Starting phenix.real_space_refine on Fri Sep 11 11:52:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nvv_12614/09_2026/7nvv_12614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvv_12614/09_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_12614/09_2026/7nvv_12614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvv_12614/09_2026/7nvv_12614.map" model { file = "/net/cci-nas-00/data/ceres_data/7nvv_12614/09_2026/7nvv_12614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvv_12614/09_2026/7nvv_12614.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nvv_12614/09_2026/7nvv_12614.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nvv_12614/09_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 1.90, 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: 1.09 Conformation dependent library (CDL) restraints added in 297.8 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: 1.23 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: 1.72 Time building geometry restraints manager: 1.02 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=" C3' DT N 49 " pdb=" C2' DT N 49 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.41e+00 ... (remaining 9353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 12705 2.19 - 4.39: 150 4.39 - 6.58: 7 6.58 - 8.78: 4 8.78 - 10.97: 6 Bond angle restraints: 12872 Sorted by residual: angle pdb=" N3 DT N 39 " pdb=" C4 DT N 39 " pdb=" O4 DT N 39 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT N 45 " pdb=" C4 DT N 45 " pdb=" O4 DT N 45 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT N 51 " pdb=" C4 DT N 51 " pdb=" O4 DT N 51 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT N 38 " pdb=" C4 DT N 38 " pdb=" O4 DT N 38 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT N 36 " pdb=" C4 DT N 36 " pdb=" O4 DT N 36 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (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 - 0.035: 1052 0.035 - 0.070: 237 0.070 - 0.104: 77 0.104 - 0.139: 51 0.139 - 0.174: 31 Chirality restraints: 1448 Sorted by residual: chirality pdb=" C3' DC N 48 " pdb=" C4' DC N 48 " pdb=" O3' DC N 48 " pdb=" C2' DC N 48 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" C3' DG N 47 " pdb=" C4' DG N 47 " pdb=" O3' DG N 47 " pdb=" C2' DG N 47 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.12e-01 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 ... (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: 7.800 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.470 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:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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= 0.581 Angle : 0.567 10.969 12872 Z= 0.368 Chirality : 0.044 0.174 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/Z covalent geometry : bond 0.00383 / 0.27 ( 9358) covalent geometry : angle 0.56741 / 0.37 (12872) hydrogen bonds : bond 0.18098 / 12.69 ( 447) hydrogen bonds : angle 6.57449 / 4.71 ( 1264) Misc. bond : bond 0.49547 / 26.08 ( 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 : 0.218 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: 0.5688 time to fit residues: 115.0931 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 : 0.283 ------------------------------------------------------------------------------- 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: 3.9990 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... 2 211 GLN 2 224 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 7 668 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.162781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115659 restraints weight = 12164.901| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.07 r_work: 0.3370 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9359 Z= 0.241 Angle : 0.670 12.444 12872 Z= 0.358 Chirality : 0.045 0.161 1448 Planarity : 0.005 0.038 1459 Dihedral : 18.570 110.464 1632 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.54 % Allowed : 12.95 % Favored : 84.51 % 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: 0.45 (0.27), residues: 961 helix: 1.24 (0.24), residues: 483 sheet: -0.69 (0.43), residues: 139 loop : -0.52 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 2 453 TYR 0.026 0.002 TYR 7 581 PHE 0.032 0.002 PHE 2 261 TRP 0.011 0.002 TRP 2 213 HIS 0.015 0.002 HIS 2 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 ( 9358) covalent geometry : angle 0.67043 / 0.36 (12872) hydrogen bonds : bond 0.05322 / 3.69 ( 447) hydrogen bonds : angle 4.83049 / 3.41 ( 1264) Misc. bond : bond 0.01736 / 0.91 ( 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 146 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.8016 (t-100) cc_final: 0.7576 (t-100) REVERT: 2 336 TYR cc_start: 0.9066 (m-80) cc_final: 0.8619 (m-80) REVERT: 2 452 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8762 (ptmt) REVERT: 2 456 LYS cc_start: 0.9387 (mmmt) cc_final: 0.9176 (ptmt) REVERT: 5 48 GLU cc_start: 0.8478 (pm20) cc_final: 0.8060 (pm20) REVERT: 5 51 ASN cc_start: 0.8511 (t0) cc_final: 0.8177 (m110) REVERT: 5 61 MET cc_start: 0.8777 (mmt) cc_final: 0.8528 (mmp) REVERT: 7 141 ARG cc_start: 0.7454 (mtm110) cc_final: 0.6646 (mtt-85) REVERT: 7 570 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8182 (mm-30) REVERT: 7 590 MET cc_start: 0.8488 (tpt) cc_final: 0.8202 (tpt) REVERT: 7 612 ASP cc_start: 0.8363 (p0) cc_final: 0.7936 (p0) outliers start: 22 outliers final: 9 residues processed: 134 average time/residue: 0.4941 time to fit residues: 70.8806 Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 ASN 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 686 SER 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: 0.9990 chunk 71 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 99 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 161 HIS 2 173 GLN ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 366 ASN ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 595 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.163314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116130 restraints weight = 11982.853| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.06 r_work: 0.3364 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9359 Z= 0.182 Angle : 0.597 7.589 12872 Z= 0.319 Chirality : 0.042 0.209 1448 Planarity : 0.004 0.043 1459 Dihedral : 18.882 111.762 1632 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.35 % Allowed : 15.26 % Favored : 81.39 % 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: 0.25 (0.26), residues: 961 helix: 1.12 (0.24), residues: 483 sheet: -0.77 (0.43), residues: 139 loop : -0.71 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 62 TYR 0.020 0.001 TYR 7 534 PHE 0.018 0.002 PHE 2 268 TRP 0.009 0.001 TRP 2 213 HIS 0.010 0.001 HIS 2 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 9358) covalent geometry : angle 0.59659 / 0.32 (12872) hydrogen bonds : bond 0.04505 / 3.13 ( 447) hydrogen bonds : angle 4.48818 / 3.17 ( 1264) Misc. bond : bond 0.00176 / 0.09 ( 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 152 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.8011 (t-100) cc_final: 0.7584 (t-100) REVERT: 2 234 LEU cc_start: 0.9490 (tp) cc_final: 0.9155 (pp) REVERT: 2 261 PHE cc_start: 0.8343 (t80) cc_final: 0.8111 (t80) REVERT: 2 336 TYR cc_start: 0.9064 (m-80) cc_final: 0.8836 (m-80) REVERT: 2 452 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8860 (ptmt) REVERT: 5 48 GLU cc_start: 0.8522 (pm20) cc_final: 0.8101 (pm20) REVERT: 5 61 MET cc_start: 0.8761 (mmt) cc_final: 0.8499 (mmp) REVERT: 5 63 GLN cc_start: 0.7796 (mt0) cc_final: 0.7415 (tt0) REVERT: 7 308 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7017 (mp) REVERT: 7 379 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6887 (mttp) REVERT: 7 590 MET cc_start: 0.8524 (tpt) cc_final: 0.8257 (tpt) REVERT: 7 612 ASP cc_start: 0.8331 (p0) cc_final: 0.7990 (p0) REVERT: 7 636 GLU cc_start: 0.8566 (tp30) cc_final: 0.8361 (tp30) outliers start: 29 outliers final: 11 residues processed: 136 average time/residue: 0.4814 time to fit residues: 70.3163 Evaluate side-chains 126 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 265 LEU 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 76 LEU 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 371 VAL Chi-restraints excluded: chain 7 residue 379 LYS Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 161 HIS 2 173 GLN 5 64 ASN 7 154 GLN 7 366 ASN ** 7 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.161647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114578 restraints weight = 12230.381| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.05 r_work: 0.3341 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9359 Z= 0.225 Angle : 0.628 8.508 12872 Z= 0.328 Chirality : 0.043 0.222 1448 Planarity : 0.004 0.052 1459 Dihedral : 19.144 107.488 1632 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.35 % Allowed : 17.11 % Favored : 79.54 % 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: 0.08 (0.26), residues: 961 helix: 0.98 (0.24), residues: 486 sheet: -0.92 (0.42), residues: 139 loop : -0.75 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 74 TYR 0.023 0.002 TYR 7 534 PHE 0.020 0.002 PHE 2 268 TRP 0.010 0.001 TRP 2 213 HIS 0.007 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 ( 9358) covalent geometry : angle 0.62753 / 0.33 (12872) hydrogen bonds : bond 0.04437 / 3.06 ( 447) hydrogen bonds : angle 4.43279 / 3.13 ( 1264) Misc. bond : bond 0.00083 / 0.04 ( 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 144 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.8007 (t-100) cc_final: 0.7589 (t-100) REVERT: 2 234 LEU cc_start: 0.9490 (tp) cc_final: 0.9158 (pp) REVERT: 2 402 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7700 (mtt90) REVERT: 5 11 GLU cc_start: 0.7952 (tt0) cc_final: 0.7623 (tt0) REVERT: 5 48 GLU cc_start: 0.8559 (pm20) cc_final: 0.8118 (pm20) REVERT: 5 63 GLN cc_start: 0.7785 (mt0) cc_final: 0.7415 (tt0) REVERT: 7 70 ASP cc_start: 0.8022 (t0) cc_final: 0.7416 (t0) REVERT: 7 379 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6913 (mttp) REVERT: 7 590 MET cc_start: 0.8521 (tpt) cc_final: 0.8292 (tpt) REVERT: 7 612 ASP cc_start: 0.8398 (p0) cc_final: 0.8094 (p0) outliers start: 29 outliers final: 14 residues processed: 130 average time/residue: 0.5010 time to fit residues: 69.9940 Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 265 LEU Chi-restraints excluded: chain 2 residue 402 ARG Chi-restraints excluded: chain 2 residue 438 LYS 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 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 379 LYS Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 99 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 34 optimal weight: 0.0370 chunk 67 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 161 HIS 2 173 GLN 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 = 0.4123 r_free = 0.4123 target = 0.162856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116369 restraints weight = 12134.924| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.03 r_work: 0.3366 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9359 Z= 0.159 Angle : 0.600 8.229 12872 Z= 0.313 Chirality : 0.041 0.224 1448 Planarity : 0.004 0.050 1459 Dihedral : 19.194 106.123 1632 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.47 % Allowed : 18.03 % Favored : 78.50 % 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: 0.08 (0.26), residues: 961 helix: 1.05 (0.24), residues: 483 sheet: -0.96 (0.42), residues: 139 loop : -0.85 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 645 TYR 0.021 0.001 TYR 7 534 PHE 0.021 0.002 PHE 2 236 TRP 0.010 0.001 TRP 7 77 HIS 0.005 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 9358) covalent geometry : angle 0.59965 / 0.31 (12872) hydrogen bonds : bond 0.03804 / 2.65 ( 447) hydrogen bonds : angle 4.29020 / 3.02 ( 1264) Misc. bond : bond 0.00048 / 0.03 ( 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 142 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.8003 (t-100) cc_final: 0.7583 (t-100) REVERT: 2 234 LEU cc_start: 0.9468 (tp) cc_final: 0.9139 (pp) REVERT: 2 261 PHE cc_start: 0.8415 (t80) cc_final: 0.8082 (t80) REVERT: 2 402 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7681 (mtt90) REVERT: 5 11 GLU cc_start: 0.7907 (tt0) cc_final: 0.7568 (tt0) REVERT: 5 48 GLU cc_start: 0.8518 (pm20) cc_final: 0.8061 (pm20) REVERT: 5 63 GLN cc_start: 0.7748 (mt0) cc_final: 0.7396 (tt0) REVERT: 7 70 ASP cc_start: 0.7934 (t0) cc_final: 0.7333 (t0) REVERT: 7 360 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7510 (ttp-170) REVERT: 7 379 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6870 (mttp) REVERT: 7 570 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8043 (mt-10) outliers start: 30 outliers final: 11 residues processed: 133 average time/residue: 0.4920 time to fit residues: 70.3309 Evaluate side-chains 119 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 402 ARG 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 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 308 ILE Chi-restraints excluded: chain 7 residue 379 LYS Chi-restraints excluded: chain 7 residue 570 GLU Chi-restraints excluded: chain 7 residue 604 THR 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: 0.6980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 23 optimal weight: 0.0050 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 161 HIS 2 173 GLN 2 224 GLN 5 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.163212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116412 restraints weight = 12163.991| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.05 r_work: 0.3369 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9359 Z= 0.150 Angle : 0.603 9.491 12872 Z= 0.311 Chirality : 0.041 0.311 1448 Planarity : 0.004 0.054 1459 Dihedral : 19.213 101.209 1632 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.89 % Allowed : 20.12 % 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: 0.04 (0.26), residues: 961 helix: 1.03 (0.24), residues: 484 sheet: -1.02 (0.42), residues: 139 loop : -0.85 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 285 TYR 0.021 0.001 TYR 7 534 PHE 0.041 0.002 PHE 2 236 TRP 0.012 0.001 TRP 2 455 HIS 0.005 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9358) covalent geometry : angle 0.60295 / 0.31 (12872) hydrogen bonds : bond 0.03660 / 2.54 ( 447) hydrogen bonds : angle 4.24878 / 2.97 ( 1264) Misc. bond : bond 0.00042 / 0.02 ( 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 137 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7909 (t-100) cc_final: 0.7496 (t-100) REVERT: 2 234 LEU cc_start: 0.9461 (tp) cc_final: 0.9138 (pp) REVERT: 2 258 LEU cc_start: 0.6908 (tm) cc_final: 0.6704 (tm) REVERT: 2 261 PHE cc_start: 0.8410 (t80) cc_final: 0.8110 (t80) REVERT: 2 402 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7652 (mtt90) REVERT: 5 11 GLU cc_start: 0.7906 (tt0) cc_final: 0.7563 (tt0) REVERT: 5 48 GLU cc_start: 0.8543 (pm20) cc_final: 0.8083 (pm20) REVERT: 5 63 GLN cc_start: 0.7747 (mt0) cc_final: 0.7405 (tt0) REVERT: 7 70 ASP cc_start: 0.7975 (t0) cc_final: 0.7336 (t0) REVERT: 7 379 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6870 (mttp) REVERT: 7 612 ASP cc_start: 0.8405 (p0) cc_final: 0.8075 (p0) outliers start: 25 outliers final: 14 residues processed: 129 average time/residue: 0.5208 time to fit residues: 71.9251 Evaluate side-chains 121 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 262 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 402 ARG 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 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 379 LYS 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: 1.9990 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 73 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 190 GLN 7 461 HIS 7 668 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.162189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115538 restraints weight = 12229.627| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.04 r_work: 0.3349 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9359 Z= 0.187 Angle : 0.615 8.292 12872 Z= 0.317 Chirality : 0.041 0.175 1448 Planarity : 0.004 0.056 1459 Dihedral : 19.329 100.216 1632 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.35 % Allowed : 20.00 % Favored : 76.65 % 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: 0.03 (0.26), residues: 961 helix: 1.03 (0.24), residues: 485 sheet: -0.98 (0.44), residues: 129 loop : -0.94 (0.29), residues: 347 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 0.031 0.002 PHE 2 236 TRP 0.010 0.001 TRP 2 455 HIS 0.007 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 9358) covalent geometry : angle 0.61534 / 0.32 (12872) hydrogen bonds : bond 0.03855 / 2.66 ( 447) hydrogen bonds : angle 4.27787 / 3.00 ( 1264) Misc. bond : bond 0.00055 / 0.03 ( 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 135 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7923 (t-100) cc_final: 0.7508 (t-100) REVERT: 2 258 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6665 (tm) REVERT: 2 261 PHE cc_start: 0.8415 (t80) cc_final: 0.8155 (t80) REVERT: 2 265 LEU cc_start: 0.9017 (mm) cc_final: 0.8816 (mm) REVERT: 2 402 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7655 (mtt90) REVERT: 5 11 GLU cc_start: 0.7928 (tt0) cc_final: 0.7582 (tt0) REVERT: 5 48 GLU cc_start: 0.8455 (pm20) cc_final: 0.7988 (pm20) REVERT: 5 63 GLN cc_start: 0.7718 (mt0) cc_final: 0.7358 (tt0) REVERT: 7 70 ASP cc_start: 0.7975 (t0) cc_final: 0.7332 (t0) REVERT: 7 360 ARG cc_start: 0.7897 (ttm110) cc_final: 0.7690 (ttm-80) REVERT: 7 379 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6926 (mttp) REVERT: 7 612 ASP cc_start: 0.8368 (p0) cc_final: 0.8119 (p0) outliers start: 29 outliers final: 15 residues processed: 125 average time/residue: 0.4878 time to fit residues: 65.5730 Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 262 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 402 ARG 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 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 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 379 LYS 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: 0.9990 chunk 7 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 70 optimal weight: 0.0050 chunk 56 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 7 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 677 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.160665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.113647 restraints weight = 12176.748| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.04 r_work: 0.3322 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9359 Z= 0.235 Angle : 0.652 8.733 12872 Z= 0.335 Chirality : 0.043 0.168 1448 Planarity : 0.004 0.058 1459 Dihedral : 19.531 103.758 1632 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.24 % Allowed : 20.23 % Favored : 76.53 % 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: -0.11 (0.26), residues: 961 helix: 0.93 (0.24), residues: 485 sheet: -1.15 (0.42), residues: 139 loop : -0.94 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 400 TYR 0.024 0.002 TYR 7 534 PHE 0.023 0.002 PHE 2 236 TRP 0.010 0.002 TRP 2 455 HIS 0.010 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 ( 9358) covalent geometry : angle 0.65184 / 0.33 (12872) hydrogen bonds : bond 0.04061 / 2.81 ( 447) hydrogen bonds : angle 4.34773 / 3.05 ( 1264) Misc. bond : bond 0.00057 / 0.03 ( 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 137 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7977 (t-100) cc_final: 0.7584 (t-100) REVERT: 2 258 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6709 (tm) REVERT: 2 261 PHE cc_start: 0.8402 (t80) cc_final: 0.8082 (t80) REVERT: 2 336 TYR cc_start: 0.9068 (m-80) cc_final: 0.8429 (m-80) REVERT: 2 402 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7662 (mtt90) REVERT: 5 11 GLU cc_start: 0.7935 (tt0) cc_final: 0.7576 (tt0) REVERT: 5 48 GLU cc_start: 0.8393 (pm20) cc_final: 0.7938 (pm20) REVERT: 5 63 GLN cc_start: 0.7735 (mt0) cc_final: 0.7329 (tt0) REVERT: 7 64 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6825 (mm-40) REVERT: 7 70 ASP cc_start: 0.8088 (t0) cc_final: 0.7426 (t0) REVERT: 7 360 ARG cc_start: 0.7920 (ttm110) cc_final: 0.7687 (ttp-170) REVERT: 7 379 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6937 (mttp) REVERT: 7 612 ASP cc_start: 0.8387 (p0) cc_final: 0.8088 (p0) outliers start: 28 outliers final: 15 residues processed: 127 average time/residue: 0.4962 time to fit residues: 67.8064 Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 262 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 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 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 379 LYS 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: 0.6980 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.161269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114449 restraints weight = 12127.088| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.03 r_work: 0.3331 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9359 Z= 0.208 Angle : 0.659 10.675 12872 Z= 0.335 Chirality : 0.045 0.502 1448 Planarity : 0.004 0.058 1459 Dihedral : 19.587 105.180 1632 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.35 % Allowed : 20.69 % 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: -0.17 (0.26), residues: 961 helix: 0.86 (0.24), residues: 485 sheet: -1.20 (0.41), residues: 139 loop : -0.95 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 676 TYR 0.024 0.001 TYR 7 534 PHE 0.020 0.002 PHE 2 236 TRP 0.017 0.002 TRP 2 455 HIS 0.008 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 ( 9358) covalent geometry : angle 0.65879 / 0.34 (12872) hydrogen bonds : bond 0.03851 / 2.66 ( 447) hydrogen bonds : angle 4.37899 / 3.07 ( 1264) Misc. bond : bond 0.00055 / 0.03 ( 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 136 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7989 (t-100) cc_final: 0.7613 (t-100) REVERT: 2 258 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6599 (tm) REVERT: 2 261 PHE cc_start: 0.8458 (t80) cc_final: 0.8144 (t80) REVERT: 2 336 TYR cc_start: 0.9088 (m-80) cc_final: 0.8193 (m-80) REVERT: 5 11 GLU cc_start: 0.7915 (tt0) cc_final: 0.7644 (tt0) REVERT: 5 48 GLU cc_start: 0.8388 (pm20) cc_final: 0.7925 (pm20) REVERT: 5 59 GLU cc_start: 0.6269 (pp20) cc_final: 0.5950 (tm-30) REVERT: 5 63 GLN cc_start: 0.7770 (mt0) cc_final: 0.7417 (tt0) REVERT: 7 64 GLN cc_start: 0.7259 (mm-40) cc_final: 0.6876 (mm-40) REVERT: 7 70 ASP cc_start: 0.8070 (t0) cc_final: 0.7398 (t0) REVERT: 7 360 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7727 (ttp-170) REVERT: 7 379 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6899 (mttp) REVERT: 7 612 ASP cc_start: 0.8401 (p0) cc_final: 0.8125 (p0) outliers start: 29 outliers final: 16 residues processed: 127 average time/residue: 0.4787 time to fit residues: 65.5482 Evaluate side-chains 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 262 LEU Chi-restraints excluded: chain 2 residue 382 VAL 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 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 379 LYS 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: 10.0000 chunk 79 optimal weight: 0.0980 chunk 36 optimal weight: 0.3980 chunk 76 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 4 optimal weight: 0.0000 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 545 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.163247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116615 restraints weight = 12082.293| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.03 r_work: 0.3374 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9359 Z= 0.143 Angle : 0.635 12.840 12872 Z= 0.321 Chirality : 0.042 0.408 1448 Planarity : 0.004 0.056 1459 Dihedral : 19.446 99.423 1632 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.54 % Allowed : 21.39 % Favored : 76.07 % 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: -0.07 (0.26), residues: 961 helix: 0.94 (0.24), residues: 485 sheet: -1.09 (0.41), residues: 139 loop : -0.92 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 453 TYR 0.022 0.001 TYR 7 534 PHE 0.041 0.002 PHE 2 433 TRP 0.014 0.001 TRP 2 455 HIS 0.004 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9358) covalent geometry : angle 0.63482 / 0.32 (12872) hydrogen bonds : bond 0.03441 / 2.40 ( 447) hydrogen bonds : angle 4.32408 / 3.01 ( 1264) Misc. bond : bond 0.00033 / 0.02 ( 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 132 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7920 (t-100) cc_final: 0.7566 (t-100) REVERT: 2 258 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6575 (tm) REVERT: 2 261 PHE cc_start: 0.8449 (t80) cc_final: 0.8097 (t80) REVERT: 2 336 TYR cc_start: 0.9045 (m-80) cc_final: 0.8190 (m-80) REVERT: 5 11 GLU cc_start: 0.7819 (tt0) cc_final: 0.7528 (tt0) REVERT: 5 48 GLU cc_start: 0.8360 (pm20) cc_final: 0.7904 (pm20) REVERT: 5 59 GLU cc_start: 0.6303 (pp20) cc_final: 0.6067 (pp20) REVERT: 5 63 GLN cc_start: 0.7746 (mt0) cc_final: 0.7334 (tt0) REVERT: 7 70 ASP cc_start: 0.8021 (t0) cc_final: 0.7369 (t0) REVERT: 7 360 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7673 (ttp-170) REVERT: 7 379 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6874 (mttp) REVERT: 7 612 ASP cc_start: 0.8381 (p0) cc_final: 0.8119 (p0) REVERT: 7 636 GLU cc_start: 0.8612 (tp30) cc_final: 0.8350 (tp30) outliers start: 22 outliers final: 15 residues processed: 125 average time/residue: 0.4813 time to fit residues: 64.9040 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 : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 262 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 383 LEU 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 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 379 LYS Chi-restraints excluded: chain 7 residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 76 optimal weight: 0.0970 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 64 GLN 7 545 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.162388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115440 restraints weight = 12010.245| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.03 r_work: 0.3354 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9359 Z= 0.178 Angle : 0.647 12.728 12872 Z= 0.327 Chirality : 0.043 0.361 1448 Planarity : 0.004 0.058 1459 Dihedral : 19.448 97.577 1632 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.77 % Allowed : 21.50 % Favored : 75.72 % 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: -0.13 (0.26), residues: 961 helix: 0.90 (0.24), residues: 485 sheet: -1.12 (0.41), residues: 139 loop : -0.95 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 676 TYR 0.024 0.001 TYR 7 534 PHE 0.028 0.002 PHE 2 433 TRP 0.019 0.001 TRP 2 455 HIS 0.006 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 9358) covalent geometry : angle 0.64719 / 0.33 (12872) hydrogen bonds : bond 0.03638 / 2.53 ( 447) hydrogen bonds : angle 4.33767 / 3.03 ( 1264) Misc. bond : bond 0.00061 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3542.86 seconds wall clock time: 61 minutes 18.08 seconds (3678.08 seconds total)