Starting phenix.real_space_refine on Thu Jul 2 16:06:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nvv_12614/07_2026/7nvv_12614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvv_12614/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7nvv_12614/07_2026/7nvv_12614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvv_12614/07_2026/7nvv_12614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nvv_12614/07_2026/7nvv_12614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvv_12614/07_2026/7nvv_12614.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nvv_12614/07_2026/7nvv_12614.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nvv_12614/07_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-6108/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: 1.45, per 1000 atoms: 0.16 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: 0.79 Conformation dependent library (CDL) restraints added in 202.7 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: 0.90 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: 2.03 Time building geometry restraints manager: 1.00 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: 7.770 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: 0.020 Set scattering table: 0.020 Process input model: 9.480 Find NCS groups from input model: 0.050 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:8.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.630 ------------------------------------------------------------------------------- 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= 0.580 Angle : 0.566 10.969 12872 Z= 0.367 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 0.56633 / 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 : 0.364 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: 0.5282 time to fit residues: 106.8692 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 : 0.264 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.162780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115685 restraints weight = 12170.983| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.07 r_work: 0.3371 rms_B_bonded: 2.91 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: 0.1945 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= 0.246 Angle : 0.672 12.614 12872 Z= 0.360 Chirality : 0.045 0.159 1448 Planarity : 0.005 0.038 1459 Dihedral : 18.552 110.643 1632 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.77 % Allowed : 12.72 % 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: 0.46 (0.27), residues: 961 helix: 1.24 (0.24), residues: 483 sheet: -0.68 (0.44), residues: 139 loop : -0.51 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 7 62 TYR 0.025 0.002 TYR 7 581 PHE 0.027 0.002 PHE 2 261 TRP 0.011 0.002 TRP 2 213 HIS 0.017 0.002 HIS 2 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 ( 9358) covalent geometry : angle 0.67208 / 0.36 (12872) hydrogen bonds : bond 0.05340 / 3.70 ( 447) hydrogen bonds : angle 4.84357 / 3.42 ( 1264) Misc. bond : bond 0.00715 / 0.38 ( 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 148 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.8018 (t-100) cc_final: 0.7578 (t-100) REVERT: 2 336 TYR cc_start: 0.9063 (m-80) cc_final: 0.8749 (m-80) REVERT: 2 452 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8766 (ptmt) REVERT: 2 456 LYS cc_start: 0.9379 (mmmt) cc_final: 0.9159 (ptmt) REVERT: 5 48 GLU cc_start: 0.8471 (pm20) cc_final: 0.8079 (pm20) REVERT: 5 51 ASN cc_start: 0.8513 (t0) cc_final: 0.8178 (m110) REVERT: 5 61 MET cc_start: 0.8761 (mmt) cc_final: 0.8511 (mmp) REVERT: 7 141 ARG cc_start: 0.7457 (mtm110) cc_final: 0.6648 (mtt-85) REVERT: 7 379 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7202 (mtmp) REVERT: 7 570 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8255 (tp30) REVERT: 7 590 MET cc_start: 0.8485 (tpt) cc_final: 0.8200 (tpt) REVERT: 7 612 ASP cc_start: 0.8358 (p0) cc_final: 0.7901 (p0) outliers start: 24 outliers final: 9 residues processed: 134 average time/residue: 0.4651 time to fit residues: 67.1009 Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 379 LYS 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: 0.9980 chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 99 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.163221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.116232 restraints weight = 11994.981| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.04 r_work: 0.3362 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9359 Z= 0.188 Angle : 0.600 7.601 12872 Z= 0.321 Chirality : 0.042 0.235 1448 Planarity : 0.004 0.043 1459 Dihedral : 18.936 111.807 1632 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.24 % Allowed : 14.68 % Favored : 82.08 % 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: 0.22 (0.26), residues: 961 helix: 1.09 (0.24), residues: 484 sheet: -0.80 (0.43), residues: 139 loop : -0.70 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 7 74 TYR 0.021 0.001 TYR 7 534 PHE 0.018 0.002 PHE 2 268 TRP 0.010 0.001 TRP 2 213 HIS 0.007 0.001 HIS 2 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 9358) covalent geometry : angle 0.59982 / 0.32 (12872) hydrogen bonds : bond 0.04520 / 3.14 ( 447) hydrogen bonds : angle 4.48375 / 3.17 ( 1264) Misc. bond : bond 0.00370 / 0.19 ( 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 149 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7993 (t-100) cc_final: 0.7567 (t-100) REVERT: 2 234 LEU cc_start: 0.9493 (tp) cc_final: 0.9158 (pp) REVERT: 2 261 PHE cc_start: 0.8375 (t80) cc_final: 0.8119 (t80) REVERT: 2 452 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8779 (ptmt) REVERT: 5 48 GLU cc_start: 0.8514 (pm20) cc_final: 0.8091 (pm20) REVERT: 5 61 MET cc_start: 0.8766 (mmt) cc_final: 0.8498 (mmp) REVERT: 5 63 GLN cc_start: 0.7798 (mt0) cc_final: 0.7412 (tt0) REVERT: 7 308 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.7024 (mp) REVERT: 7 590 MET cc_start: 0.8519 (tpt) cc_final: 0.8257 (tpt) REVERT: 7 636 GLU cc_start: 0.8554 (tp30) cc_final: 0.8332 (tp30) outliers start: 28 outliers final: 12 residues processed: 134 average time/residue: 0.4169 time to fit residues: 60.2316 Evaluate side-chains 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 267 THR Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL 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: 0.9980 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 90 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.161834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.114569 restraints weight = 12221.472| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.06 r_work: 0.3340 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2546 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= 0.224 Angle : 0.622 8.415 12872 Z= 0.326 Chirality : 0.043 0.222 1448 Planarity : 0.004 0.051 1459 Dihedral : 19.162 108.292 1632 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.35 % Allowed : 16.76 % Favored : 79.88 % 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: 0.97 (0.24), residues: 486 sheet: -0.96 (0.42), residues: 139 loop : -0.74 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 7 74 TYR 0.021 0.002 TYR 7 534 PHE 0.016 0.002 PHE 2 433 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 0.00526 / 0.22 ( 9358) covalent geometry : angle 0.62159 / 0.33 (12872) hydrogen bonds : bond 0.04413 / 3.04 ( 447) hydrogen bonds : angle 4.45144 / 3.15 ( 1264) Misc. bond : bond 0.00153 / 0.08 ( 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 142 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.8008 (t-100) cc_final: 0.7591 (t-100) REVERT: 2 234 LEU cc_start: 0.9480 (tp) cc_final: 0.9144 (pp) REVERT: 2 402 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7657 (mtt90) REVERT: 2 456 LYS cc_start: 0.9335 (ptmt) cc_final: 0.9039 (mmmt) REVERT: 5 11 GLU cc_start: 0.7936 (tt0) cc_final: 0.7614 (tt0) REVERT: 5 48 GLU cc_start: 0.8548 (pm20) cc_final: 0.8110 (pm20) REVERT: 5 63 GLN cc_start: 0.7797 (mt0) cc_final: 0.7425 (tt0) REVERT: 7 70 ASP cc_start: 0.8012 (t0) cc_final: 0.7404 (t0) REVERT: 7 379 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7192 (mtmp) REVERT: 7 590 MET cc_start: 0.8510 (tpt) cc_final: 0.8284 (tpt) REVERT: 7 612 ASP cc_start: 0.8407 (p0) cc_final: 0.8094 (p0) REVERT: 7 636 GLU cc_start: 0.8589 (tp30) cc_final: 0.8371 (tp30) outliers start: 29 outliers final: 13 residues processed: 129 average time/residue: 0.4521 time to fit residues: 62.6384 Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.161589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114517 restraints weight = 12148.579| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.04 r_work: 0.3339 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9359 Z= 0.204 Angle : 0.614 8.264 12872 Z= 0.323 Chirality : 0.042 0.245 1448 Planarity : 0.004 0.054 1459 Dihedral : 19.320 108.599 1632 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.58 % Allowed : 18.27 % Favored : 78.15 % 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: -0.02 (0.26), residues: 961 helix: 0.97 (0.24), residues: 484 sheet: -0.96 (0.43), residues: 129 loop : -0.92 (0.29), residues: 348 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 0.018 0.002 PHE 2 268 TRP 0.010 0.001 TRP 2 213 HIS 0.008 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 9358) covalent geometry : angle 0.61407 / 0.32 (12872) hydrogen bonds : bond 0.04091 / 2.83 ( 447) hydrogen bonds : angle 4.35412 / 3.08 ( 1264) Misc. bond : bond 0.00083 / 0.04 ( 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: 31 poor density : 111 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.8001 (t-100) cc_final: 0.7586 (t-100) REVERT: 2 234 LEU cc_start: 0.9470 (tp) cc_final: 0.9138 (pp) REVERT: 2 261 PHE cc_start: 0.8407 (t80) cc_final: 0.8040 (t80) REVERT: 2 402 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7640 (mtt90) REVERT: 2 456 LYS cc_start: 0.9381 (ptmt) cc_final: 0.9053 (mmmt) REVERT: 5 48 GLU cc_start: 0.8520 (pm20) cc_final: 0.8067 (pm20) REVERT: 5 63 GLN cc_start: 0.7771 (mt0) cc_final: 0.7408 (tt0) REVERT: 7 70 ASP cc_start: 0.7955 (t0) cc_final: 0.7336 (t0) REVERT: 7 287 LEU cc_start: 0.8700 (mt) cc_final: 0.8491 (mp) REVERT: 7 590 MET cc_start: 0.8508 (tpt) cc_final: 0.8301 (tpt) REVERT: 7 612 ASP cc_start: 0.8416 (p0) cc_final: 0.8100 (p0) REVERT: 7 636 GLU cc_start: 0.8602 (tp30) cc_final: 0.8353 (tp30) outliers start: 31 outliers final: 12 residues processed: 133 average time/residue: 0.4253 time to fit residues: 60.9954 Evaluate side-chains 119 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 371 VAL 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: 3.9990 chunk 72 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 chunk 23 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 161 HIS 2 173 GLN 2 224 GLN 5 64 ASN 7 461 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.162497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115644 restraints weight = 12187.075| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.04 r_work: 0.3356 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9359 Z= 0.163 Angle : 0.592 8.365 12872 Z= 0.309 Chirality : 0.042 0.315 1448 Planarity : 0.004 0.055 1459 Dihedral : 19.343 105.689 1632 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.89 % Allowed : 19.65 % Favored : 77.46 % 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: -1.05 (0.42), residues: 139 loop : -0.88 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 62 TYR 0.023 0.001 TYR 7 534 PHE 0.017 0.002 PHE 2 268 TRP 0.010 0.001 TRP 7 77 HIS 0.006 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9358) covalent geometry : angle 0.59187 / 0.31 (12872) hydrogen bonds : bond 0.03790 / 2.63 ( 447) hydrogen bonds : angle 4.27880 / 3.00 ( 1264) Misc. bond : bond 0.00034 / 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 132 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7989 (t-100) cc_final: 0.7580 (t-100) REVERT: 2 234 LEU cc_start: 0.9457 (tp) cc_final: 0.9172 (pp) REVERT: 2 261 PHE cc_start: 0.8368 (t80) cc_final: 0.8082 (t80) REVERT: 2 456 LYS cc_start: 0.9370 (ptmt) cc_final: 0.9048 (mmmt) REVERT: 5 11 GLU cc_start: 0.7924 (tt0) cc_final: 0.7670 (tt0) REVERT: 5 48 GLU cc_start: 0.8529 (pm20) cc_final: 0.8066 (pm20) REVERT: 5 63 GLN cc_start: 0.7775 (mt0) cc_final: 0.7445 (tt0) REVERT: 7 70 ASP cc_start: 0.7975 (t0) cc_final: 0.7334 (t0) REVERT: 7 287 LEU cc_start: 0.8689 (mt) cc_final: 0.8439 (mt) REVERT: 7 612 ASP cc_start: 0.8408 (p0) cc_final: 0.8133 (p0) REVERT: 7 636 GLU cc_start: 0.8607 (tp30) cc_final: 0.8361 (tp30) outliers start: 25 outliers final: 14 residues processed: 122 average time/residue: 0.4466 time to fit residues: 58.8897 Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 382 VAL 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 285 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 73 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 3 ASN 5 64 ASN 7 190 GLN 7 668 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115840 restraints weight = 12205.144| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.03 r_work: 0.3359 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2961 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= 0.164 Angle : 0.590 8.740 12872 Z= 0.307 Chirality : 0.041 0.167 1448 Planarity : 0.004 0.057 1459 Dihedral : 19.363 102.290 1632 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.24 % Allowed : 19.88 % Favored : 76.88 % 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: 1.04 (0.24), residues: 486 sheet: -1.06 (0.42), residues: 139 loop : -0.89 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 7 62 TYR 0.022 0.001 TYR 7 534 PHE 0.016 0.002 PHE 2 268 TRP 0.009 0.001 TRP 7 77 HIS 0.006 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 9358) covalent geometry : angle 0.59023 / 0.31 (12872) hydrogen bonds : bond 0.03703 / 2.56 ( 447) hydrogen bonds : angle 4.25566 / 2.98 ( 1264) Misc. bond : bond 0.00040 / 0.02 ( 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 132 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7933 (t-100) cc_final: 0.7517 (t-100) REVERT: 2 261 PHE cc_start: 0.8344 (t80) cc_final: 0.8110 (t80) REVERT: 2 336 TYR cc_start: 0.9044 (m-80) cc_final: 0.8315 (m-80) REVERT: 2 402 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7661 (mtt90) REVERT: 2 456 LYS cc_start: 0.9384 (ptmt) cc_final: 0.9055 (mmmt) REVERT: 5 11 GLU cc_start: 0.7912 (tt0) cc_final: 0.7600 (tt0) REVERT: 5 48 GLU cc_start: 0.8483 (pm20) cc_final: 0.8016 (pm20) REVERT: 5 63 GLN cc_start: 0.7737 (mt0) cc_final: 0.7389 (tt0) REVERT: 7 70 ASP cc_start: 0.7979 (t0) cc_final: 0.7318 (t0) REVERT: 7 287 LEU cc_start: 0.8692 (mt) cc_final: 0.8447 (mt) REVERT: 7 612 ASP cc_start: 0.8403 (p0) cc_final: 0.8136 (p0) outliers start: 28 outliers final: 14 residues processed: 124 average time/residue: 0.4495 time to fit residues: 59.9556 Evaluate side-chains 118 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 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 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 285 ILE Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL 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: 0.7980 chunk 7 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.160789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.113584 restraints weight = 12164.291| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.04 r_work: 0.3328 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9359 Z= 0.223 Angle : 0.638 9.988 12872 Z= 0.329 Chirality : 0.044 0.396 1448 Planarity : 0.004 0.059 1459 Dihedral : 19.543 104.427 1632 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.58 % Allowed : 19.54 % Favored : 76.88 % 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: 0.95 (0.24), residues: 486 sheet: -1.12 (0.42), residues: 139 loop : -0.95 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 285 TYR 0.024 0.002 TYR 7 534 PHE 0.017 0.002 PHE 2 268 TRP 0.009 0.001 TRP 2 213 HIS 0.009 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 ( 9358) covalent geometry : angle 0.63805 / 0.33 (12872) hydrogen bonds : bond 0.04017 / 2.78 ( 447) hydrogen bonds : angle 4.29855 / 3.02 ( 1264) Misc. bond : bond 0.00065 / 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 136 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.8025 (t-100) cc_final: 0.7642 (t-100) REVERT: 2 261 PHE cc_start: 0.8428 (t80) cc_final: 0.8191 (t80) REVERT: 2 336 TYR cc_start: 0.9110 (m-80) cc_final: 0.8186 (m-80) REVERT: 2 402 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7668 (mtt90) REVERT: 2 456 LYS cc_start: 0.9369 (ptmt) cc_final: 0.9153 (pttm) REVERT: 5 11 GLU cc_start: 0.7944 (tt0) cc_final: 0.7585 (tt0) REVERT: 5 48 GLU cc_start: 0.8386 (pm20) cc_final: 0.7936 (pm20) REVERT: 5 63 GLN cc_start: 0.7780 (mt0) cc_final: 0.7388 (tt0) REVERT: 7 64 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6796 (mm-40) REVERT: 7 70 ASP cc_start: 0.8046 (t0) cc_final: 0.7391 (t0) REVERT: 7 287 LEU cc_start: 0.8684 (mt) cc_final: 0.8458 (mt) REVERT: 7 612 ASP cc_start: 0.8414 (p0) cc_final: 0.8138 (p0) outliers start: 31 outliers final: 15 residues processed: 129 average time/residue: 0.3830 time to fit residues: 53.3745 Evaluate side-chains 120 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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 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 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: 0.0770 chunk 27 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 3 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.162365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.115448 restraints weight = 12094.953| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.04 r_work: 0.3356 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9359 Z= 0.162 Angle : 0.617 12.188 12872 Z= 0.316 Chirality : 0.042 0.388 1448 Planarity : 0.004 0.058 1459 Dihedral : 19.509 102.440 1632 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.77 % Allowed : 20.46 % Favored : 76.76 % 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: -0.09 (0.26), residues: 961 helix: 0.96 (0.24), residues: 485 sheet: -1.11 (0.42), residues: 139 loop : -0.97 (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 0.015 0.002 PHE 2 367 TRP 0.011 0.001 TRP 7 77 HIS 0.006 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 9358) covalent geometry : angle 0.61694 / 0.32 (12872) hydrogen bonds : bond 0.03547 / 2.46 ( 447) hydrogen bonds : angle 4.27037 / 2.99 ( 1264) Misc. bond : bond 0.00037 / 0.02 ( 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 128 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7946 (t-100) cc_final: 0.7585 (t-100) REVERT: 2 261 PHE cc_start: 0.8446 (t80) cc_final: 0.8191 (t80) REVERT: 2 336 TYR cc_start: 0.9077 (m-80) cc_final: 0.8175 (m-80) REVERT: 2 456 LYS cc_start: 0.9386 (ptmt) cc_final: 0.9071 (mmmt) REVERT: 5 11 GLU cc_start: 0.7904 (tt0) cc_final: 0.7636 (tt0) REVERT: 5 48 GLU cc_start: 0.8383 (pm20) cc_final: 0.7920 (pm20) REVERT: 5 59 GLU cc_start: 0.6254 (pp20) cc_final: 0.5964 (tm-30) REVERT: 5 63 GLN cc_start: 0.7764 (mt0) cc_final: 0.7423 (tt0) REVERT: 7 70 ASP cc_start: 0.7953 (t0) cc_final: 0.7302 (t0) REVERT: 7 287 LEU cc_start: 0.8661 (mt) cc_final: 0.8430 (mt) REVERT: 7 612 ASP cc_start: 0.8416 (p0) cc_final: 0.8132 (p0) outliers start: 24 outliers final: 15 residues processed: 121 average time/residue: 0.4510 time to fit residues: 58.9545 Evaluate side-chains 116 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 9.9990 chunk 79 optimal weight: 0.1980 chunk 36 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 4 optimal weight: 0.0170 chunk 80 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.162840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115900 restraints weight = 12080.489| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.04 r_work: 0.3358 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9359 Z= 0.157 Angle : 0.643 13.758 12872 Z= 0.322 Chirality : 0.043 0.397 1448 Planarity : 0.004 0.059 1459 Dihedral : 19.464 99.215 1632 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.20 % Allowed : 21.39 % Favored : 76.42 % 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: 0.95 (0.24), residues: 485 sheet: -1.09 (0.42), residues: 139 loop : -0.97 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 530 TYR 0.023 0.001 TYR 7 534 PHE 0.015 0.001 PHE 2 367 TRP 0.009 0.001 TRP 2 213 HIS 0.005 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 9358) covalent geometry : angle 0.64340 / 0.32 (12872) hydrogen bonds : bond 0.03580 / 2.46 ( 447) hydrogen bonds : angle 4.28897 / 3.00 ( 1264) Misc. bond : bond 0.00049 / 0.03 ( 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 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7921 (t-100) cc_final: 0.7567 (t-100) REVERT: 2 261 PHE cc_start: 0.8438 (t80) cc_final: 0.8225 (t80) REVERT: 2 336 TYR cc_start: 0.9074 (m-80) cc_final: 0.8200 (m-80) REVERT: 2 402 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7679 (mtt90) REVERT: 2 456 LYS cc_start: 0.9387 (ptmt) cc_final: 0.9168 (pttm) REVERT: 5 11 GLU cc_start: 0.7898 (tt0) cc_final: 0.7562 (tt0) REVERT: 5 48 GLU cc_start: 0.8350 (pm20) cc_final: 0.7896 (pm20) REVERT: 5 59 GLU cc_start: 0.6224 (pp20) cc_final: 0.5974 (pp20) REVERT: 5 63 GLN cc_start: 0.7738 (mt0) cc_final: 0.7309 (tt0) REVERT: 7 70 ASP cc_start: 0.8028 (t0) cc_final: 0.7368 (t0) REVERT: 7 287 LEU cc_start: 0.8647 (mt) cc_final: 0.8414 (mt) REVERT: 7 612 ASP cc_start: 0.8412 (p0) cc_final: 0.8134 (p0) outliers start: 19 outliers final: 15 residues processed: 119 average time/residue: 0.4309 time to fit residues: 55.4029 Evaluate side-chains 119 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 383 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 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 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: 0.6980 chunk 14 optimal weight: 0.5980 chunk 76 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.162226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115108 restraints weight = 11986.466| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.02 r_work: 0.3346 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3238 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= 0.181 Angle : 0.647 13.190 12872 Z= 0.325 Chirality : 0.043 0.402 1448 Planarity : 0.004 0.059 1459 Dihedral : 19.501 98.419 1632 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.77 % Allowed : 20.92 % Favored : 76.30 % 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: 0.94 (0.24), residues: 485 sheet: -1.10 (0.42), residues: 139 loop : -1.00 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 360 TYR 0.025 0.001 TYR 7 534 PHE 0.031 0.002 PHE 2 433 TRP 0.009 0.001 TRP 2 213 HIS 0.007 0.001 HIS 7 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 9358) covalent geometry : angle 0.64669 / 0.32 (12872) hydrogen bonds : bond 0.03690 / 2.56 ( 447) hydrogen bonds : angle 4.30729 / 3.01 ( 1264) Misc. bond : bond 0.00057 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3100.79 seconds wall clock time: 53 minutes 28.71 seconds (3208.71 seconds total)