Starting phenix.real_space_refine on Sat Aug 23 16:42:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9q_39867/08_2025/8z9q_39867.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9q_39867/08_2025/8z9q_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z9q_39867/08_2025/8z9q_39867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9q_39867/08_2025/8z9q_39867.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z9q_39867/08_2025/8z9q_39867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9q_39867/08_2025/8z9q_39867.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.09, per 1000 atoms: 0.25 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: 0.95 Conformation dependent library (CDL) restraints added in 602.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.43 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: 1.80 Time building geometry restraints manager: 1.31 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: 17027 2.28 - 4.56: 141 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=" 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=" CA ARG A 147 " pdb=" CB ARG A 147 " pdb=" CG ARG A 147 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.63e+00 angle pdb=" CG1 ILE B 452 " pdb=" CB ILE B 452 " pdb=" CG2 ILE B 452 " ideal model delta sigma weight residual 110.70 102.97 7.73 3.00e+00 1.11e-01 6.63e+00 angle pdb=" CA LEU B 487 " pdb=" CB LEU B 487 " pdb=" CG LEU B 487 " ideal model delta sigma weight residual 116.30 124.66 -8.36 3.50e+00 8.16e-02 5.71e+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: 1354 0.036 - 0.072: 417 0.072 - 0.108: 115 0.108 - 0.145: 31 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 12.070 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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= 0.116 Angle : 0.534 11.412 17184 Z= 0.277 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 aren 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 covalent geometry : bond 0.00261 (12656) covalent geometry : angle 0.53447 (17184) hydrogen bonds : bond 0.15861 ( 544) hydrogen bonds : angle 6.19319 ( 1533) Misc. bond : bond 0.00044 ( 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 : 0.418 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: 0.7509 time to fit residues: 181.8208 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 : 0.300 ------------------------------------------------------------------------------- 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: 6.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 433 HIS B 506 ASN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104884 restraints weight = 15239.682| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.12 r_work: 0.3221 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12657 Z= 0.116 Angle : 0.536 7.697 17184 Z= 0.282 Chirality : 0.039 0.131 1919 Planarity : 0.005 0.042 2158 Dihedral : 8.581 80.564 1797 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.85 % Allowed : 7.77 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.22), residues: 1489 helix: 1.43 (0.21), residues: 691 sheet: 0.58 (0.48), residues: 118 loop : -0.31 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 92 TYR 0.017 0.001 TYR B 533 PHE 0.024 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 covalent geometry : bond 0.00253 (12656) covalent geometry : angle 0.53647 (17184) hydrogen bonds : bond 0.04149 ( 544) hydrogen bonds : angle 4.84129 ( 1533) Misc. bond : bond 0.00052 ( 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 213 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.515 Fit side-chains REVERT: A 9 ASP cc_start: 0.8043 (p0) cc_final: 0.7608 (t70) REVERT: A 17 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7598 (tp30) REVERT: A 47 ASN cc_start: 0.7737 (t0) cc_final: 0.7510 (t0) REVERT: A 49 HIS cc_start: 0.7922 (m90) cc_final: 0.7644 (m90) REVERT: A 64 ASP cc_start: 0.7154 (t0) cc_final: 0.6903 (t0) REVERT: A 86 ASP cc_start: 0.7921 (m-30) cc_final: 0.7669 (m-30) REVERT: A 122 GLU cc_start: 0.7780 (pm20) cc_final: 0.7573 (pm20) REVERT: A 139 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7073 (tm-30) REVERT: A 163 GLU cc_start: 0.8407 (tp30) cc_final: 0.7915 (tp30) REVERT: B 100 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7522 (pt0) REVERT: B 283 LYS cc_start: 0.8560 (tptt) cc_final: 0.8180 (tppt) REVERT: B 287 LYS cc_start: 0.7933 (tmtt) cc_final: 0.7679 (tmtt) REVERT: B 469 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 482 ASN cc_start: 0.8704 (t0) cc_final: 0.8443 (t0) REVERT: B 576 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: B 672 GLN cc_start: 0.7931 (mt0) cc_final: 0.7317 (pt0) REVERT: B 693 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7597 (tm-30) REVERT: C 201 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 210 GLU cc_start: 0.7941 (pm20) cc_final: 0.7690 (mp0) outliers start: 25 outliers final: 5 residues processed: 199 average time/residue: 0.6470 time to fit residues: 138.1866 Evaluate side-chains 189 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 B residue 576 GLU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 126 GLU 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: 0.9990 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 507 GLN B 302 GLN B 336 ASN B 397 ASN B 506 ASN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.134159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103085 restraints weight = 15355.455| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.17 r_work: 0.3190 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12657 Z= 0.123 Angle : 0.523 6.268 17184 Z= 0.274 Chirality : 0.039 0.130 1919 Planarity : 0.004 0.042 2158 Dihedral : 8.311 78.106 1797 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.85 % Allowed : 9.39 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.22), residues: 1489 helix: 1.57 (0.21), residues: 685 sheet: 0.41 (0.47), residues: 118 loop : -0.28 (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 0.024 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 covalent geometry : bond 0.00279 (12656) covalent geometry : angle 0.52349 (17184) hydrogen bonds : bond 0.03829 ( 544) hydrogen bonds : angle 4.52785 ( 1533) Misc. bond : bond 0.00030 ( 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 218 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.487 Fit side-chains REVERT: A 9 ASP cc_start: 0.7932 (p0) cc_final: 0.7524 (t70) REVERT: A 18 THR cc_start: 0.8685 (m) cc_final: 0.8380 (p) REVERT: A 47 ASN cc_start: 0.7851 (t0) cc_final: 0.7559 (t0) REVERT: A 49 HIS cc_start: 0.7948 (m90) cc_final: 0.7682 (m90) REVERT: A 86 ASP cc_start: 0.8039 (m-30) cc_final: 0.7708 (m-30) REVERT: A 122 GLU cc_start: 0.7680 (pm20) cc_final: 0.7424 (pm20) REVERT: A 139 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7122 (tm-30) REVERT: A 163 GLU cc_start: 0.8422 (tp30) cc_final: 0.7900 (tp30) REVERT: B 93 ARG cc_start: 0.7540 (mtm110) cc_final: 0.7305 (mtm110) REVERT: B 100 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7526 (pt0) REVERT: B 144 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7529 (tm-30) REVERT: B 283 LYS cc_start: 0.8552 (tptt) cc_final: 0.8184 (tppt) REVERT: B 469 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 482 ASN cc_start: 0.8754 (t0) cc_final: 0.8471 (t0) REVERT: B 672 GLN cc_start: 0.8008 (mt0) cc_final: 0.7316 (pt0) REVERT: C 127 ASP cc_start: 0.7938 (t0) cc_final: 0.7531 (m-30) REVERT: C 146 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7313 (mtt) REVERT: C 201 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7848 (tm-30) REVERT: C 210 GLU cc_start: 0.8049 (pm20) cc_final: 0.7767 (mp0) outliers start: 25 outliers final: 9 residues processed: 207 average time/residue: 0.7293 time to fit residues: 160.9363 Evaluate side-chains 187 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 550 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 670 LEU 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: 4.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.0040 chunk 105 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.5730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 397 ASN B 506 ASN C 113 GLN C 154 GLN C 214 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103621 restraints weight = 15161.577| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.12 r_work: 0.3198 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12657 Z= 0.113 Angle : 0.510 5.830 17184 Z= 0.267 Chirality : 0.039 0.128 1919 Planarity : 0.004 0.043 2158 Dihedral : 8.128 77.784 1797 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.00 % Allowed : 10.43 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.22), residues: 1489 helix: 1.61 (0.21), residues: 685 sheet: 0.31 (0.46), residues: 118 loop : -0.31 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 92 TYR 0.018 0.001 TYR B 533 PHE 0.023 0.001 PHE C 41 TRP 0.010 0.001 TRP A 336 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00256 (12656) covalent geometry : angle 0.50979 (17184) hydrogen bonds : bond 0.03554 ( 544) hydrogen bonds : angle 4.41369 ( 1533) Misc. bond : bond 0.00033 ( 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 212 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.578 Fit side-chains REVERT: A 9 ASP cc_start: 0.7919 (p0) cc_final: 0.7539 (t70) REVERT: A 18 THR cc_start: 0.8688 (m) cc_final: 0.8396 (p) REVERT: A 47 ASN cc_start: 0.7821 (t0) cc_final: 0.7563 (t0) REVERT: A 49 HIS cc_start: 0.7961 (m90) cc_final: 0.7653 (m90) REVERT: A 64 ASP cc_start: 0.7206 (t0) cc_final: 0.6810 (t0) REVERT: A 86 ASP cc_start: 0.8071 (m-30) cc_final: 0.7733 (m-30) REVERT: A 139 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7185 (tm-30) REVERT: A 153 VAL cc_start: 0.8546 (t) cc_final: 0.8293 (m) REVERT: A 163 GLU cc_start: 0.8418 (tp30) cc_final: 0.7899 (tp30) REVERT: B 93 ARG cc_start: 0.7514 (mtm110) cc_final: 0.7244 (mtm110) REVERT: B 100 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7517 (pt0) REVERT: B 283 LYS cc_start: 0.8526 (tptt) cc_final: 0.8141 (tppt) REVERT: B 469 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7846 (tm-30) REVERT: B 482 ASN cc_start: 0.8747 (t0) cc_final: 0.8461 (t0) REVERT: B 576 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: B 672 GLN cc_start: 0.7988 (mt0) cc_final: 0.7273 (pt0) REVERT: C 75 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7848 (pt) REVERT: C 127 ASP cc_start: 0.7937 (t0) cc_final: 0.7556 (m-30) REVERT: C 146 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7231 (mtt) REVERT: C 201 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7893 (tm-30) REVERT: C 210 GLU cc_start: 0.8067 (pm20) cc_final: 0.7759 (mp0) REVERT: C 222 SER cc_start: 0.8422 (t) cc_final: 0.8193 (m) outliers start: 27 outliers final: 7 residues processed: 200 average time/residue: 0.6606 time to fit residues: 141.8980 Evaluate side-chains 192 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 576 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: 1.9990 chunk 88 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 307 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 397 ASN C 154 GLN C 214 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099801 restraints weight = 15265.505| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.15 r_work: 0.3139 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12657 Z= 0.170 Angle : 0.562 8.167 17184 Z= 0.295 Chirality : 0.041 0.134 1919 Planarity : 0.005 0.049 2158 Dihedral : 8.235 82.700 1797 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.00 % Allowed : 11.32 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.22), residues: 1489 helix: 1.49 (0.21), residues: 686 sheet: 0.18 (0.46), residues: 118 loop : -0.35 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 92 TYR 0.019 0.002 TYR B 533 PHE 0.026 0.002 PHE C 41 TRP 0.012 0.001 TRP A 253 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00401 (12656) covalent geometry : angle 0.56217 (17184) hydrogen bonds : bond 0.04122 ( 544) hydrogen bonds : angle 4.45020 ( 1533) Misc. bond : bond 0.00005 ( 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 210 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.490 Fit side-chains REVERT: A 9 ASP cc_start: 0.7935 (p0) cc_final: 0.7597 (t70) REVERT: A 18 THR cc_start: 0.8830 (m) cc_final: 0.8529 (p) REVERT: A 49 HIS cc_start: 0.7926 (m90) cc_final: 0.7648 (m90) REVERT: A 64 ASP cc_start: 0.7264 (t0) cc_final: 0.6939 (t0) REVERT: A 86 ASP cc_start: 0.8100 (m-30) cc_final: 0.7662 (m-30) REVERT: A 139 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7200 (tm-30) REVERT: A 163 GLU cc_start: 0.8442 (tp30) cc_final: 0.7932 (tp30) REVERT: A 205 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6596 (mm-30) REVERT: A 212 MET cc_start: 0.7911 (ttp) cc_final: 0.7658 (ttm) REVERT: B 93 ARG cc_start: 0.7549 (mtm110) cc_final: 0.7260 (mtm110) REVERT: B 100 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7492 (pt0) REVERT: B 283 LYS cc_start: 0.8545 (tptt) cc_final: 0.8185 (tppt) REVERT: B 469 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7870 (tm-30) REVERT: B 482 ASN cc_start: 0.8795 (t0) cc_final: 0.8566 (t0) REVERT: B 576 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: B 672 GLN cc_start: 0.7938 (mt0) cc_final: 0.7200 (pt0) REVERT: B 682 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6868 (mt-10) REVERT: C 75 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7902 (pt) REVERT: C 127 ASP cc_start: 0.8017 (t0) cc_final: 0.7603 (m-30) REVERT: C 146 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7281 (mtt) REVERT: C 201 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 210 GLU cc_start: 0.8103 (pm20) cc_final: 0.7765 (mp0) outliers start: 27 outliers final: 10 residues processed: 195 average time/residue: 0.6895 time to fit residues: 143.3930 Evaluate side-chains 191 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 B residue 670 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 54 GLN 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: 0.1980 chunk 19 optimal weight: 0.0030 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 129 optimal weight: 0.2980 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 123 GLN 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 = 0.3735 r_free = 0.3735 target = 0.135035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104179 restraints weight = 15246.865| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.15 r_work: 0.3206 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1733 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= 0.101 Angle : 0.499 6.584 17184 Z= 0.262 Chirality : 0.038 0.128 1919 Planarity : 0.004 0.041 2158 Dihedral : 7.964 77.541 1797 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.92 % Allowed : 11.98 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.22), residues: 1489 helix: 1.64 (0.21), residues: 685 sheet: -0.10 (0.45), residues: 122 loop : -0.31 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 56 TYR 0.019 0.001 TYR B 104 PHE 0.021 0.001 PHE C 41 TRP 0.011 0.001 TRP B 330 HIS 0.007 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00222 (12656) covalent geometry : angle 0.49870 (17184) hydrogen bonds : bond 0.03268 ( 544) hydrogen bonds : angle 4.31609 ( 1533) Misc. bond : bond 0.00043 ( 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 211 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.330 Fit side-chains REVERT: A 9 ASP cc_start: 0.7893 (p0) cc_final: 0.7558 (t70) REVERT: A 18 THR cc_start: 0.8709 (m) cc_final: 0.8414 (p) REVERT: A 64 ASP cc_start: 0.7295 (t0) cc_final: 0.6896 (t0) REVERT: A 86 ASP cc_start: 0.8085 (m-30) cc_final: 0.7693 (m-30) REVERT: A 139 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7213 (tm-30) REVERT: A 147 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7152 (ptm-80) REVERT: A 153 VAL cc_start: 0.8504 (t) cc_final: 0.8269 (m) REVERT: A 163 GLU cc_start: 0.8441 (tp30) cc_final: 0.7924 (tp30) REVERT: A 212 MET cc_start: 0.7809 (ttp) cc_final: 0.7590 (ttm) REVERT: B 93 ARG cc_start: 0.7505 (mtm110) cc_final: 0.7219 (mtm110) REVERT: B 100 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7482 (pt0) REVERT: B 283 LYS cc_start: 0.8524 (tptt) cc_final: 0.8145 (tppt) REVERT: B 348 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7636 (t70) REVERT: B 469 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7651 (tm-30) REVERT: B 576 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: B 672 GLN cc_start: 0.7948 (mt0) cc_final: 0.7240 (pt0) REVERT: C 127 ASP cc_start: 0.7964 (t0) cc_final: 0.7603 (m-30) REVERT: C 146 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7205 (mtt) REVERT: C 201 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7864 (tm-30) REVERT: C 210 GLU cc_start: 0.8093 (pm20) cc_final: 0.7778 (mp0) REVERT: C 222 SER cc_start: 0.8440 (t) cc_final: 0.8190 (m) outliers start: 26 outliers final: 10 residues processed: 201 average time/residue: 0.6257 time to fit residues: 134.9080 Evaluate side-chains 188 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 147 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 348 ASP Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain C residue 73 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 82 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 311 GLN B 232 HIS C 80 ASN C 154 GLN C 214 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102699 restraints weight = 15103.948| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.15 r_work: 0.3186 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12657 Z= 0.120 Angle : 0.520 9.486 17184 Z= 0.271 Chirality : 0.039 0.139 1919 Planarity : 0.004 0.050 2158 Dihedral : 7.958 78.823 1797 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.70 % Allowed : 12.57 % Favored : 85.72 % 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 aren not related in a simple way. whole: 0.86 (0.22), residues: 1489 helix: 1.61 (0.21), residues: 690 sheet: 0.05 (0.45), residues: 118 loop : -0.37 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 582 TYR 0.018 0.001 TYR B 533 PHE 0.022 0.001 PHE C 41 TRP 0.010 0.001 TRP A 253 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00280 (12656) covalent geometry : angle 0.51961 (17184) hydrogen bonds : bond 0.03499 ( 544) hydrogen bonds : angle 4.28717 ( 1533) Misc. bond : bond 0.00023 ( 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 201 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.524 Fit side-chains REVERT: A 9 ASP cc_start: 0.7879 (p0) cc_final: 0.7536 (t70) REVERT: A 18 THR cc_start: 0.8716 (m) cc_final: 0.8418 (p) REVERT: A 64 ASP cc_start: 0.7275 (t0) cc_final: 0.6879 (t0) REVERT: A 86 ASP cc_start: 0.8070 (m-30) cc_final: 0.7697 (m-30) REVERT: A 139 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 153 VAL cc_start: 0.8486 (t) cc_final: 0.8253 (m) REVERT: A 163 GLU cc_start: 0.8456 (tp30) cc_final: 0.7945 (tp30) REVERT: B 93 ARG cc_start: 0.7532 (mtm110) cc_final: 0.7233 (mtm110) REVERT: B 100 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7503 (pt0) REVERT: B 283 LYS cc_start: 0.8526 (tptt) cc_final: 0.8149 (tppt) REVERT: B 469 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7625 (tm-30) REVERT: B 576 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: B 672 GLN cc_start: 0.7947 (mt0) cc_final: 0.7200 (pt0) REVERT: C 127 ASP cc_start: 0.8021 (t0) cc_final: 0.7637 (m-30) REVERT: C 146 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7217 (mtt) REVERT: C 201 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 210 GLU cc_start: 0.8077 (pm20) cc_final: 0.7766 (mp0) REVERT: C 222 SER cc_start: 0.8462 (t) cc_final: 0.8214 (m) outliers start: 23 outliers final: 11 residues processed: 194 average time/residue: 0.6073 time to fit residues: 126.6418 Evaluate side-chains 187 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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 73 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 147 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 107 optimal weight: 0.0770 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 154 GLN C 214 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102782 restraints weight = 15190.921| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.17 r_work: 0.3187 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12657 Z= 0.117 Angle : 0.515 6.386 17184 Z= 0.271 Chirality : 0.039 0.128 1919 Planarity : 0.004 0.044 2158 Dihedral : 7.929 79.201 1797 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.18 % Allowed : 13.46 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.22), residues: 1489 helix: 1.62 (0.21), residues: 690 sheet: 0.03 (0.45), residues: 118 loop : -0.38 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 147 TYR 0.019 0.001 TYR B 30 PHE 0.022 0.001 PHE C 41 TRP 0.010 0.001 TRP B 330 HIS 0.007 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00272 (12656) covalent geometry : angle 0.51484 (17184) hydrogen bonds : bond 0.03452 ( 544) hydrogen bonds : angle 4.26561 ( 1533) Misc. bond : bond 0.00023 ( 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 197 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.527 Fit side-chains REVERT: A 9 ASP cc_start: 0.7864 (p0) cc_final: 0.7561 (t70) REVERT: A 18 THR cc_start: 0.8739 (m) cc_final: 0.8451 (p) REVERT: A 64 ASP cc_start: 0.7299 (t0) cc_final: 0.6881 (t0) REVERT: A 86 ASP cc_start: 0.8067 (m-30) cc_final: 0.7628 (m-30) REVERT: A 139 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7246 (tm-30) REVERT: A 153 VAL cc_start: 0.8535 (t) cc_final: 0.8334 (m) REVERT: A 163 GLU cc_start: 0.8464 (tp30) cc_final: 0.7958 (tp30) REVERT: B 93 ARG cc_start: 0.7468 (mtm110) cc_final: 0.7177 (mtm110) REVERT: B 100 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7515 (pt0) REVERT: B 283 LYS cc_start: 0.8534 (tptt) cc_final: 0.8131 (tppt) REVERT: B 348 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7648 (t70) REVERT: B 469 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 576 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: B 672 GLN cc_start: 0.7979 (mt0) cc_final: 0.7211 (pt0) REVERT: C 127 ASP cc_start: 0.8017 (t0) cc_final: 0.7646 (m-30) REVERT: C 194 GLU cc_start: 0.7837 (tt0) cc_final: 0.7571 (tm-30) REVERT: C 201 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7901 (tm-30) REVERT: C 210 GLU cc_start: 0.8083 (pm20) cc_final: 0.7773 (mp0) REVERT: C 222 SER cc_start: 0.8462 (t) cc_final: 0.8211 (m) outliers start: 16 outliers final: 9 residues processed: 191 average time/residue: 0.6838 time to fit residues: 139.9956 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 : 0.366 ------------------------------------------------------------------------------- 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 348 ASP Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 131 optimal weight: 0.0070 chunk 85 optimal weight: 0.7980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 154 GLN 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 = 0.133219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102763 restraints weight = 15186.741| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.11 r_work: 0.3179 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: 0.8232 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12657 Z= 0.125 Angle : 0.530 10.683 17184 Z= 0.276 Chirality : 0.039 0.129 1919 Planarity : 0.004 0.045 2158 Dihedral : 7.933 80.408 1797 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.04 % Allowed : 13.68 % 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 aren not related in a simple way. whole: 0.85 (0.22), residues: 1489 helix: 1.63 (0.21), residues: 690 sheet: 0.01 (0.45), residues: 118 loop : -0.40 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 147 TYR 0.021 0.001 TYR B 104 PHE 0.022 0.001 PHE C 41 TRP 0.011 0.001 TRP A 253 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00294 (12656) covalent geometry : angle 0.53049 (17184) hydrogen bonds : bond 0.03530 ( 544) hydrogen bonds : angle 4.26890 ( 1533) Misc. bond : bond 0.00019 ( 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: 14 poor density : 175 time to evaluate : 0.549 Fit side-chains REVERT: A 9 ASP cc_start: 0.7875 (p0) cc_final: 0.7541 (t70) REVERT: A 18 THR cc_start: 0.8764 (m) cc_final: 0.8486 (p) REVERT: A 64 ASP cc_start: 0.7291 (t0) cc_final: 0.6865 (t0) REVERT: A 86 ASP cc_start: 0.8069 (m-30) cc_final: 0.7608 (m-30) REVERT: A 139 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7270 (tm-30) REVERT: A 153 VAL cc_start: 0.8527 (t) cc_final: 0.8325 (m) REVERT: A 163 GLU cc_start: 0.8461 (tp30) cc_final: 0.7959 (tp30) REVERT: A 579 MET cc_start: 0.8549 (mtt) cc_final: 0.8344 (mtt) REVERT: B 93 ARG cc_start: 0.7461 (mtm110) cc_final: 0.7167 (mtm110) REVERT: B 100 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7582 (pt0) REVERT: B 283 LYS cc_start: 0.8534 (tptt) cc_final: 0.8131 (tppt) REVERT: B 469 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 576 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: B 672 GLN cc_start: 0.7973 (mt0) cc_final: 0.7180 (pt0) REVERT: C 127 ASP cc_start: 0.8032 (t0) cc_final: 0.7657 (m-30) REVERT: C 201 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7898 (tm-30) REVERT: C 210 GLU cc_start: 0.8090 (pm20) cc_final: 0.7769 (mp0) REVERT: C 222 SER cc_start: 0.8463 (t) cc_final: 0.8207 (m) outliers start: 14 outliers final: 10 residues processed: 184 average time/residue: 0.5907 time to fit residues: 116.9168 Evaluate side-chains 183 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 232 HIS ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100627 restraints weight = 15230.927| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.16 r_work: 0.3155 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12657 Z= 0.150 Angle : 0.547 7.024 17184 Z= 0.289 Chirality : 0.040 0.133 1919 Planarity : 0.005 0.046 2158 Dihedral : 8.044 83.559 1797 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.33 % Allowed : 13.61 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.22), residues: 1489 helix: 1.60 (0.21), residues: 686 sheet: 0.06 (0.46), residues: 115 loop : -0.38 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 582 TYR 0.018 0.001 TYR B 533 PHE 0.024 0.002 PHE C 41 TRP 0.012 0.001 TRP A 253 HIS 0.008 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00355 (12656) covalent geometry : angle 0.54737 (17184) hydrogen bonds : bond 0.03813 ( 544) hydrogen bonds : angle 4.33097 ( 1533) Misc. bond : bond 0.00008 ( 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 194 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.538 Fit side-chains REVERT: A 9 ASP cc_start: 0.7877 (p0) cc_final: 0.7571 (t70) REVERT: A 18 THR cc_start: 0.8805 (m) cc_final: 0.8538 (p) REVERT: A 64 ASP cc_start: 0.7321 (t0) cc_final: 0.6899 (t0) REVERT: A 86 ASP cc_start: 0.8144 (m-30) cc_final: 0.7657 (m-30) REVERT: A 139 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7272 (tm-30) REVERT: A 146 CYS cc_start: 0.6356 (m) cc_final: 0.5482 (p) REVERT: A 153 VAL cc_start: 0.8518 (t) cc_final: 0.8303 (m) REVERT: A 163 GLU cc_start: 0.8460 (tp30) cc_final: 0.7960 (tp30) REVERT: A 579 MET cc_start: 0.8608 (mtt) cc_final: 0.8386 (mtt) REVERT: B 93 ARG cc_start: 0.7512 (mtm110) cc_final: 0.7214 (mtm110) REVERT: B 100 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7564 (pt0) REVERT: B 283 LYS cc_start: 0.8545 (tptt) cc_final: 0.8143 (tppt) REVERT: B 348 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7698 (t70) REVERT: B 469 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 576 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: B 672 GLN cc_start: 0.7906 (mt0) cc_final: 0.7126 (pt0) REVERT: B 682 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: C 127 ASP cc_start: 0.7998 (t0) cc_final: 0.7620 (m-30) REVERT: C 201 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7872 (tm-30) REVERT: C 210 GLU cc_start: 0.8081 (pm20) cc_final: 0.7728 (mp0) REVERT: C 222 SER cc_start: 0.8463 (t) cc_final: 0.8208 (m) outliers start: 18 outliers final: 9 residues processed: 188 average time/residue: 0.6216 time to fit residues: 125.7132 Evaluate side-chains 184 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 348 ASP Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 682 GLU 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: 0.0870 chunk 28 optimal weight: 0.2980 chunk 123 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 232 HIS ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 131 GLN C 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102616 restraints weight = 15214.910| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.11 r_work: 0.3182 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12657 Z= 0.121 Angle : 0.539 10.899 17184 Z= 0.281 Chirality : 0.039 0.129 1919 Planarity : 0.004 0.044 2158 Dihedral : 7.969 82.345 1797 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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 aren not related in a simple way. whole: 0.84 (0.22), residues: 1489 helix: 1.63 (0.21), residues: 685 sheet: 0.04 (0.46), residues: 115 loop : -0.41 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 92 TYR 0.022 0.001 TYR B 104 PHE 0.023 0.001 PHE C 41 TRP 0.011 0.001 TRP B 330 HIS 0.007 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00281 (12656) covalent geometry : angle 0.53862 (17184) hydrogen bonds : bond 0.03511 ( 544) hydrogen bonds : angle 4.31446 ( 1533) Misc. bond : bond 0.00025 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5148.61 seconds wall clock time: 88 minutes 13.02 seconds (5293.02 seconds total)