Starting phenix.real_space_refine on Thu Aug 6 03:57:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9q_39867/08_2026/8z9q_39867.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9q_39867/08_2026/8z9q_39867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9q_39867/08_2026/8z9q_39867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9q_39867/08_2026/8z9q_39867.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9q_39867/08_2026/8z9q_39867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9q_39867/08_2026/8z9q_39867.cif" } resolution = 2.33 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= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 74 5.16 5 C 7803 2.51 5 N 2153 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12362 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5020 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain: "B" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5190 Classifications: {'peptide': 647} Link IDs: {'PTRANS': 33, 'TRANS': 613} Chain breaks: 4 Chain: "C" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1926 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain breaks: 1 Chain: "D" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 226 Unusual residues: {'ATP': 1} Classifications: {'RNA': 9, 'undetermined': 1} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 5, None: 1} Not linked: pdbres="ATP D 1 " pdbres=" G D 2 " Time building chain proxies: 2.57, per 1000 atoms: 0.21 Number of scatterers: 12362 At special positions: 0 Unit cell: (91.104, 100.74, 134.028, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 12 15.00 O 2320 8.00 N 2153 7.00 C 7803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 521.2 milliseconds 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2878 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 50.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 4.964A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 80 through 84 removed outlier: 4.024A pdb=" N THR A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.559A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 305 through 316 removed outlier: 4.121A pdb=" N GLN A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.879A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.375A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 Processing helix chain 'A' and resid 485 through 493 removed outlier: 3.593A pdb=" N ASN A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 Processing helix chain 'A' and resid 498 through 517 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.458A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 4.052A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 11 through 16 removed outlier: 3.527A pdb=" N THR B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 33 through 47 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.946A pdb=" N LYS B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.398A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.797A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 Proline residue: B 338 - end of helix removed outlier: 3.541A pdb=" N SER B 344 " --> pdb=" O MET B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 removed outlier: 4.315A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 removed outlier: 3.543A pdb=" N SER B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 449 Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 587 through 595 Processing helix chain 'B' and resid 648 through 662 Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.505A pdb=" N VAL B 669 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 694 Processing helix chain 'B' and resid 698 through 708 removed outlier: 3.559A pdb=" N ARG B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 33 through 36 removed outlier: 6.158A pdb=" N THR C 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 33 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.853A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 126 through 135 Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.525A pdb=" N LYS C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.598A pdb=" N ILE C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.789A pdb=" N GLU C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.926A pdb=" N CYS C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 238 removed outlier: 4.255A pdb=" N ILE A 450 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 423 through 431 current: chain 'A' and resid 463 through 469 removed outlier: 6.777A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.345A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 442 through 451 current: chain 'A' and resid 290 through 291 Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.502A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 227 through 230 Processing sheet with id=AA9, first strand: chain 'B' and resid 380 through 381 Processing sheet with id=AB1, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.867A pdb=" N THR C 97 " --> pdb=" O MET C 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 143 removed outlier: 4.900A pdb=" N HIS C 252 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE C 141 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR C 250 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.605A pdb=" N LYS C 151 " --> pdb=" O LEU C 227 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1533 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: 2.14 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3994 1.34 - 1.46: 1800 1.46 - 1.57: 6720 1.57 - 1.69: 22 1.69 - 1.81: 120 Bond restraints: 12656 Sorted by residual: bond pdb=" CB ARG B 315 " pdb=" CG ARG B 315 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" CB ILE B 452 " pdb=" CG2 ILE B 452 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CA ARG A 147 " pdb=" CB ARG A 147 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.17e+00 bond pdb=" CG1 ILE A 606 " pdb=" CD1 ILE A 606 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.14e-01 bond pdb=" N LYS B 357 " pdb=" CA LYS B 357 " ideal model delta sigma weight residual 1.468 1.458 0.010 1.24e-02 6.50e+03 6.12e-01 ... (remaining 12651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 17017 2.28 - 4.56: 151 4.56 - 6.85: 13 6.85 - 9.13: 2 9.13 - 11.41: 1 Bond angle restraints: 17184 Sorted by residual: angle pdb=" C CYS A 146 " pdb=" N ARG A 147 " pdb=" CA ARG A 147 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" O5' A D 7 " pdb=" C5' A D 7 " pdb=" C4' A D 7 " ideal model delta sigma weight residual 109.40 112.85 -3.45 8.00e-01 1.56e+00 1.86e+01 angle pdb=" N ARG A 147 " pdb=" CA ARG A 147 " pdb=" CB ARG A 147 " ideal model delta sigma weight residual 110.49 115.74 -5.25 1.69e+00 3.50e-01 9.64e+00 angle pdb=" O5' A D 5 " pdb=" C5' A D 5 " pdb=" C4' A D 5 " ideal model delta sigma weight residual 109.40 111.83 -2.43 8.00e-01 1.56e+00 9.22e+00 angle pdb=" O5' A D 10 " pdb=" C5' A D 10 " pdb=" C4' A D 10 " ideal model delta sigma weight residual 109.40 111.72 -2.32 8.00e-01 1.56e+00 8.43e+00 ... (remaining 17179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7114 17.77 - 35.53: 493 35.53 - 53.30: 87 53.30 - 71.07: 25 71.07 - 88.83: 14 Dihedral angle restraints: 7733 sinusoidal: 3307 harmonic: 4426 Sorted by residual: dihedral pdb=" CA ARG A 147 " pdb=" C ARG A 147 " pdb=" N ALA A 148 " pdb=" CA ALA A 148 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LEU A 145 " pdb=" C LEU A 145 " pdb=" N CYS A 146 " pdb=" CA CYS A 146 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS C 233 " pdb=" C HIS C 233 " pdb=" N THR C 234 " pdb=" CA THR C 234 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1345 0.036 - 0.072: 417 0.072 - 0.108: 118 0.108 - 0.145: 37 0.145 - 0.181: 2 Chirality restraints: 1919 Sorted by residual: chirality pdb=" CB ILE B 452 " pdb=" CA ILE B 452 " pdb=" CG1 ILE B 452 " pdb=" CG2 ILE B 452 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CG LEU A 550 " pdb=" CB LEU A 550 " pdb=" CD1 LEU A 550 " pdb=" CD2 LEU A 550 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ARG A 147 " pdb=" N ARG A 147 " pdb=" C ARG A 147 " pdb=" CB ARG A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1916 not shown) Planarity restraints: 2158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 463 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 464 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 464 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 464 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 604 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 605 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 11 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO B 12 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 12 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 12 " -0.023 5.00e-02 4.00e+02 ... (remaining 2155 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 234 2.67 - 3.23: 11908 3.23 - 3.79: 19866 3.79 - 4.34: 28172 4.34 - 4.90: 45310 Nonbonded interactions: 105490 Sorted by model distance: nonbonded pdb=" OG SER B 472 " pdb=" O VAL B 483 " model vdw 2.117 3.040 nonbonded pdb=" OD2 ASP B 500 " pdb=" OH TYR B 537 " model vdw 2.134 3.040 nonbonded pdb=" O ASN C 163 " pdb=" OG SER C 166 " model vdw 2.211 3.040 nonbonded pdb=" O THR A 269 " pdb=" OG SER A 463 " model vdw 2.238 3.040 nonbonded pdb=" OD1 ASP B 172 " pdb=" NH2 ARG B 216 " model vdw 2.243 3.120 ... (remaining 105485 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 0.003 0.036 12657 Z= 0.118 Angle : 0.542 11.412 17184 Z= 0.287 Chirality : 0.040 0.181 1919 Planarity : 0.005 0.042 2158 Dihedral : 13.208 88.832 4855 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 0.58 (0.22), residues: 1489 helix: 1.12 (0.20), residues: 688 sheet: 0.62 (0.47), residues: 124 loop : -0.35 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 686 TYR 0.019 0.001 TYR B 104 PHE 0.027 0.002 PHE A 483 TRP 0.013 0.001 TRP A 336 HIS 0.006 0.001 HIS A 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (12656) covalent geometry : angle 0.54163 / 0.29 (17184) hydrogen bonds : bond 0.15861 / 10.64 ( 544) hydrogen bonds : angle 6.19319 / 4.39 ( 1533) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.369 Fit side-chains REVERT: A 86 ASP cc_start: 0.7653 (m-30) cc_final: 0.7424 (m-30) REVERT: A 139 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 163 GLU cc_start: 0.8261 (tp30) cc_final: 0.7851 (tp30) REVERT: A 307 GLN cc_start: 0.7293 (pp30) cc_final: 0.7090 (pp30) REVERT: B 30 TYR cc_start: 0.7834 (m-80) cc_final: 0.7596 (m-80) REVERT: B 243 ILE cc_start: 0.9069 (pt) cc_final: 0.8855 (pp) REVERT: B 283 LYS cc_start: 0.8272 (tptt) cc_final: 0.8033 (tppt) REVERT: B 287 LYS cc_start: 0.7869 (tmtt) cc_final: 0.7626 (tmtt) REVERT: B 672 GLN cc_start: 0.7878 (mt0) cc_final: 0.7360 (pt0) REVERT: C 127 ASP cc_start: 0.7121 (t0) cc_final: 0.6828 (t0) REVERT: C 201 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7583 (tm-30) REVERT: C 210 GLU cc_start: 0.7759 (pm20) cc_final: 0.7545 (mp0) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.7727 time to fit residues: 186.9412 Evaluate side-chains 174 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.0040 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 156 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 123 GLN B 232 HIS B 302 GLN B 397 ASN B 433 HIS B 506 ASN C 214 HIS C 252 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.135272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104766 restraints weight = 15229.750| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.12 r_work: 0.3222 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12657 Z= 0.121 Angle : 0.552 7.336 17184 Z= 0.291 Chirality : 0.039 0.134 1919 Planarity : 0.005 0.045 2158 Dihedral : 8.600 84.093 1797 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.00 % Allowed : 7.77 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1489 helix: 1.40 (0.21), residues: 690 sheet: 0.54 (0.48), residues: 118 loop : -0.35 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 512 TYR 0.019 0.001 TYR B 533 PHE 0.023 0.002 PHE C 41 TRP 0.011 0.001 TRP A 336 HIS 0.007 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12656) covalent geometry : angle 0.55235 / 0.29 (17184) hydrogen bonds : bond 0.04261 / 2.98 ( 544) hydrogen bonds : angle 4.93700 / 3.50 ( 1533) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.475 Fit side-chains REVERT: A 9 ASP cc_start: 0.8062 (p0) cc_final: 0.7652 (t70) REVERT: A 17 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7569 (tp30) REVERT: A 86 ASP cc_start: 0.7902 (m-30) cc_final: 0.7654 (m-30) REVERT: A 139 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7081 (tm-30) REVERT: A 163 GLU cc_start: 0.8422 (tp30) cc_final: 0.7936 (tp30) REVERT: B 100 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7532 (pt0) REVERT: B 283 LYS cc_start: 0.8567 (tptt) cc_final: 0.8188 (tppt) REVERT: B 287 LYS cc_start: 0.7943 (tmtt) cc_final: 0.7693 (tmtt) REVERT: B 348 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7642 (t70) REVERT: B 369 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8153 (mtp) REVERT: B 482 ASN cc_start: 0.8750 (t0) cc_final: 0.8456 (t0) REVERT: B 576 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: B 672 GLN cc_start: 0.7950 (mt0) cc_final: 0.7350 (pt0) REVERT: B 693 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7739 (tm-30) REVERT: C 201 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7878 (tm-30) outliers start: 27 outliers final: 7 residues processed: 203 average time/residue: 0.6432 time to fit residues: 140.0163 Evaluate side-chains 187 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 163 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 125 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 336 ASN B 397 ASN B 506 ASN C 214 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097985 restraints weight = 15346.097| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.16 r_work: 0.3114 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12657 Z= 0.227 Angle : 0.623 6.702 17184 Z= 0.328 Chirality : 0.044 0.151 1919 Planarity : 0.005 0.053 2158 Dihedral : 8.623 84.481 1797 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.29 % Allowed : 9.39 % Favored : 88.31 % 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: 0.56 (0.22), residues: 1489 helix: 1.23 (0.20), residues: 687 sheet: 0.28 (0.47), residues: 118 loop : -0.43 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 576 TYR 0.019 0.002 TYR B 533 PHE 0.029 0.002 PHE C 41 TRP 0.012 0.002 TRP A 336 HIS 0.013 0.002 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (12656) covalent geometry : angle 0.62287 / 0.33 (17184) hydrogen bonds : bond 0.04866 / 3.37 ( 544) hydrogen bonds : angle 4.75548 / 3.40 ( 1533) Misc. bond : bond 0.00049 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.459 Fit side-chains REVERT: A 9 ASP cc_start: 0.8072 (p0) cc_final: 0.7691 (t70) REVERT: A 17 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: A 49 HIS cc_start: 0.7862 (m90) cc_final: 0.7607 (m90) REVERT: A 86 ASP cc_start: 0.8082 (m-30) cc_final: 0.7735 (m-30) REVERT: A 139 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 147 ARG cc_start: 0.8029 (ptm-80) cc_final: 0.7666 (ptm-80) REVERT: A 163 GLU cc_start: 0.8441 (tp30) cc_final: 0.7940 (tp30) REVERT: A 205 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6609 (mm-30) REVERT: A 320 GLU cc_start: 0.8288 (mp0) cc_final: 0.8086 (mp0) REVERT: B 93 ARG cc_start: 0.7532 (mtm110) cc_final: 0.7277 (mtm110) REVERT: B 100 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7518 (pt0) REVERT: B 144 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: B 283 LYS cc_start: 0.8549 (tptt) cc_final: 0.8197 (tppt) REVERT: B 469 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 672 GLN cc_start: 0.7861 (mt0) cc_final: 0.7198 (pt0) REVERT: C 127 ASP cc_start: 0.8035 (t0) cc_final: 0.7591 (m-30) REVERT: C 146 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7319 (mtt) REVERT: C 201 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7885 (tm-30) outliers start: 31 outliers final: 12 residues processed: 205 average time/residue: 0.6654 time to fit residues: 146.1524 Evaluate side-chains 196 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 94 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 86 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.1359 > 50:) chunk 105 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN B 55 GLN B 123 GLN B 397 ASN B 506 ASN B 663 ASN C 214 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100294 restraints weight = 15133.354| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.09 r_work: 0.3152 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12657 Z= 0.139 Angle : 0.545 6.213 17184 Z= 0.287 Chirality : 0.040 0.134 1919 Planarity : 0.005 0.051 2158 Dihedral : 8.432 83.390 1797 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.92 % Allowed : 11.09 % Favored : 86.98 % 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: 0.68 (0.22), residues: 1489 helix: 1.39 (0.21), residues: 686 sheet: 0.19 (0.46), residues: 118 loop : -0.42 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 92 TYR 0.018 0.001 TYR B 533 PHE 0.024 0.002 PHE C 41 TRP 0.012 0.001 TRP B 330 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (12656) covalent geometry : angle 0.54500 / 0.29 (17184) hydrogen bonds : bond 0.03999 / 2.77 ( 544) hydrogen bonds : angle 4.59006 / 3.28 ( 1533) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.486 Fit side-chains REVERT: A 9 ASP cc_start: 0.8013 (p0) cc_final: 0.7624 (t70) REVERT: A 18 THR cc_start: 0.8840 (m) cc_final: 0.8549 (p) REVERT: A 49 HIS cc_start: 0.7948 (m90) cc_final: 0.7705 (m90) REVERT: A 64 ASP cc_start: 0.7277 (t70) cc_final: 0.6923 (t0) REVERT: A 86 ASP cc_start: 0.8124 (m-30) cc_final: 0.7774 (m-30) REVERT: A 139 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 163 GLU cc_start: 0.8434 (tp30) cc_final: 0.7921 (tp30) REVERT: A 320 GLU cc_start: 0.8259 (mp0) cc_final: 0.8048 (mp0) REVERT: B 93 ARG cc_start: 0.7550 (mtm110) cc_final: 0.7285 (mtm110) REVERT: B 100 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7498 (pt0) REVERT: B 283 LYS cc_start: 0.8549 (tptt) cc_final: 0.8170 (tppt) REVERT: B 469 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 672 GLN cc_start: 0.7898 (mt0) cc_final: 0.7193 (pt0) REVERT: B 685 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8021 (tptp) REVERT: C 18 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8289 (tp30) REVERT: C 25 LYS cc_start: 0.8471 (ttpp) cc_final: 0.8236 (ttpp) REVERT: C 75 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7897 (pt) REVERT: C 127 ASP cc_start: 0.7984 (t0) cc_final: 0.7577 (m-30) REVERT: C 146 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7277 (mtt) REVERT: C 201 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7827 (tm-30) outliers start: 26 outliers final: 7 residues processed: 200 average time/residue: 0.7003 time to fit residues: 149.5923 Evaluate side-chains 185 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 685 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 146 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 66 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN A 307 GLN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100306 restraints weight = 15298.442| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.14 r_work: 0.3150 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12657 Z= 0.137 Angle : 0.540 7.897 17184 Z= 0.284 Chirality : 0.040 0.132 1919 Planarity : 0.004 0.049 2158 Dihedral : 8.309 83.299 1797 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.00 % Allowed : 11.76 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.22), residues: 1489 helix: 1.43 (0.21), residues: 686 sheet: 0.13 (0.46), residues: 118 loop : -0.43 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 92 TYR 0.018 0.001 TYR B 533 PHE 0.023 0.002 PHE C 41 TRP 0.011 0.001 TRP B 230 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (12656) covalent geometry : angle 0.54021 / 0.28 (17184) hydrogen bonds : bond 0.03897 / 2.70 ( 544) hydrogen bonds : angle 4.51121 / 3.23 ( 1533) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.511 Fit side-chains REVERT: A 9 ASP cc_start: 0.8011 (p0) cc_final: 0.7617 (t70) REVERT: A 18 THR cc_start: 0.8759 (m) cc_final: 0.8470 (p) REVERT: A 49 HIS cc_start: 0.7912 (m90) cc_final: 0.7653 (m90) REVERT: A 86 ASP cc_start: 0.8129 (m-30) cc_final: 0.7767 (m-30) REVERT: A 139 GLN cc_start: 0.7698 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 163 GLU cc_start: 0.8436 (tp30) cc_final: 0.7919 (tp30) REVERT: A 205 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6546 (mm-30) REVERT: A 212 MET cc_start: 0.7817 (ttp) cc_final: 0.7535 (ttm) REVERT: A 320 GLU cc_start: 0.8280 (mp0) cc_final: 0.8041 (mp0) REVERT: B 93 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7263 (mtm110) REVERT: B 100 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7489 (pt0) REVERT: B 283 LYS cc_start: 0.8533 (tptt) cc_final: 0.8151 (tppt) REVERT: B 287 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7578 (tmtt) REVERT: B 469 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 576 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: B 672 GLN cc_start: 0.7876 (mt0) cc_final: 0.7151 (pt0) REVERT: C 18 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: C 75 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7959 (pt) REVERT: C 127 ASP cc_start: 0.7980 (t0) cc_final: 0.7577 (m-30) REVERT: C 146 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7245 (mtt) REVERT: C 201 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7876 (tm-30) outliers start: 27 outliers final: 8 residues processed: 196 average time/residue: 0.7038 time to fit residues: 147.9818 Evaluate side-chains 188 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.0170 chunk 77 optimal weight: 0.3980 chunk 30 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 214 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.102279 restraints weight = 15246.137| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.15 r_work: 0.3178 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12657 Z= 0.109 Angle : 0.517 6.125 17184 Z= 0.272 Chirality : 0.039 0.142 1919 Planarity : 0.004 0.046 2158 Dihedral : 8.127 81.397 1797 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.63 % Allowed : 12.43 % Favored : 85.95 % 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 (0.22), residues: 1489 helix: 1.57 (0.21), residues: 684 sheet: 0.09 (0.46), residues: 118 loop : -0.37 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 92 TYR 0.019 0.001 TYR B 104 PHE 0.021 0.001 PHE C 41 TRP 0.012 0.001 TRP B 330 HIS 0.007 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (12656) covalent geometry : angle 0.51735 / 0.27 (17184) hydrogen bonds : bond 0.03505 / 2.44 ( 544) hydrogen bonds : angle 4.40287 / 3.14 ( 1533) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.528 Fit side-chains REVERT: A 9 ASP cc_start: 0.7976 (p0) cc_final: 0.7600 (t70) REVERT: A 18 THR cc_start: 0.8782 (m) cc_final: 0.8510 (p) REVERT: A 64 ASP cc_start: 0.7292 (t70) cc_final: 0.6895 (t0) REVERT: A 86 ASP cc_start: 0.8130 (m-30) cc_final: 0.7766 (m-30) REVERT: A 139 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 163 GLU cc_start: 0.8442 (tp30) cc_final: 0.7923 (tp30) REVERT: A 212 MET cc_start: 0.7851 (ttp) cc_final: 0.7563 (ttm) REVERT: A 320 GLU cc_start: 0.8279 (mp0) cc_final: 0.8006 (mp0) REVERT: B 93 ARG cc_start: 0.7553 (mtm110) cc_final: 0.7285 (mtm110) REVERT: B 100 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7468 (pt0) REVERT: B 283 LYS cc_start: 0.8529 (tptt) cc_final: 0.8145 (tppt) REVERT: B 469 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7878 (tm-30) REVERT: B 576 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: B 672 GLN cc_start: 0.7937 (mt0) cc_final: 0.7159 (pt0) REVERT: B 682 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7268 (mp0) REVERT: C 75 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7973 (pt) REVERT: C 127 ASP cc_start: 0.7955 (t0) cc_final: 0.7566 (m-30) REVERT: C 201 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7869 (tm-30) REVERT: C 222 SER cc_start: 0.8472 (t) cc_final: 0.8247 (m) outliers start: 22 outliers final: 8 residues processed: 199 average time/residue: 0.7070 time to fit residues: 150.8075 Evaluate side-chains 186 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 129 optimal weight: 0.0870 chunk 93 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 214 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102228 restraints weight = 15095.912| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.14 r_work: 0.3178 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12657 Z= 0.113 Angle : 0.525 10.037 17184 Z= 0.274 Chirality : 0.039 0.138 1919 Planarity : 0.004 0.045 2158 Dihedral : 8.020 81.355 1797 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.48 % Allowed : 12.87 % Favored : 85.65 % 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: 0.84 (0.22), residues: 1489 helix: 1.59 (0.21), residues: 684 sheet: 0.06 (0.45), residues: 118 loop : -0.36 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 92 TYR 0.018 0.001 TYR B 533 PHE 0.021 0.001 PHE C 41 TRP 0.011 0.001 TRP B 330 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (12656) covalent geometry : angle 0.52544 / 0.27 (17184) hydrogen bonds : bond 0.03522 / 2.45 ( 544) hydrogen bonds : angle 4.34533 / 3.11 ( 1533) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.461 Fit side-chains REVERT: A 9 ASP cc_start: 0.7945 (p0) cc_final: 0.7599 (t70) REVERT: A 18 THR cc_start: 0.8761 (m) cc_final: 0.8479 (p) REVERT: A 64 ASP cc_start: 0.7284 (t70) cc_final: 0.6908 (t0) REVERT: A 86 ASP cc_start: 0.8125 (m-30) cc_final: 0.7761 (m-30) REVERT: A 139 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 163 GLU cc_start: 0.8440 (tp30) cc_final: 0.7923 (tp30) REVERT: A 212 MET cc_start: 0.7879 (ttp) cc_final: 0.7576 (ttm) REVERT: A 320 GLU cc_start: 0.8266 (mp0) cc_final: 0.7972 (mp0) REVERT: B 93 ARG cc_start: 0.7499 (mtm110) cc_final: 0.7220 (mtm110) REVERT: B 100 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7472 (pt0) REVERT: B 283 LYS cc_start: 0.8514 (tptt) cc_final: 0.8135 (tppt) REVERT: B 469 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 576 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: B 672 GLN cc_start: 0.7963 (mt0) cc_final: 0.7188 (pt0) REVERT: B 682 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7208 (mp0) REVERT: C 75 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7995 (pt) REVERT: C 127 ASP cc_start: 0.8008 (t0) cc_final: 0.7613 (m-30) REVERT: C 201 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7866 (tm-30) REVERT: C 222 SER cc_start: 0.8458 (t) cc_final: 0.8225 (m) outliers start: 20 outliers final: 9 residues processed: 187 average time/residue: 0.7199 time to fit residues: 144.4686 Evaluate side-chains 184 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 180 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 147 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN A 507 GLN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 214 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.101917 restraints weight = 15171.684| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.13 r_work: 0.3172 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12657 Z= 0.123 Angle : 0.525 7.547 17184 Z= 0.274 Chirality : 0.039 0.134 1919 Planarity : 0.004 0.046 2158 Dihedral : 7.991 82.067 1797 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.18 % Allowed : 13.24 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.84 (0.22), residues: 1489 helix: 1.60 (0.21), residues: 684 sheet: 0.04 (0.45), residues: 118 loop : -0.37 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 92 TYR 0.018 0.001 TYR B 533 PHE 0.022 0.001 PHE C 41 TRP 0.011 0.001 TRP B 330 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (12656) covalent geometry : angle 0.52494 / 0.27 (17184) hydrogen bonds : bond 0.03578 / 2.49 ( 544) hydrogen bonds : angle 4.31034 / 3.09 ( 1533) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.620 Fit side-chains REVERT: A 9 ASP cc_start: 0.7945 (p0) cc_final: 0.7605 (t70) REVERT: A 18 THR cc_start: 0.8781 (m) cc_final: 0.8505 (p) REVERT: A 64 ASP cc_start: 0.7284 (t70) cc_final: 0.6906 (t0) REVERT: A 86 ASP cc_start: 0.8127 (m-30) cc_final: 0.7678 (m-30) REVERT: A 139 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7228 (tm-30) REVERT: A 153 VAL cc_start: 0.8576 (t) cc_final: 0.8346 (m) REVERT: A 163 GLU cc_start: 0.8444 (tp30) cc_final: 0.7932 (tp30) REVERT: A 320 GLU cc_start: 0.8270 (mp0) cc_final: 0.7974 (mp0) REVERT: B 93 ARG cc_start: 0.7514 (mtm110) cc_final: 0.7228 (mtm110) REVERT: B 100 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7481 (pt0) REVERT: B 283 LYS cc_start: 0.8530 (tptt) cc_final: 0.8145 (tppt) REVERT: B 469 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7664 (tm-30) REVERT: B 576 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: B 672 GLN cc_start: 0.7975 (mt0) cc_final: 0.7181 (pt0) REVERT: C 75 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7971 (pt) REVERT: C 127 ASP cc_start: 0.8015 (t0) cc_final: 0.7635 (m-30) REVERT: C 201 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7860 (tm-30) REVERT: C 222 SER cc_start: 0.8458 (t) cc_final: 0.8227 (m) outliers start: 16 outliers final: 10 residues processed: 191 average time/residue: 0.6833 time to fit residues: 140.1832 Evaluate side-chains 182 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 85 optimal weight: 0.0270 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN A 311 GLN B 55 GLN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 214 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101924 restraints weight = 15138.718| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.13 r_work: 0.3173 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12657 Z= 0.121 Angle : 0.532 9.801 17184 Z= 0.279 Chirality : 0.039 0.135 1919 Planarity : 0.004 0.045 2158 Dihedral : 7.955 82.260 1797 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.33 % Allowed : 13.46 % Favored : 85.21 % 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: 0.85 (0.22), residues: 1489 helix: 1.60 (0.21), residues: 685 sheet: 0.02 (0.45), residues: 118 loop : -0.35 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 92 TYR 0.018 0.001 TYR B 533 PHE 0.022 0.001 PHE C 41 TRP 0.011 0.001 TRP B 330 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (12656) covalent geometry : angle 0.53247 / 0.28 (17184) hydrogen bonds : bond 0.03551 / 2.47 ( 544) hydrogen bonds : angle 4.30322 / 3.08 ( 1533) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.514 Fit side-chains REVERT: A 9 ASP cc_start: 0.7924 (p0) cc_final: 0.7592 (t70) REVERT: A 18 THR cc_start: 0.8769 (m) cc_final: 0.8492 (p) REVERT: A 64 ASP cc_start: 0.7290 (t70) cc_final: 0.6909 (t0) REVERT: A 86 ASP cc_start: 0.8125 (m-30) cc_final: 0.7653 (m-30) REVERT: A 139 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7246 (tm-30) REVERT: A 153 VAL cc_start: 0.8563 (t) cc_final: 0.8335 (m) REVERT: A 163 GLU cc_start: 0.8440 (tp30) cc_final: 0.7930 (tp30) REVERT: A 320 GLU cc_start: 0.8265 (mp0) cc_final: 0.7967 (mp0) REVERT: B 93 ARG cc_start: 0.7455 (mtm110) cc_final: 0.7167 (mtm110) REVERT: B 100 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7463 (pt0) REVERT: B 283 LYS cc_start: 0.8532 (tptt) cc_final: 0.8150 (tppt) REVERT: B 469 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 576 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: B 672 GLN cc_start: 0.7930 (mt0) cc_final: 0.7124 (pt0) REVERT: C 75 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7969 (pt) REVERT: C 127 ASP cc_start: 0.8016 (t0) cc_final: 0.7624 (m-30) REVERT: C 194 GLU cc_start: 0.7885 (tt0) cc_final: 0.7600 (tm-30) REVERT: C 201 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7860 (tm-30) REVERT: C 222 SER cc_start: 0.8457 (t) cc_final: 0.8222 (m) outliers start: 18 outliers final: 10 residues processed: 183 average time/residue: 0.7299 time to fit residues: 143.3852 Evaluate side-chains 179 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 144 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101829 restraints weight = 15192.541| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.14 r_work: 0.3171 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12657 Z= 0.124 Angle : 0.535 7.382 17184 Z= 0.280 Chirality : 0.039 0.137 1919 Planarity : 0.004 0.046 2158 Dihedral : 7.935 82.654 1797 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.96 % Allowed : 13.76 % Favored : 85.28 % 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: 0.85 (0.22), residues: 1489 helix: 1.60 (0.21), residues: 685 sheet: 0.03 (0.45), residues: 118 loop : -0.36 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 92 TYR 0.018 0.001 TYR B 533 PHE 0.022 0.001 PHE C 41 TRP 0.011 0.001 TRP B 330 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (12656) covalent geometry : angle 0.53470 / 0.28 (17184) hydrogen bonds : bond 0.03566 / 2.49 ( 544) hydrogen bonds : angle 4.29077 / 3.07 ( 1533) Misc. bond : bond 0.00022 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.406 Fit side-chains REVERT: A 9 ASP cc_start: 0.7922 (p0) cc_final: 0.7592 (t70) REVERT: A 18 THR cc_start: 0.8765 (m) cc_final: 0.8482 (p) REVERT: A 64 ASP cc_start: 0.7250 (t70) cc_final: 0.6877 (t0) REVERT: A 86 ASP cc_start: 0.8127 (m-30) cc_final: 0.7658 (m-30) REVERT: A 139 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7247 (tm-30) REVERT: A 153 VAL cc_start: 0.8553 (t) cc_final: 0.8329 (m) REVERT: A 163 GLU cc_start: 0.8447 (tp30) cc_final: 0.7936 (tp30) REVERT: A 320 GLU cc_start: 0.8260 (mp0) cc_final: 0.7941 (mp0) REVERT: B 93 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7170 (mtm110) REVERT: B 100 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7478 (pt0) REVERT: B 283 LYS cc_start: 0.8535 (tptt) cc_final: 0.8147 (tppt) REVERT: B 469 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 576 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: B 672 GLN cc_start: 0.7925 (mt0) cc_final: 0.7104 (pt0) REVERT: C 75 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7983 (pt) REVERT: C 127 ASP cc_start: 0.8004 (t0) cc_final: 0.7621 (m-30) REVERT: C 201 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 222 SER cc_start: 0.8456 (t) cc_final: 0.8219 (m) outliers start: 13 outliers final: 9 residues processed: 177 average time/residue: 0.6706 time to fit residues: 127.3924 Evaluate side-chains 176 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 68 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.101075 restraints weight = 15171.478| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.15 r_work: 0.3162 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12657 Z= 0.135 Angle : 0.549 11.731 17184 Z= 0.286 Chirality : 0.040 0.132 1919 Planarity : 0.004 0.046 2158 Dihedral : 7.952 83.599 1797 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.18 % Allowed : 13.91 % Favored : 84.91 % 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: 0.81 (0.22), residues: 1489 helix: 1.57 (0.21), residues: 685 sheet: 0.02 (0.45), residues: 118 loop : -0.38 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 92 TYR 0.018 0.001 TYR B 533 PHE 0.023 0.002 PHE C 41 TRP 0.011 0.001 TRP A 253 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (12656) covalent geometry : angle 0.54886 / 0.29 (17184) hydrogen bonds : bond 0.03670 / 2.55 ( 544) hydrogen bonds : angle 4.29594 / 3.08 ( 1533) Misc. bond : bond 0.00013 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5526.93 seconds wall clock time: 94 minutes 39.98 seconds (5679.98 seconds total)