Starting phenix.real_space_refine on Tue Mar 3 23:18:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nvv_12614/03_2026/7nvv_12614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvv_12614/03_2026/7nvv_12614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nvv_12614/03_2026/7nvv_12614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvv_12614/03_2026/7nvv_12614.map" model { file = "/net/cci-nas-00/data/ceres_data/7nvv_12614/03_2026/7nvv_12614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvv_12614/03_2026/7nvv_12614.cif" } resolution = 2.9 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= -0.002 sd= 0.953 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 P 52 5.49 5 Mg 1 5.21 5 S 42 5.16 5 Be 1 3.05 5 C 5635 2.51 5 N 1579 2.21 5 O 1758 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9071 Number of models: 1 Model: "" Number of chains: 9 Chain: "2" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2357 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "5" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "7" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4890 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Chain: "N" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 505 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "T" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 520 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "W" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.95, per 1000 atoms: 0.21 Number of scatterers: 9071 At special positions: 0 Unit cell: (142.8, 90.3, 115.5, 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) S 42 16.00 P 52 15.00 Mg 1 11.99 F 3 9.00 O 1758 8.00 N 1579 7.00 C 5635 6.00 Be 1 4.00 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: 0.71 Conformation dependent library (CDL) restraints added in 236.5 milliseconds 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1912 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 52.2% alpha, 15.2% beta 25 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain '2' and resid 145 through 164 removed outlier: 3.557A pdb=" N ASP 2 149 " --> pdb=" O VAL 2 145 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS 2 150 " --> pdb=" O PRO 2 146 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 181 Processing helix chain '2' and resid 197 through 206 removed outlier: 3.705A pdb=" N GLN 2 202 " --> pdb=" O SER 2 198 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU 2 206 " --> pdb=" O GLN 2 202 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 227 removed outlier: 3.801A pdb=" N GLN 2 224 " --> pdb=" O LEU 2 220 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER 2 225 " --> pdb=" O GLN 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 229 through 242 removed outlier: 3.645A pdb=" N ILE 2 233 " --> pdb=" O ASP 2 229 " (cutoff:3.500A) Processing helix chain '2' and resid 256 through 268 Processing helix chain '2' and resid 284 through 289 removed outlier: 3.889A pdb=" N ILE 2 288 " --> pdb=" O THR 2 284 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN 2 289 " --> pdb=" O ARG 2 285 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 284 through 289' Processing helix chain '2' and resid 321 through 331 removed outlier: 3.561A pdb=" N ILE 2 325 " --> pdb=" O SER 2 321 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE 2 331 " --> pdb=" O LEU 2 327 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 358 Processing helix chain '2' and resid 360 through 371 Processing helix chain '2' and resid 373 through 379 removed outlier: 4.021A pdb=" N LYS 2 378 " --> pdb=" O PRO 2 374 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN 2 379 " --> pdb=" O VAL 2 375 " (cutoff:3.500A) Processing helix chain '2' and resid 384 through 399 removed outlier: 3.694A pdb=" N ARG 2 398 " --> pdb=" O TRP 2 394 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP 2 399 " --> pdb=" O GLU 2 395 " (cutoff:3.500A) Processing helix chain '2' and resid 414 through 429 removed outlier: 3.705A pdb=" N GLU 2 419 " --> pdb=" O GLN 2 415 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU 2 420 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing helix chain '2' and resid 447 through 458 Processing helix chain '5' and resid 13 through 27 Processing helix chain '5' and resid 49 through 64 removed outlier: 3.522A pdb=" N GLU 5 55 " --> pdb=" O ASN 5 51 " (cutoff:3.500A) Processing helix chain '7' and resid 92 through 104 removed outlier: 3.512A pdb=" N ALA 7 102 " --> pdb=" O ASP 7 98 " (cutoff:3.500A) Processing helix chain '7' and resid 119 through 130 Processing helix chain '7' and resid 132 through 144 Processing helix chain '7' and resid 149 through 159 Processing helix chain '7' and resid 181 through 191 removed outlier: 3.571A pdb=" N ILE 7 185 " --> pdb=" O HIS 7 181 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP 7 191 " --> pdb=" O HIS 7 187 " (cutoff:3.500A) Processing helix chain '7' and resid 191 through 197 Processing helix chain '7' and resid 273 through 275 No H-bonds generated for 'chain '7' and resid 273 through 275' Processing helix chain '7' and resid 276 through 287 Processing helix chain '7' and resid 296 through 300 Processing helix chain '7' and resid 317 through 328 Processing helix chain '7' and resid 345 through 358 Processing helix chain '7' and resid 367 through 382 Processing helix chain '7' and resid 410 through 415 Processing helix chain '7' and resid 420 through 432 removed outlier: 3.653A pdb=" N VAL 7 426 " --> pdb=" O GLU 7 422 " (cutoff:3.500A) Processing helix chain '7' and resid 443 through 446 Processing helix chain '7' and resid 452 through 458 removed outlier: 4.094A pdb=" N THR 7 456 " --> pdb=" O ARG 7 452 " (cutoff:3.500A) Processing helix chain '7' and resid 476 through 478 No H-bonds generated for 'chain '7' and resid 476 through 478' Processing helix chain '7' and resid 479 through 484 Processing helix chain '7' and resid 492 through 499 Processing helix chain '7' and resid 515 through 525 removed outlier: 3.542A pdb=" N GLU 7 521 " --> pdb=" O GLU 7 517 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA 7 524 " --> pdb=" O ARG 7 520 " (cutoff:3.500A) Processing helix chain '7' and resid 529 through 536 Processing helix chain '7' and resid 537 through 553 Processing helix chain '7' and resid 564 through 576 Processing helix chain '7' and resid 585 through 599 Processing helix chain '7' and resid 609 through 613 removed outlier: 3.647A pdb=" N ASP 7 612 " --> pdb=" O LYS 7 609 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR 7 613 " --> pdb=" O VAL 7 610 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 609 through 613' Processing helix chain '7' and resid 632 through 641 Processing helix chain '7' and resid 642 through 644 No H-bonds generated for 'chain '7' and resid 642 through 644' Processing helix chain '7' and resid 667 through 677 removed outlier: 3.961A pdb=" N ALA 7 671 " --> pdb=" O THR 7 667 " (cutoff:3.500A) Processing helix chain '7' and resid 677 through 683 Processing helix chain '7' and resid 705 through 720 Processing helix chain 'W' and resid 278 through 283 Processing sheet with id=AA1, first strand: chain '2' and resid 185 through 186 removed outlier: 3.855A pdb=" N LYS 2 186 " --> pdb=" O CYS 2 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 271 through 272 Processing sheet with id=AA3, first strand: chain '2' and resid 307 through 309 removed outlier: 6.952A pdb=" N MET 2 341 " --> pdb=" O ARG 2 337 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG 2 337 " --> pdb=" O MET 2 341 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL 2 343 " --> pdb=" O LEU 2 335 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N LYS 7 59 " --> pdb=" O GLU 2 333 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU 2 335 " --> pdb=" O LYS 7 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 431 through 435 removed outlier: 3.589A pdb=" N PHE 2 433 " --> pdb=" O VAL 2 442 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET 2 441 " --> pdb=" O TYR 2 409 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N HIS 5 42 " --> pdb=" O ASP 5 37 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP 5 37 " --> pdb=" O HIS 5 42 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE 5 44 " --> pdb=" O ILE 5 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '7' and resid 76 through 78 removed outlier: 6.722A pdb=" N GLU 7 115 " --> pdb=" O VAL 7 107 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU 7 105 " --> pdb=" O LYS 7 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '7' and resid 268 through 272 removed outlier: 4.167A pdb=" N TYR 7 175 " --> pdb=" O VAL 7 272 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL 7 166 " --> pdb=" O LEU 7 292 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '7' and resid 294 through 295 Processing sheet with id=AA8, first strand: chain '7' and resid 389 through 392 removed outlier: 4.163A pdb=" N THR 7 409 " --> pdb=" O PHE 7 392 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY 7 336 " --> pdb=" O GLY 7 465 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR 7 467 " --> pdb=" O GLY 7 336 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE 7 338 " --> pdb=" O THR 7 467 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL 7 337 " --> pdb=" O LYS 7 487 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR 7 489 " --> pdb=" O VAL 7 337 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '7' and resid 434 through 435 Processing sheet with id=AB1, first strand: chain '7' and resid 579 through 580 removed outlier: 6.573A pdb=" N ILE 7 558 " --> pdb=" O ILE 7 605 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE 7 607 " --> pdb=" O ILE 7 558 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL 7 560 " --> pdb=" O ILE 7 607 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU 7 623 " --> pdb=" O TYR 7 660 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '7' and resid 579 through 580 removed outlier: 6.573A pdb=" N ILE 7 558 " --> pdb=" O ILE 7 605 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE 7 607 " --> pdb=" O ILE 7 558 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL 7 560 " --> pdb=" O ILE 7 607 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU 7 623 " --> pdb=" O TYR 7 660 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 0.91 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: 2696 1.34 - 1.45: 1554 1.45 - 1.57: 4939 1.57 - 1.69: 101 1.69 - 1.81: 68 Bond restraints: 9358 Sorted by residual: bond pdb=" C4 ADP 7 901 " pdb=" C5 ADP 7 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" F2 BEF 7 903 " pdb="BE BEF 7 903 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C5 ADP 7 901 " pdb=" C6 ADP 7 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" F3 BEF 7 903 " pdb="BE BEF 7 903 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" F1 BEF 7 903 " pdb="BE BEF 7 903 " ideal model delta sigma weight residual 1.476 1.532 -0.056 2.00e-02 2.50e+03 7.97e+00 ... (remaining 9353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 12749 2.19 - 4.39: 106 4.39 - 6.58: 7 6.58 - 8.78: 4 8.78 - 10.97: 6 Bond angle restraints: 12872 Sorted by residual: angle pdb=" PA ADP 7 901 " pdb=" O3A ADP 7 901 " pdb=" PB ADP 7 901 " ideal model delta sigma weight residual 120.50 131.47 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C2' ADP 7 901 " pdb=" C3' ADP 7 901 " pdb=" C4' ADP 7 901 " ideal model delta sigma weight residual 111.00 100.21 10.79 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C1' ADP 7 901 " pdb=" C2' ADP 7 901 " pdb=" C3' ADP 7 901 " ideal model delta sigma weight residual 111.00 100.53 10.47 3.00e+00 1.11e-01 1.22e+01 angle pdb=" F2 BEF 7 903 " pdb="BE BEF 7 903 " pdb=" F3 BEF 7 903 " ideal model delta sigma weight residual 119.96 109.73 10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N1 ADP 7 901 " pdb=" C2 ADP 7 901 " pdb=" N3 ADP 7 901 " ideal model delta sigma weight residual 120.00 129.29 -9.29 3.00e+00 1.11e-01 9.59e+00 ... (remaining 12867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 4965 23.52 - 47.03: 433 47.03 - 70.55: 97 70.55 - 94.06: 9 94.06 - 117.58: 1 Dihedral angle restraints: 5505 sinusoidal: 2566 harmonic: 2939 Sorted by residual: dihedral pdb=" C5' ADP 7 901 " pdb=" O5' ADP 7 901 " pdb=" PA ADP 7 901 " pdb=" O2A ADP 7 901 " ideal model delta sinusoidal sigma weight residual -60.00 -177.57 117.58 1 2.00e+01 2.50e-03 3.51e+01 dihedral pdb=" O1B ADP 7 901 " pdb=" O3A ADP 7 901 " pdb=" PB ADP 7 901 " pdb=" PA ADP 7 901 " ideal model delta sinusoidal sigma weight residual -60.00 -128.87 68.87 1 2.00e+01 2.50e-03 1.53e+01 dihedral pdb=" CA ASP 7 563 " pdb=" CB ASP 7 563 " pdb=" CG ASP 7 563 " pdb=" OD1 ASP 7 563 " ideal model delta sinusoidal sigma weight residual -30.00 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1047 0.033 - 0.066: 246 0.066 - 0.099: 101 0.099 - 0.132: 52 0.132 - 0.165: 2 Chirality restraints: 1448 Sorted by residual: chirality pdb=" C3' ADP 7 901 " pdb=" C2' ADP 7 901 " pdb=" C4' ADP 7 901 " pdb=" O3' ADP 7 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE 7 580 " pdb=" N ILE 7 580 " pdb=" C ILE 7 580 " pdb=" CB ILE 7 580 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE 7 559 " pdb=" N ILE 7 559 " pdb=" C ILE 7 559 " pdb=" CB ILE 7 559 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 1445 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 7 62 " 0.172 9.50e-02 1.11e+02 7.70e-02 3.83e+00 pdb=" NE ARG 7 62 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG 7 62 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG 7 62 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG 7 62 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE 2 338 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO 2 339 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO 2 339 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO 2 339 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR 7 581 " 0.009 2.00e-02 2.50e+03 9.58e-03 1.84e+00 pdb=" CG TYR 7 581 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR 7 581 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR 7 581 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 7 581 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR 7 581 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR 7 581 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR 7 581 " 0.000 2.00e-02 2.50e+03 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 66 2.57 - 3.15: 7366 3.15 - 3.73: 15099 3.73 - 4.32: 21014 4.32 - 4.90: 33957 Nonbonded interactions: 77502 Sorted by model distance: nonbonded pdb=" O LYS 7 165 " pdb=" OG SER 7 179 " model vdw 1.984 3.040 nonbonded pdb=" OG SER 2 172 " pdb=" OD1 ASP 2 174 " model vdw 2.000 3.040 nonbonded pdb="MG MG 7 902 " pdb=" F1 BEF 7 903 " model vdw 2.009 2.120 nonbonded pdb=" OH TYR 7 319 " pdb=" O ALA 7 344 " model vdw 2.014 3.040 nonbonded pdb=" O PHE 7 378 " pdb=" OG SER 7 382 " model vdw 2.018 3.040 ... (remaining 77497 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: 8.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.006 0.495 9359 Z= 0.534 Angle : 0.519 10.969 12872 Z= 0.261 Chirality : 0.038 0.165 1448 Planarity : 0.003 0.077 1459 Dihedral : 17.438 117.575 3593 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.30 (0.28), residues: 961 helix: 1.96 (0.25), residues: 468 sheet: -0.30 (0.45), residues: 144 loop : -0.04 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 7 62 TYR 0.023 0.001 TYR 7 581 PHE 0.009 0.001 PHE 7 482 TRP 0.006 0.001 TRP W 280 HIS 0.002 0.000 HIS 7 114 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9358) covalent geometry : angle 0.51887 (12872) hydrogen bonds : bond 0.18098 ( 447) hydrogen bonds : angle 6.57449 ( 1264) Misc. bond : bond 0.49547 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7789 (t-100) cc_final: 0.7485 (t-100) REVERT: 2 336 TYR cc_start: 0.8502 (m-80) cc_final: 0.8175 (m-80) REVERT: 7 495 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7080 (mm-30) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.6441 time to fit residues: 130.0736 Evaluate side-chains 116 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 173 GLN 2 211 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 352 GLN ** 2 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 190 GLN 7 366 ASN 7 388 GLN 7 564 ASN 7 595 ASN 7 668 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.162294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.115101 restraints weight = 12174.398| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.07 r_work: 0.3360 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9359 Z= 0.244 Angle : 0.632 10.571 12872 Z= 0.331 Chirality : 0.043 0.155 1448 Planarity : 0.004 0.033 1459 Dihedral : 18.571 111.781 1632 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.89 % Allowed : 13.29 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.63 (0.27), residues: 961 helix: 1.44 (0.24), residues: 484 sheet: -0.68 (0.44), residues: 139 loop : -0.48 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 7 62 TYR 0.024 0.002 TYR 7 581 PHE 0.032 0.002 PHE 2 261 TRP 0.009 0.001 TRP 2 213 HIS 0.012 0.002 HIS 7 286 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 9358) covalent geometry : angle 0.63238 (12872) hydrogen bonds : bond 0.05068 ( 447) hydrogen bonds : angle 4.74926 ( 1264) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.8017 (t-100) cc_final: 0.7603 (t-100) REVERT: 2 258 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7269 (tm) REVERT: 2 262 LEU cc_start: 0.9065 (tp) cc_final: 0.8865 (mm) REVERT: 2 336 TYR cc_start: 0.9075 (m-80) cc_final: 0.8842 (m-80) REVERT: 2 452 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8807 (ptmt) REVERT: 5 48 GLU cc_start: 0.8488 (pm20) cc_final: 0.8086 (pm20) REVERT: 5 51 ASN cc_start: 0.8460 (t0) cc_final: 0.8088 (m110) REVERT: 5 61 MET cc_start: 0.8812 (mmt) cc_final: 0.8540 (mmp) REVERT: 7 76 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8689 (tp) REVERT: 7 141 ARG cc_start: 0.7502 (mtm110) cc_final: 0.6667 (mtt-85) REVERT: 7 379 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7194 (mtmp) REVERT: 7 590 MET cc_start: 0.8490 (tpt) cc_final: 0.8185 (tpt) REVERT: 7 612 ASP cc_start: 0.8417 (p0) cc_final: 0.8088 (p0) outliers start: 25 outliers final: 9 residues processed: 139 average time/residue: 0.5488 time to fit residues: 81.7205 Evaluate side-chains 125 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 265 LEU Chi-restraints excluded: chain 2 residue 421 LEU Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 379 LYS Chi-restraints excluded: chain 7 residue 686 SER Chi-restraints excluded: chain W residue 279 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 2 optimal weight: 0.0070 chunk 34 optimal weight: 0.0270 chunk 80 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 38 optimal weight: 0.3980 overall best weight: 0.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 366 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.165309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.118826 restraints weight = 12003.550| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.05 r_work: 0.3406 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9359 Z= 0.135 Angle : 0.568 8.575 12872 Z= 0.294 Chirality : 0.040 0.227 1448 Planarity : 0.004 0.039 1459 Dihedral : 18.560 101.434 1632 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.89 % Allowed : 16.07 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 961 helix: 1.34 (0.24), residues: 484 sheet: -0.69 (0.43), residues: 139 loop : -0.61 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 74 TYR 0.023 0.001 TYR 7 534 PHE 0.015 0.001 PHE 2 261 TRP 0.009 0.001 TRP 2 213 HIS 0.007 0.001 HIS 7 286 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9358) covalent geometry : angle 0.56848 (12872) hydrogen bonds : bond 0.03658 ( 447) hydrogen bonds : angle 4.31135 ( 1264) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7819 (t-100) cc_final: 0.7403 (t-100) REVERT: 2 261 PHE cc_start: 0.8253 (t80) cc_final: 0.7955 (t80) REVERT: 2 336 TYR cc_start: 0.9066 (m-80) cc_final: 0.8835 (m-80) REVERT: 2 341 MET cc_start: 0.8790 (tmm) cc_final: 0.8566 (tmm) REVERT: 2 456 LYS cc_start: 0.9330 (ptmt) cc_final: 0.9046 (mmmt) REVERT: 5 48 GLU cc_start: 0.8502 (pm20) cc_final: 0.8076 (pm20) REVERT: 5 59 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6574 (tm-30) REVERT: 5 61 MET cc_start: 0.8728 (mmt) cc_final: 0.8457 (mmp) REVERT: 5 63 GLN cc_start: 0.7785 (mt0) cc_final: 0.7414 (tt0) REVERT: 7 287 LEU cc_start: 0.8683 (mt) cc_final: 0.8415 (mt) REVERT: 7 308 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.6997 (mp) REVERT: 7 570 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7840 (mt-10) REVERT: 7 590 MET cc_start: 0.8515 (tpt) cc_final: 0.8227 (tpt) REVERT: 7 612 ASP cc_start: 0.8345 (p0) cc_final: 0.7962 (p0) outliers start: 25 outliers final: 8 residues processed: 130 average time/residue: 0.5404 time to fit residues: 75.4227 Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 438 LYS Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 552 GLU Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain W residue 279 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 90 optimal weight: 0.0970 chunk 2 optimal weight: 0.0170 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN 2 424 HIS 5 64 ASN 7 366 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.164552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.118142 restraints weight = 12259.372| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.05 r_work: 0.3391 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9359 Z= 0.144 Angle : 0.561 8.830 12872 Z= 0.288 Chirality : 0.040 0.175 1448 Planarity : 0.004 0.044 1459 Dihedral : 18.607 93.560 1632 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.01 % Allowed : 17.92 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.41 (0.27), residues: 961 helix: 1.28 (0.24), residues: 483 sheet: -0.69 (0.43), residues: 139 loop : -0.68 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 348 TYR 0.022 0.001 TYR 7 534 PHE 0.017 0.002 PHE 2 261 TRP 0.007 0.001 TRP 2 213 HIS 0.004 0.001 HIS 7 286 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9358) covalent geometry : angle 0.56122 (12872) hydrogen bonds : bond 0.03531 ( 447) hydrogen bonds : angle 4.17455 ( 1264) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7827 (t-100) cc_final: 0.7275 (t-100) REVERT: 2 261 PHE cc_start: 0.8127 (t80) cc_final: 0.7744 (t80) REVERT: 2 265 LEU cc_start: 0.9100 (mm) cc_final: 0.8899 (mm) REVERT: 2 336 TYR cc_start: 0.9056 (m-80) cc_final: 0.8843 (m-80) REVERT: 2 341 MET cc_start: 0.8795 (tmm) cc_final: 0.8522 (tmm) REVERT: 2 402 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7632 (mtt90) REVERT: 2 456 LYS cc_start: 0.9371 (ptmt) cc_final: 0.9058 (mmmt) REVERT: 5 48 GLU cc_start: 0.8473 (pm20) cc_final: 0.7997 (pm20) REVERT: 5 63 GLN cc_start: 0.7842 (mt0) cc_final: 0.7501 (tt0) REVERT: 7 54 ASP cc_start: 0.7368 (m-30) cc_final: 0.7031 (m-30) REVERT: 7 70 ASP cc_start: 0.7965 (t0) cc_final: 0.7462 (t0) REVERT: 7 287 LEU cc_start: 0.8690 (mt) cc_final: 0.8392 (mt) REVERT: 7 570 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7963 (mt-10) REVERT: 7 590 MET cc_start: 0.8539 (tpt) cc_final: 0.8263 (tpt) REVERT: 7 612 ASP cc_start: 0.8333 (p0) cc_final: 0.7946 (p0) REVERT: 7 706 LYS cc_start: 0.7419 (tptt) cc_final: 0.7193 (tptt) outliers start: 26 outliers final: 14 residues processed: 136 average time/residue: 0.5476 time to fit residues: 79.6712 Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 402 ARG Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 285 ILE Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 552 GLU Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Chi-restraints excluded: chain W residue 279 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 0.0570 chunk 51 optimal weight: 0.0980 chunk 99 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN 2 224 GLN 5 64 ASN 7 190 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115855 restraints weight = 12185.155| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.03 r_work: 0.3353 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9359 Z= 0.193 Angle : 0.589 8.114 12872 Z= 0.303 Chirality : 0.041 0.171 1448 Planarity : 0.004 0.049 1459 Dihedral : 18.889 97.009 1632 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.01 % Allowed : 19.42 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.27 (0.27), residues: 961 helix: 1.20 (0.24), residues: 484 sheet: -0.84 (0.43), residues: 139 loop : -0.77 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 285 TYR 0.023 0.001 TYR 7 534 PHE 0.015 0.002 PHE 2 367 TRP 0.008 0.001 TRP 2 213 HIS 0.007 0.001 HIS 7 114 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9358) covalent geometry : angle 0.58948 (12872) hydrogen bonds : bond 0.03669 ( 447) hydrogen bonds : angle 4.20624 ( 1264) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7901 (t-100) cc_final: 0.7344 (t-100) REVERT: 2 402 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7621 (mtt90) REVERT: 2 456 LYS cc_start: 0.9385 (ptmt) cc_final: 0.9070 (mmmt) REVERT: 5 48 GLU cc_start: 0.8467 (pm20) cc_final: 0.7974 (pm20) REVERT: 5 63 GLN cc_start: 0.7787 (mt0) cc_final: 0.7448 (tt0) REVERT: 5 64 ASN cc_start: 0.8414 (m110) cc_final: 0.8210 (m-40) REVERT: 7 54 ASP cc_start: 0.7371 (m-30) cc_final: 0.6988 (m-30) REVERT: 7 70 ASP cc_start: 0.7976 (t0) cc_final: 0.7380 (t0) REVERT: 7 287 LEU cc_start: 0.8645 (mt) cc_final: 0.8384 (mt) REVERT: 7 590 MET cc_start: 0.8542 (tpt) cc_final: 0.8280 (tpt) REVERT: 7 612 ASP cc_start: 0.8369 (p0) cc_final: 0.8110 (p0) outliers start: 26 outliers final: 15 residues processed: 133 average time/residue: 0.5281 time to fit residues: 75.4065 Evaluate side-chains 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 402 ARG Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 285 ILE Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 39 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 461 HIS 7 668 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.161843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114944 restraints weight = 12203.860| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.03 r_work: 0.3342 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9359 Z= 0.197 Angle : 0.585 7.743 12872 Z= 0.302 Chirality : 0.041 0.173 1448 Planarity : 0.004 0.056 1459 Dihedral : 19.039 99.080 1632 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.82 % Allowed : 19.19 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.17 (0.27), residues: 961 helix: 1.15 (0.24), residues: 485 sheet: -0.91 (0.42), residues: 139 loop : -0.85 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 676 TYR 0.021 0.001 TYR 7 534 PHE 0.033 0.002 PHE 2 261 TRP 0.009 0.001 TRP 7 77 HIS 0.007 0.001 HIS 7 114 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 9358) covalent geometry : angle 0.58509 (12872) hydrogen bonds : bond 0.03647 ( 447) hydrogen bonds : angle 4.22248 ( 1264) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7911 (t-100) cc_final: 0.7374 (t-100) REVERT: 2 261 PHE cc_start: 0.8305 (t80) cc_final: 0.7809 (t80) REVERT: 2 265 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8812 (mm) REVERT: 2 336 TYR cc_start: 0.9085 (m-80) cc_final: 0.8190 (m-80) REVERT: 2 456 LYS cc_start: 0.9360 (ptmt) cc_final: 0.9055 (mmmt) REVERT: 5 11 GLU cc_start: 0.7914 (tt0) cc_final: 0.7686 (tt0) REVERT: 5 48 GLU cc_start: 0.8419 (pm20) cc_final: 0.7903 (pm20) REVERT: 5 63 GLN cc_start: 0.7831 (mt0) cc_final: 0.7459 (tt0) REVERT: 5 64 ASN cc_start: 0.8348 (m110) cc_final: 0.8103 (m-40) REVERT: 7 64 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6739 (mm-40) REVERT: 7 70 ASP cc_start: 0.8028 (t0) cc_final: 0.7398 (t0) REVERT: 7 287 LEU cc_start: 0.8644 (mt) cc_final: 0.8395 (mt) REVERT: 7 590 MET cc_start: 0.8525 (tpt) cc_final: 0.8278 (tpt) REVERT: 7 612 ASP cc_start: 0.8371 (p0) cc_final: 0.8075 (p0) outliers start: 33 outliers final: 20 residues processed: 130 average time/residue: 0.5126 time to fit residues: 71.8061 Evaluate side-chains 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 237 LEU Chi-restraints excluded: chain 2 residue 265 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 139 TYR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 285 ILE Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 56 optimal weight: 0.1980 chunk 73 optimal weight: 0.0980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.164244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.117819 restraints weight = 12221.243| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.04 r_work: 0.3386 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9359 Z= 0.133 Angle : 0.561 8.320 12872 Z= 0.287 Chirality : 0.039 0.211 1448 Planarity : 0.004 0.056 1459 Dihedral : 18.880 91.549 1632 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.47 % Allowed : 19.54 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.24 (0.27), residues: 961 helix: 1.22 (0.24), residues: 485 sheet: -0.84 (0.42), residues: 139 loop : -0.87 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 348 TYR 0.021 0.001 TYR 7 534 PHE 0.020 0.001 PHE 2 261 TRP 0.010 0.001 TRP 7 77 HIS 0.004 0.001 HIS 7 114 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9358) covalent geometry : angle 0.56089 (12872) hydrogen bonds : bond 0.03119 ( 447) hydrogen bonds : angle 4.10468 ( 1264) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7838 (t-100) cc_final: 0.7202 (t-100) REVERT: 2 258 LEU cc_start: 0.6885 (tm) cc_final: 0.6680 (tp) REVERT: 2 261 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7713 (t80) REVERT: 2 265 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8756 (mm) REVERT: 2 336 TYR cc_start: 0.9076 (m-80) cc_final: 0.8129 (m-80) REVERT: 2 402 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7660 (mtt90) REVERT: 2 456 LYS cc_start: 0.9361 (ptmt) cc_final: 0.9058 (mmmt) REVERT: 5 11 GLU cc_start: 0.7903 (tt0) cc_final: 0.7640 (tt0) REVERT: 5 48 GLU cc_start: 0.8413 (pm20) cc_final: 0.7905 (pm20) REVERT: 5 63 GLN cc_start: 0.7845 (mt0) cc_final: 0.7486 (tt0) REVERT: 5 64 ASN cc_start: 0.8420 (m110) cc_final: 0.8182 (m-40) REVERT: 7 54 ASP cc_start: 0.7264 (m-30) cc_final: 0.6909 (m-30) REVERT: 7 70 ASP cc_start: 0.8053 (t0) cc_final: 0.7394 (t0) REVERT: 7 287 LEU cc_start: 0.8679 (mt) cc_final: 0.8435 (mt) REVERT: 7 612 ASP cc_start: 0.8387 (p0) cc_final: 0.8041 (p0) outliers start: 30 outliers final: 12 residues processed: 134 average time/residue: 0.5269 time to fit residues: 75.9738 Evaluate side-chains 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 237 LEU Chi-restraints excluded: chain 2 residue 261 PHE Chi-restraints excluded: chain 2 residue 265 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 402 ARG Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 139 TYR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 677 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.160826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113600 restraints weight = 12154.089| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.03 r_work: 0.3317 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9359 Z= 0.238 Angle : 0.654 12.277 12872 Z= 0.329 Chirality : 0.043 0.218 1448 Planarity : 0.004 0.058 1459 Dihedral : 19.243 101.289 1632 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.82 % Allowed : 20.23 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.01 (0.26), residues: 961 helix: 1.03 (0.24), residues: 484 sheet: -1.06 (0.42), residues: 139 loop : -0.96 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 2 285 TYR 0.023 0.002 TYR 7 534 PHE 0.020 0.002 PHE 2 261 TRP 0.008 0.001 TRP 7 511 HIS 0.009 0.001 HIS 7 114 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 9358) covalent geometry : angle 0.65427 (12872) hydrogen bonds : bond 0.03986 ( 447) hydrogen bonds : angle 4.31578 ( 1264) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.8029 (t-100) cc_final: 0.7683 (t-100) REVERT: 2 261 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7629 (t80) REVERT: 2 336 TYR cc_start: 0.9111 (m-80) cc_final: 0.8126 (m-80) REVERT: 2 402 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7681 (mtt90) REVERT: 2 456 LYS cc_start: 0.9354 (ptmt) cc_final: 0.9110 (mmmt) REVERT: 5 11 GLU cc_start: 0.7945 (tt0) cc_final: 0.7673 (tt0) REVERT: 5 48 GLU cc_start: 0.8292 (pm20) cc_final: 0.7845 (pm20) REVERT: 5 63 GLN cc_start: 0.7851 (mt0) cc_final: 0.7479 (tt0) REVERT: 5 64 ASN cc_start: 0.8440 (m110) cc_final: 0.8206 (m-40) REVERT: 7 70 ASP cc_start: 0.8095 (t0) cc_final: 0.7416 (t0) REVERT: 7 287 LEU cc_start: 0.8666 (mt) cc_final: 0.8438 (mt) REVERT: 7 612 ASP cc_start: 0.8402 (p0) cc_final: 0.8131 (p0) outliers start: 33 outliers final: 16 residues processed: 132 average time/residue: 0.5326 time to fit residues: 75.3715 Evaluate side-chains 125 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 2 residue 237 LEU Chi-restraints excluded: chain 2 residue 261 PHE Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 402 ARG Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 285 ILE Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 62 optimal weight: 0.0670 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 64 GLN 7 190 GLN ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.161640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.114693 restraints weight = 12107.962| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.03 r_work: 0.3336 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9359 Z= 0.195 Angle : 0.635 11.527 12872 Z= 0.320 Chirality : 0.042 0.214 1448 Planarity : 0.004 0.060 1459 Dihedral : 19.246 100.895 1632 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.89 % Allowed : 21.50 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.01 (0.27), residues: 961 helix: 1.05 (0.24), residues: 485 sheet: -1.14 (0.42), residues: 139 loop : -0.96 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 676 TYR 0.022 0.001 TYR 7 534 PHE 0.037 0.002 PHE 2 162 TRP 0.009 0.001 TRP 2 213 HIS 0.007 0.001 HIS 7 114 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 9358) covalent geometry : angle 0.63514 (12872) hydrogen bonds : bond 0.03562 ( 447) hydrogen bonds : angle 4.27715 ( 1264) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: 2 162 PHE cc_start: 0.8205 (t80) cc_final: 0.7989 (t80) REVERT: 2 213 TRP cc_start: 0.8023 (t-100) cc_final: 0.7692 (t-100) REVERT: 2 336 TYR cc_start: 0.9081 (m-80) cc_final: 0.8160 (m-80) REVERT: 2 402 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7655 (mtt90) REVERT: 2 452 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8291 (ptpt) REVERT: 5 11 GLU cc_start: 0.7933 (tt0) cc_final: 0.7656 (tt0) REVERT: 5 48 GLU cc_start: 0.8297 (pm20) cc_final: 0.7852 (pm20) REVERT: 5 63 GLN cc_start: 0.7872 (mt0) cc_final: 0.7550 (tt0) REVERT: 5 64 ASN cc_start: 0.8576 (m110) cc_final: 0.8320 (m-40) REVERT: 7 70 ASP cc_start: 0.8001 (t0) cc_final: 0.7343 (t0) REVERT: 7 153 MET cc_start: 0.7651 (mmm) cc_final: 0.7340 (mmt) REVERT: 7 287 LEU cc_start: 0.8648 (mt) cc_final: 0.8420 (mt) REVERT: 7 612 ASP cc_start: 0.8397 (p0) cc_final: 0.8082 (p0) outliers start: 25 outliers final: 15 residues processed: 124 average time/residue: 0.5213 time to fit residues: 69.5218 Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 2 residue 237 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 402 ARG Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 2 residue 452 LYS Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 285 ILE Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 76 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 62 optimal weight: 0.0470 chunk 68 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 80 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 3 ASN 7 64 GLN ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.164335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.118321 restraints weight = 12087.683| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.02 r_work: 0.3388 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9359 Z= 0.139 Angle : 0.625 11.434 12872 Z= 0.312 Chirality : 0.040 0.194 1448 Planarity : 0.004 0.058 1459 Dihedral : 18.992 91.832 1632 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.89 % Allowed : 21.97 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.00 (0.27), residues: 961 helix: 1.03 (0.24), residues: 486 sheet: -0.92 (0.42), residues: 144 loop : -1.02 (0.30), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 457 TYR 0.023 0.001 TYR 7 534 PHE 0.037 0.002 PHE 2 261 TRP 0.008 0.001 TRP 2 213 HIS 0.004 0.001 HIS 7 114 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9358) covalent geometry : angle 0.62507 (12872) hydrogen bonds : bond 0.03156 ( 447) hydrogen bonds : angle 4.18898 ( 1264) Misc. bond : bond 0.00036 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7931 (t-100) cc_final: 0.7295 (t-100) REVERT: 2 336 TYR cc_start: 0.9008 (m-80) cc_final: 0.8147 (m-80) REVERT: 2 402 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7651 (mtt90) REVERT: 2 456 LYS cc_start: 0.9313 (pttm) cc_final: 0.8993 (mmmt) REVERT: 5 11 GLU cc_start: 0.7894 (tt0) cc_final: 0.7602 (tt0) REVERT: 5 48 GLU cc_start: 0.8214 (pm20) cc_final: 0.7775 (pm20) REVERT: 5 63 GLN cc_start: 0.7879 (mt0) cc_final: 0.7537 (tt0) REVERT: 5 64 ASN cc_start: 0.8432 (m110) cc_final: 0.8165 (m-40) REVERT: 7 52 LYS cc_start: 0.7182 (tppt) cc_final: 0.6201 (ttmt) REVERT: 7 54 ASP cc_start: 0.7164 (m-30) cc_final: 0.6761 (m-30) REVERT: 7 64 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7023 (mm110) REVERT: 7 70 ASP cc_start: 0.7961 (t0) cc_final: 0.7279 (t0) REVERT: 7 153 MET cc_start: 0.7568 (mmm) cc_final: 0.7312 (mmm) REVERT: 7 287 LEU cc_start: 0.8677 (mt) cc_final: 0.8441 (mt) REVERT: 7 450 MET cc_start: 0.8421 (mpm) cc_final: 0.8166 (mpp) REVERT: 7 612 ASP cc_start: 0.8410 (p0) cc_final: 0.8083 (p0) outliers start: 25 outliers final: 16 residues processed: 128 average time/residue: 0.5092 time to fit residues: 70.3189 Evaluate side-chains 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 2 residue 237 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 402 ARG Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 2 residue 448 HIS Chi-restraints excluded: chain 5 residue 3 ASN Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 92 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 0.0870 chunk 22 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 3 ASN ** 5 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.164030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118198 restraints weight = 12051.056| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.01 r_work: 0.3385 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.264 9359 Z= 0.258 Angle : 0.940 59.199 12872 Z= 0.519 Chirality : 0.051 1.199 1448 Planarity : 0.004 0.073 1459 Dihedral : 18.991 91.826 1632 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.43 % Allowed : 22.20 % Favored : 75.38 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.50 % 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: -0.02 (0.27), residues: 961 helix: 1.01 (0.24), residues: 486 sheet: -0.91 (0.42), residues: 144 loop : -1.03 (0.30), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 348 TYR 0.022 0.001 TYR 7 534 PHE 0.031 0.002 PHE 2 261 TRP 0.008 0.001 TRP 2 213 HIS 0.007 0.001 HIS 2 448 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 9358) covalent geometry : angle 0.93990 (12872) hydrogen bonds : bond 0.03165 ( 447) hydrogen bonds : angle 4.18954 ( 1264) Misc. bond : bond 0.00041 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3702.91 seconds wall clock time: 63 minutes 36.48 seconds (3816.48 seconds total)