Starting phenix.real_space_refine on Sat Jul 4 17:37:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lc3_23268/07_2026/7lc3_23268_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lc3_23268/07_2026/7lc3_23268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lc3_23268/07_2026/7lc3_23268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lc3_23268/07_2026/7lc3_23268.map" model { file = "/net/cci-nas-00/data/ceres_data/7lc3_23268/07_2026/7lc3_23268_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lc3_23268/07_2026/7lc3_23268_trim.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 6984 2.51 5 N 1824 2.21 5 O 1979 1.98 5 H 11144 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21999 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8444 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 10173 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 26, 'TRANS': 646} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 2848 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 13, 'TRANS': 174} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 421 Classifications: {'peptide': 27} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {' MG': 1, '9Y0': 1, 'ACP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 3.74, per 1000 atoms: 0.17 Number of scatterers: 21999 At special positions: 0 Unit cell: (73.485, 111.78, 157.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 2 19.00 S 61 16.00 P 4 15.00 Mg 1 11.99 O 1979 8.00 N 1824 7.00 C 6984 6.00 H 11144 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 669.8 milliseconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 9 sheets defined 65.2% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 39 through 51 removed outlier: 4.117A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.630A pdb=" N GLN A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 218 through 229 removed outlier: 4.157A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.299A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.068A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.000A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 Processing helix chain 'A' and resid 410 through 436 removed outlier: 4.298A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.824A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 509 Proline residue: A 499 - end of helix removed outlier: 4.040A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 550 Proline residue: A 545 - end of helix removed outlier: 3.618A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 11 through 24 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.511A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 102 removed outlier: 4.062A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 198 through 208 removed outlier: 3.627A pdb=" N MET B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 247 removed outlier: 3.852A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 285 removed outlier: 4.939A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.853A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 343 removed outlier: 4.333A pdb=" N ALA B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 452 through 461 removed outlier: 3.524A pdb=" N ALA B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.573A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 556 through 595 removed outlier: 3.829A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 Processing helix chain 'B' and resid 612 through 638 removed outlier: 4.366A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 645 through 680 removed outlier: 3.905A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 662 " --> pdb=" O GLY B 658 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 4 through 34 removed outlier: 4.494A pdb=" N TYR C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.758A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.609A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.610A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.587A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 109 Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 134 removed outlier: 6.296A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 164 through 168 Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 3.579A pdb=" N MET B 548 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET B 535 " --> pdb=" O MET B 515 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLY B 517 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B 512 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 303 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 324 removed outlier: 6.987A pdb=" N ALA B 444 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE B 322 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 442 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LEU B 440 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N MET B 383 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE B 377 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.720A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.539A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 11132 1.01 - 1.21: 15 1.21 - 1.42: 4353 1.42 - 1.62: 6572 1.62 - 1.82: 114 Bond restraints: 22186 Sorted by residual: bond pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 1.333 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" O3A ACP B 803 " pdb=" PB ACP B 803 " ideal model delta sigma weight residual 1.698 1.596 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O2A ACP B 803 " pdb=" PA ACP B 803 " ideal model delta sigma weight residual 1.505 1.605 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O2B ACP B 803 " pdb=" PB ACP B 803 " ideal model delta sigma weight residual 1.507 1.603 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 9Y0 B 801 " pdb=" O7 9Y0 B 801 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.04e+01 ... (remaining 22181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.45: 40163 6.45 - 12.89: 55 12.89 - 19.34: 6 19.34 - 25.78: 3 25.78 - 32.23: 3 Bond angle restraints: 40230 Sorted by residual: angle pdb=" HB1 ALA B 498 " pdb=" CB ALA B 498 " pdb=" HB3 ALA B 498 " ideal model delta sigma weight residual 110.00 77.77 32.23 3.00e+00 1.11e-01 1.15e+02 angle pdb=" HB2 ALA B 498 " pdb=" CB ALA B 498 " pdb=" HB3 ALA B 498 " ideal model delta sigma weight residual 110.00 78.94 31.06 3.00e+00 1.11e-01 1.07e+02 angle pdb=" CA ALA B 498 " pdb=" CB ALA B 498 " pdb=" HB2 ALA B 498 " ideal model delta sigma weight residual 109.00 81.70 27.30 3.00e+00 1.11e-01 8.28e+01 angle pdb=" CA ALA B 498 " pdb=" CB ALA B 498 " pdb=" HB1 ALA B 498 " ideal model delta sigma weight residual 109.00 84.13 24.87 3.00e+00 1.11e-01 6.88e+01 angle pdb=" HB1 ALA B 498 " pdb=" CB ALA B 498 " pdb=" HB2 ALA B 498 " ideal model delta sigma weight residual 110.00 133.66 -23.66 3.00e+00 1.11e-01 6.22e+01 ... (remaining 40225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 9684 24.54 - 49.08: 512 49.08 - 73.62: 188 73.62 - 98.16: 14 98.16 - 122.69: 2 Dihedral angle restraints: 10400 sinusoidal: 5743 harmonic: 4657 Sorted by residual: dihedral pdb=" O1B ACP B 803 " pdb=" C3B ACP B 803 " pdb=" PB ACP B 803 " pdb=" PG ACP B 803 " ideal model delta sinusoidal sigma weight residual -52.82 69.87 -122.69 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C27 9Y0 B 801 " pdb=" C28 9Y0 B 801 " pdb=" C29 9Y0 B 801 " pdb=" C30 9Y0 B 801 " ideal model delta sinusoidal sigma weight residual -178.88 -62.49 -116.39 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C ALA C 73 " pdb=" N ALA C 73 " pdb=" CA ALA C 73 " pdb=" CB ALA C 73 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 10397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1392 0.071 - 0.141: 352 0.141 - 0.211: 56 0.211 - 0.282: 4 0.282 - 0.352: 2 Chirality restraints: 1806 Sorted by residual: chirality pdb=" CA ALA C 73 " pdb=" N ALA C 73 " pdb=" C ALA C 73 " pdb=" CB ALA C 73 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA TRP A 176 " pdb=" N TRP A 176 " pdb=" C TRP A 176 " pdb=" CB TRP A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB VAL A 508 " pdb=" CA VAL A 508 " pdb=" CG1 VAL A 508 " pdb=" CG2 VAL A 508 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1803 not shown) Planarity restraints: 3275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 606 " 0.068 2.00e-02 2.50e+03 8.96e-02 1.20e+02 pdb=" CG ASN B 606 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 606 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 606 " -0.143 2.00e-02 2.50e+03 pdb="HD21 ASN B 606 " -0.019 2.00e-02 2.50e+03 pdb="HD22 ASN B 606 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 239 " 0.065 2.00e-02 2.50e+03 8.40e-02 1.06e+02 pdb=" CG ASN A 239 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 239 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 239 " -0.134 2.00e-02 2.50e+03 pdb="HD21 ASN A 239 " -0.014 2.00e-02 2.50e+03 pdb="HD22 ASN A 239 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 361 " 0.051 2.00e-02 2.50e+03 7.52e-02 8.49e+01 pdb=" CG ASN B 361 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN B 361 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN B 361 " -0.122 2.00e-02 2.50e+03 pdb="HD21 ASN B 361 " -0.023 2.00e-02 2.50e+03 pdb="HD22 ASN B 361 " 0.124 2.00e-02 2.50e+03 ... (remaining 3272 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.30: 4716 2.30 - 3.01: 63351 3.01 - 3.72: 85658 3.72 - 4.43: 131974 4.43 - 5.14: 205273 Nonbonded interactions: 490972 Sorted by model distance: nonbonded pdb=" O ASN B 361 " pdb="HD21 ASN B 361 " model vdw 1.591 2.450 nonbonded pdb=" O ARG C 68 " pdb=" HH TYR C 77 " model vdw 1.632 2.450 nonbonded pdb=" H THR A 401 " pdb=" OD2 ASP B 300 " model vdw 1.638 2.450 nonbonded pdb=" OD1 ASP B 143 " pdb=" H GLY B 178 " model vdw 1.678 2.450 nonbonded pdb=" O THR A 105 " pdb=" HG SER A 108 " model vdw 1.682 2.450 ... (remaining 490967 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.210 Find NCS groups from input model: 0.050 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.012 0.209 11042 Z= 0.513 Angle : 1.154 18.724 15024 Z= 0.627 Chirality : 0.063 0.352 1806 Planarity : 0.007 0.075 1898 Dihedral : 15.226 122.695 3966 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.12 % Allowed : 10.53 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.20), residues: 1437 helix: -0.72 (0.16), residues: 877 sheet: -1.95 (0.46), residues: 88 loop : -2.16 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 651 TYR 0.040 0.005 TYR A 126 PHE 0.022 0.003 PHE A 149 TRP 0.030 0.003 TRP A 115 HIS 0.012 0.003 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.01194 / 0.51 (11042) covalent geometry : angle 1.15401 / 0.63 (15024) hydrogen bonds : bond 0.12582 / 8.71 ( 710) hydrogen bonds : angle 6.19980 / 4.42 ( 2067) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8898 (mtt) cc_final: 0.8670 (mtp) REVERT: A 412 ARG cc_start: 0.7228 (tmm-80) cc_final: 0.6573 (ttt90) REVERT: B 125 GLN cc_start: 0.7162 (tt0) cc_final: 0.6932 (tp40) REVERT: B 318 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7400 (tt0) REVERT: B 530 ASP cc_start: 0.7143 (t70) cc_final: 0.6745 (t0) REVERT: B 570 MET cc_start: 0.8418 (mmt) cc_final: 0.7924 (mmt) REVERT: B 647 SER cc_start: 0.8546 (m) cc_final: 0.8279 (p) outliers start: 24 outliers final: 10 residues processed: 259 average time/residue: 0.2416 time to fit residues: 86.5230 Evaluate side-chains 155 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0010 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN B 554 ASN B 653 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.158848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120186 restraints weight = 37044.551| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.59 r_work: 0.3315 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11042 Z= 0.154 Angle : 0.582 6.479 15024 Z= 0.304 Chirality : 0.040 0.152 1806 Planarity : 0.004 0.051 1898 Dihedral : 9.405 90.781 1612 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.24 % Allowed : 12.21 % Favored : 86.55 % 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: -0.66 (0.21), residues: 1437 helix: 0.34 (0.16), residues: 877 sheet: -2.04 (0.45), residues: 94 loop : -1.45 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 317 TYR 0.021 0.002 TYR A 381 PHE 0.013 0.001 PHE A 47 TRP 0.018 0.001 TRP B 245 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11042) covalent geometry : angle 0.58193 / 0.30 (15024) hydrogen bonds : bond 0.05181 / 3.65 ( 710) hydrogen bonds : angle 5.14607 / 3.70 ( 2067) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8091 (mmt) cc_final: 0.7699 (mmt) REVERT: A 160 MET cc_start: 0.8882 (tpp) cc_final: 0.8609 (mmm) REVERT: B 83 GLU cc_start: 0.7799 (tt0) cc_final: 0.7595 (tt0) REVERT: B 125 GLN cc_start: 0.7699 (tt0) cc_final: 0.7347 (tp-100) REVERT: B 318 GLN cc_start: 0.7402 (mm-40) cc_final: 0.7094 (tt0) REVERT: B 647 SER cc_start: 0.8525 (m) cc_final: 0.8300 (p) REVERT: C 161 LYS cc_start: 0.8656 (tttt) cc_final: 0.8382 (tttm) outliers start: 14 outliers final: 9 residues processed: 163 average time/residue: 0.2051 time to fit residues: 49.1414 Evaluate side-chains 136 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 564 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112620 restraints weight = 37378.590| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.51 r_work: 0.3129 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11042 Z= 0.209 Angle : 0.568 6.040 15024 Z= 0.298 Chirality : 0.040 0.153 1806 Planarity : 0.004 0.044 1898 Dihedral : 8.526 83.522 1604 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.59 % Allowed : 12.48 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1437 helix: 0.78 (0.17), residues: 892 sheet: -1.65 (0.47), residues: 97 loop : -1.44 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 317 TYR 0.022 0.002 TYR A 381 PHE 0.012 0.001 PHE A 149 TRP 0.015 0.001 TRP B 245 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (11042) covalent geometry : angle 0.56769 / 0.30 (15024) hydrogen bonds : bond 0.04861 / 3.42 ( 710) hydrogen bonds : angle 4.88744 / 3.52 ( 2067) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8326 (mm-30) REVERT: A 116 ARG cc_start: 0.7570 (mtm110) cc_final: 0.7239 (ptt90) REVERT: A 160 MET cc_start: 0.8803 (tpp) cc_final: 0.8445 (mtp) REVERT: A 412 ARG cc_start: 0.7695 (tmm-80) cc_final: 0.6559 (ttt90) REVERT: B 83 GLU cc_start: 0.7744 (tt0) cc_final: 0.7537 (tt0) REVERT: B 125 GLN cc_start: 0.7889 (tt0) cc_final: 0.7347 (tp-100) REVERT: B 318 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7252 (tt0) REVERT: B 455 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8256 (tm-30) REVERT: B 570 MET cc_start: 0.8587 (mtt) cc_final: 0.8240 (mtt) REVERT: B 574 SER cc_start: 0.8102 (OUTLIER) cc_final: 0.7866 (m) REVERT: B 647 SER cc_start: 0.8512 (m) cc_final: 0.8216 (p) REVERT: B 649 MET cc_start: 0.8500 (tpp) cc_final: 0.8295 (tpt) outliers start: 18 outliers final: 9 residues processed: 148 average time/residue: 0.2014 time to fit residues: 43.4115 Evaluate side-chains 136 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 530 ASP Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 606 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 chunk 128 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114175 restraints weight = 37682.430| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.48 r_work: 0.3192 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11042 Z= 0.199 Angle : 0.547 5.491 15024 Z= 0.286 Chirality : 0.040 0.147 1806 Planarity : 0.004 0.047 1898 Dihedral : 8.129 79.275 1600 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.33 % Allowed : 13.01 % Favored : 85.66 % 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: 0.18 (0.21), residues: 1437 helix: 1.02 (0.17), residues: 890 sheet: -1.44 (0.49), residues: 97 loop : -1.25 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.022 0.002 TYR A 381 PHE 0.012 0.001 PHE A 149 TRP 0.016 0.001 TRP B 245 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (11042) covalent geometry : angle 0.54688 / 0.29 (15024) hydrogen bonds : bond 0.04576 / 3.23 ( 710) hydrogen bonds : angle 4.73575 / 3.43 ( 2067) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 160 MET cc_start: 0.8935 (tpp) cc_final: 0.8685 (mtp) REVERT: A 412 ARG cc_start: 0.7826 (tmm-80) cc_final: 0.6706 (ttt90) REVERT: B 83 GLU cc_start: 0.7733 (tt0) cc_final: 0.7523 (tt0) REVERT: B 125 GLN cc_start: 0.7733 (tt0) cc_final: 0.7281 (tp-100) REVERT: B 282 MET cc_start: 0.8442 (tpt) cc_final: 0.7660 (tpt) REVERT: B 318 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7257 (tt0) REVERT: B 455 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8270 (tm-30) REVERT: B 570 MET cc_start: 0.8746 (mtt) cc_final: 0.8372 (mtt) REVERT: B 574 SER cc_start: 0.8048 (OUTLIER) cc_final: 0.7841 (m) REVERT: B 647 SER cc_start: 0.8607 (m) cc_final: 0.8276 (p) outliers start: 15 outliers final: 13 residues processed: 141 average time/residue: 0.2314 time to fit residues: 48.3799 Evaluate side-chains 139 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 530 ASP Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain C residue 133 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 122 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.113508 restraints weight = 37027.174| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.52 r_work: 0.3106 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11042 Z= 0.155 Angle : 0.513 5.331 15024 Z= 0.266 Chirality : 0.039 0.149 1806 Planarity : 0.004 0.048 1898 Dihedral : 7.870 76.549 1600 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.88 % Allowed : 14.25 % Favored : 84.87 % 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: 0.42 (0.22), residues: 1437 helix: 1.21 (0.17), residues: 890 sheet: -1.31 (0.50), residues: 97 loop : -1.18 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 651 TYR 0.022 0.001 TYR A 381 PHE 0.009 0.001 PHE A 270 TRP 0.013 0.001 TRP B 245 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (11042) covalent geometry : angle 0.51282 / 0.27 (15024) hydrogen bonds : bond 0.04309 / 3.03 ( 710) hydrogen bonds : angle 4.55606 / 3.30 ( 2067) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8841 (tpp) cc_final: 0.8575 (mtp) REVERT: A 205 ASN cc_start: 0.7788 (t0) cc_final: 0.7078 (t0) REVERT: A 412 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.6502 (ttt90) REVERT: B 125 GLN cc_start: 0.7806 (tt0) cc_final: 0.7298 (tp-100) REVERT: B 318 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7190 (tt0) REVERT: B 455 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 570 MET cc_start: 0.8724 (mtt) cc_final: 0.8392 (mtt) REVERT: B 647 SER cc_start: 0.8535 (m) cc_final: 0.8165 (p) outliers start: 10 outliers final: 8 residues processed: 141 average time/residue: 0.2589 time to fit residues: 52.6497 Evaluate side-chains 135 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 411 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 26 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 127 optimal weight: 0.1980 chunk 128 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.155006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117634 restraints weight = 38075.474| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.51 r_work: 0.3395 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11042 Z= 0.153 Angle : 0.502 5.408 15024 Z= 0.261 Chirality : 0.038 0.142 1806 Planarity : 0.004 0.047 1898 Dihedral : 7.624 77.227 1598 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.33 % Allowed : 13.89 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.22), residues: 1437 helix: 1.35 (0.17), residues: 891 sheet: -1.28 (0.51), residues: 97 loop : -1.07 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.022 0.001 TYR A 381 PHE 0.009 0.001 PHE A 149 TRP 0.013 0.001 TRP B 245 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (11042) covalent geometry : angle 0.50223 / 0.26 (15024) hydrogen bonds : bond 0.04204 / 2.95 ( 710) hydrogen bonds : angle 4.46424 / 3.24 ( 2067) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8822 (tpp) cc_final: 0.8606 (mtp) REVERT: A 205 ASN cc_start: 0.7710 (t0) cc_final: 0.7265 (t0) REVERT: A 412 ARG cc_start: 0.7856 (ttm-80) cc_final: 0.6779 (ttt90) REVERT: B 125 GLN cc_start: 0.7552 (tt0) cc_final: 0.6774 (tp-100) REVERT: B 455 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 647 SER cc_start: 0.8582 (m) cc_final: 0.8303 (p) outliers start: 15 outliers final: 12 residues processed: 142 average time/residue: 0.2339 time to fit residues: 49.2479 Evaluate side-chains 137 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116587 restraints weight = 38308.631| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.57 r_work: 0.3387 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11042 Z= 0.153 Angle : 0.501 5.452 15024 Z= 0.260 Chirality : 0.038 0.142 1806 Planarity : 0.004 0.045 1898 Dihedral : 7.472 78.296 1598 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.24 % Allowed : 13.98 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.22), residues: 1437 helix: 1.43 (0.17), residues: 891 sheet: -1.22 (0.52), residues: 95 loop : -1.00 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.022 0.001 TYR A 381 PHE 0.008 0.001 PHE A 149 TRP 0.011 0.001 TRP B 245 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (11042) covalent geometry : angle 0.50058 / 0.26 (15024) hydrogen bonds : bond 0.04142 / 2.90 ( 710) hydrogen bonds : angle 4.39825 / 3.19 ( 2067) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8842 (tpp) cc_final: 0.8612 (mtp) REVERT: A 205 ASN cc_start: 0.7735 (t0) cc_final: 0.7409 (t0) REVERT: A 412 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.6738 (ttt90) REVERT: B 455 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 647 SER cc_start: 0.8595 (m) cc_final: 0.8321 (p) REVERT: C 72 THR cc_start: 0.8762 (m) cc_final: 0.8527 (p) outliers start: 14 outliers final: 13 residues processed: 138 average time/residue: 0.2380 time to fit residues: 48.6697 Evaluate side-chains 138 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 603 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 96 optimal weight: 4.9990 chunk 71 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.155203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117004 restraints weight = 38163.656| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.58 r_work: 0.3391 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11042 Z= 0.133 Angle : 0.493 7.952 15024 Z= 0.253 Chirality : 0.038 0.140 1806 Planarity : 0.004 0.045 1898 Dihedral : 7.244 80.008 1598 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.24 % Allowed : 14.42 % Favored : 84.34 % 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: 0.86 (0.22), residues: 1437 helix: 1.54 (0.17), residues: 890 sheet: -1.31 (0.48), residues: 108 loop : -0.89 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.022 0.001 TYR A 381 PHE 0.010 0.001 PHE A 270 TRP 0.012 0.001 TRP B 245 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11042) covalent geometry : angle 0.49254 / 0.25 (15024) hydrogen bonds : bond 0.04027 / 2.82 ( 710) hydrogen bonds : angle 4.31407 / 3.14 ( 2067) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8848 (tpp) cc_final: 0.8600 (mtp) REVERT: A 205 ASN cc_start: 0.7708 (t0) cc_final: 0.7411 (t0) REVERT: B 380 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7782 (mp10) REVERT: B 455 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 647 SER cc_start: 0.8572 (m) cc_final: 0.8324 (p) outliers start: 14 outliers final: 11 residues processed: 140 average time/residue: 0.2259 time to fit residues: 47.8921 Evaluate side-chains 136 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 432 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 106 optimal weight: 0.9990 chunk 78 optimal weight: 0.0980 chunk 128 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.154911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117891 restraints weight = 38061.307| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.50 r_work: 0.3388 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11042 Z= 0.137 Angle : 0.495 6.116 15024 Z= 0.255 Chirality : 0.038 0.160 1806 Planarity : 0.004 0.044 1898 Dihedral : 6.987 82.850 1597 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.15 % Allowed : 14.34 % Favored : 84.51 % 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: 0.92 (0.22), residues: 1437 helix: 1.59 (0.17), residues: 891 sheet: -1.26 (0.48), residues: 108 loop : -0.88 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.022 0.001 TYR A 381 PHE 0.008 0.001 PHE A 527 TRP 0.010 0.001 TRP B 245 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (11042) covalent geometry : angle 0.49472 / 0.25 (15024) hydrogen bonds : bond 0.03994 / 2.79 ( 710) hydrogen bonds : angle 4.27650 / 3.11 ( 2067) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8814 (tpp) cc_final: 0.8565 (mtp) REVERT: A 205 ASN cc_start: 0.7706 (t0) cc_final: 0.7457 (t0) REVERT: B 47 THR cc_start: 0.8451 (t) cc_final: 0.8016 (m) REVERT: B 124 ASP cc_start: 0.8395 (m-30) cc_final: 0.8029 (p0) REVERT: B 380 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7846 (mp10) REVERT: B 455 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8108 (tm-30) REVERT: B 647 SER cc_start: 0.8535 (m) cc_final: 0.8281 (p) REVERT: C 72 THR cc_start: 0.8656 (m) cc_final: 0.8424 (p) outliers start: 13 outliers final: 12 residues processed: 141 average time/residue: 0.2250 time to fit residues: 47.5526 Evaluate side-chains 138 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 432 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 95 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 18 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.154948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116994 restraints weight = 38390.988| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.56 r_work: 0.3380 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11042 Z= 0.140 Angle : 0.501 6.983 15024 Z= 0.258 Chirality : 0.038 0.141 1806 Planarity : 0.004 0.045 1898 Dihedral : 6.842 86.954 1597 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.97 % Allowed : 14.51 % Favored : 84.51 % 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: 0.95 (0.22), residues: 1437 helix: 1.61 (0.17), residues: 891 sheet: -1.06 (0.50), residues: 102 loop : -0.94 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.022 0.001 TYR A 381 PHE 0.021 0.001 PHE B 412 TRP 0.010 0.001 TRP B 245 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (11042) covalent geometry : angle 0.50150 / 0.26 (15024) hydrogen bonds : bond 0.03979 / 2.78 ( 710) hydrogen bonds : angle 4.24779 / 3.09 ( 2067) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8815 (tpp) cc_final: 0.8562 (mtp) REVERT: A 205 ASN cc_start: 0.7702 (t0) cc_final: 0.7456 (t0) REVERT: B 47 THR cc_start: 0.8441 (t) cc_final: 0.8023 (m) REVERT: B 124 ASP cc_start: 0.8494 (m-30) cc_final: 0.8067 (p0) REVERT: B 380 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7869 (mp10) REVERT: B 455 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 647 SER cc_start: 0.8512 (m) cc_final: 0.8282 (p) outliers start: 11 outliers final: 10 residues processed: 138 average time/residue: 0.2371 time to fit residues: 48.8895 Evaluate side-chains 139 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 120 optimal weight: 0.1980 chunk 80 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.155630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117781 restraints weight = 38180.755| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.56 r_work: 0.3396 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11042 Z= 0.125 Angle : 0.489 6.862 15024 Z= 0.251 Chirality : 0.038 0.139 1806 Planarity : 0.003 0.044 1898 Dihedral : 6.575 86.999 1597 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.88 % Allowed : 14.60 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.22), residues: 1437 helix: 1.68 (0.17), residues: 891 sheet: -1.17 (0.49), residues: 104 loop : -0.89 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 50 TYR 0.023 0.001 TYR A 381 PHE 0.012 0.001 PHE B 412 TRP 0.012 0.001 TRP B 245 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (11042) covalent geometry : angle 0.48921 / 0.25 (15024) hydrogen bonds : bond 0.03885 / 2.72 ( 710) hydrogen bonds : angle 4.20160 / 3.05 ( 2067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5132.83 seconds wall clock time: 87 minutes 58.58 seconds (5278.58 seconds total)