpp) outliers start: 14 outliers final: 9 residues processed: 119 average time/residue: 0.1518 time to fit residues: 27.6812 Evaluate side-chains 115 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.195089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145192 restraints weight = 34799.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142879 restraints weight = 29981.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.146440 restraints weight = 24405.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146404 restraints weight = 14611.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.147025 restraints weight = 13541.146| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10038 Z= 0.175 Angle : 0.500 6.708 13607 Z= 0.277 Chirality : 0.038 0.166 1540 Planarity : 0.004 0.057 1713 Dihedral : 7.956 87.485 1431 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.27 % Allowed : 13.81 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1233 helix: 1.38 (0.18), residues: 785 sheet: -1.70 (0.54), residues: 81 loop : -1.77 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 521 TYR 0.016 0.001 TYR D 495 PHE 0.011 0.001 PHE C 77 TRP 0.014 0.001 TRP C 78 HIS 0.006 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00384 (10038) covalent geometry : angle 0.50002 (13607) hydrogen bonds : bond 0.03719 ( 624) hydrogen bonds : angle 4.48797 ( 1821) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.7880 (tpp) cc_final: 0.7436 (tpp) REVERT: C 545 MET cc_start: 0.5512 (ttm) cc_final: 0.5177 (ttm) REVERT: C 556 HIS cc_start: 0.5902 (p90) cc_final: 0.5617 (p90) REVERT: D 162 PHE cc_start: 0.7094 (m-80) cc_final: 0.6838 (m-80) REVERT: D 661 MET cc_start: 0.4266 (OUTLIER) cc_final: 0.3885 (mpp) outliers start: 13 outliers final: 8 residues processed: 114 average time/residue: 0.1554 time to fit residues: 27.3876 Evaluate side-chains 109 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.196261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.147377 restraints weight = 34516.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.144199 restraints weight = 28130.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146887 restraints weight = 22812.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.147367 restraints weight = 14540.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.147869 restraints weight = 14216.017| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10038 Z= 0.124 Angle : 0.473 5.350 13607 Z= 0.261 Chirality : 0.037 0.137 1540 Planarity : 0.004 0.055 1713 Dihedral : 7.699 88.413 1429 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.08 % Allowed : 13.91 % Favored : 85.01 % 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 are not related in a simple way. whole: 0.59 (0.24), residues: 1233 helix: 1.55 (0.18), residues: 785 sheet: -1.65 (0.54), residues: 81 loop : -1.69 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 521 TYR 0.012 0.001 TYR C 15 PHE 0.028 0.001 PHE D 139 TRP 0.014 0.001 TRP C 78 HIS 0.005 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00264 (10038) covalent geometry : angle 0.47331 (13607) hydrogen bonds : bond 0.03564 ( 624) hydrogen bonds : angle 4.37579 ( 1821) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.7861 (tpp) cc_final: 0.7412 (tpp) REVERT: C 545 MET cc_start: 0.5586 (ttm) cc_final: 0.5240 (ttm) REVERT: D 162 PHE cc_start: 0.7026 (m-80) cc_final: 0.6772 (m-80) REVERT: D 661 MET cc_start: 0.4292 (OUTLIER) cc_final: 0.3951 (mpp) outliers start: 11 outliers final: 8 residues processed: 108 average time/residue: 0.1538 time to fit residues: 25.9860 Evaluate side-chains 106 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.195499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146330 restraints weight = 34414.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143742 restraints weight = 28516.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147196 restraints weight = 22576.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147326 restraints weight = 13388.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.147758 restraints weight = 12599.491| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10038 Z= 0.146 Angle : 0.481 5.869 13607 Z= 0.267 Chirality : 0.037 0.135 1540 Planarity : 0.004 0.055 1713 Dihedral : 7.636 89.778 1429 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.08 % Allowed : 14.20 % Favored : 84.72 % 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 are not related in a simple way. whole: 0.60 (0.24), residues: 1233 helix: 1.54 (0.18), residues: 785 sheet: -1.63 (0.54), residues: 81 loop : -1.64 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 521 TYR 0.013 0.001 TYR C 434 PHE 0.016 0.001 PHE D 139 TRP 0.014 0.001 TRP C 78 HIS 0.012 0.001 HIS C 556 Details of bonding type rmsd covalent geometry : bond 0.00319 (10038) covalent geometry : angle 0.48110 (13607) hydrogen bonds : bond 0.03577 ( 624) hydrogen bonds : angle 4.36180 ( 1821) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.7883 (tpp) cc_final: 0.7433 (tpp) REVERT: C 545 MET cc_start: 0.5683 (ttm) cc_final: 0.5387 (ttm) REVERT: D 661 MET cc_start: 0.4274 (OUTLIER) cc_final: 0.3917 (mpp) outliers start: 11 outliers final: 8 residues processed: 113 average time/residue: 0.1630 time to fit residues: 28.1637 Evaluate side-chains 108 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 109 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.196371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.147674 restraints weight = 34552.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.144248 restraints weight = 28642.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147152 restraints weight = 24816.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.147449 restraints weight = 15756.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.148036 restraints weight = 14271.930| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10038 Z= 0.112 Angle : 0.469 6.232 13607 Z= 0.258 Chirality : 0.037 0.135 1540 Planarity : 0.004 0.053 1713 Dihedral : 7.537 89.772 1429 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.78 % Allowed : 14.40 % Favored : 84.82 % 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 are not related in a simple way. whole: 0.82 (0.24), residues: 1233 helix: 1.70 (0.18), residues: 782 sheet: -1.56 (0.54), residues: 81 loop : -1.49 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 521 TYR 0.013 0.001 TYR C 214 PHE 0.034 0.001 PHE D 139 TRP 0.014 0.001 TRP C 78 HIS 0.013 0.001 HIS C 556 Details of bonding type rmsd covalent geometry : bond 0.00236 (10038) covalent geometry : angle 0.46900 (13607) hydrogen bonds : bond 0.03457 ( 624) hydrogen bonds : angle 4.27167 ( 1821) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.7863 (tpp) cc_final: 0.7414 (tpp) REVERT: C 545 MET cc_start: 0.5657 (ttm) cc_final: 0.5361 (ttm) REVERT: D 661 MET cc_start: 0.4205 (OUTLIER) cc_final: 0.3884 (mpp) outliers start: 8 outliers final: 6 residues processed: 106 average time/residue: 0.1629 time to fit residues: 26.6308 Evaluate side-chains 106 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.194498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.145527 restraints weight = 34683.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143131 restraints weight = 29894.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.146165 restraints weight = 24560.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.146352 restraints weight = 15417.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147154 restraints weight = 14525.324| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10038 Z= 0.169 Angle : 0.497 6.398 13607 Z= 0.276 Chirality : 0.038 0.134 1540 Planarity : 0.004 0.054 1713 Dihedral : 7.457 88.468 1427 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.88 % Allowed : 14.79 % Favored : 84.33 % 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 are not related in a simple way. whole: 0.69 (0.24), residues: 1233 helix: 1.58 (0.18), residues: 783 sheet: -1.58 (0.54), residues: 81 loop : -1.53 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 521 TYR 0.012 0.001 TYR C 15 PHE 0.016 0.001 PHE D 139 TRP 0.015 0.001 TRP C 78 HIS 0.015 0.001 HIS C 556 Details of bonding type rmsd covalent geometry : bond 0.00372 (10038) covalent geometry : angle 0.49703 (13607) hydrogen bonds : bond 0.03612 ( 624) hydrogen bonds : angle 4.34634 ( 1821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.00 seconds wall clock time: 43 minutes 32.88 seconds (2612.88 seconds total)