Starting phenix.real_space_refine on Thu Mar 13 20:38:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nvv_12614/03_2025/7nvv_12614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvv_12614/03_2025/7nvv_12614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nvv_12614/03_2025/7nvv_12614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvv_12614/03_2025/7nvv_12614.map" model { file = "/net/cci-nas-00/data/ceres_data/7nvv_12614/03_2025/7nvv_12614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvv_12614/03_2025/7nvv_12614.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.62, per 1000 atoms: 0.84 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: 2.62 Conformation dependent library (CDL) restraints added in 923.8 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: 3.71 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: 3.84 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2696 1.34 - 1.45: 1554 1.45 - 1.57: 4939 1.57 - 1.69: 101 1.69 - 1.81: 68 Bond restraints: 9358 Sorted by residual: bond pdb=" C4 ADP 7 901 " pdb=" C5 ADP 7 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" F2 BEF 7 903 " pdb="BE BEF 7 903 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C5 ADP 7 901 " pdb=" C6 ADP 7 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" F3 BEF 7 903 " pdb="BE BEF 7 903 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" F1 BEF 7 903 " pdb="BE BEF 7 903 " ideal model delta sigma weight residual 1.476 1.532 -0.056 2.00e-02 2.50e+03 7.97e+00 ... (remaining 9353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 12749 2.19 - 4.39: 106 4.39 - 6.58: 7 6.58 - 8.78: 4 8.78 - 10.97: 6 Bond angle restraints: 12872 Sorted by residual: angle pdb=" PA ADP 7 901 " pdb=" O3A ADP 7 901 " pdb=" PB ADP 7 901 " ideal model delta sigma weight residual 120.50 131.47 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C2' ADP 7 901 " pdb=" C3' ADP 7 901 " pdb=" C4' ADP 7 901 " ideal model delta sigma weight residual 111.00 100.21 10.79 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C1' ADP 7 901 " pdb=" C2' ADP 7 901 " pdb=" C3' ADP 7 901 " ideal model delta sigma weight residual 111.00 100.53 10.47 3.00e+00 1.11e-01 1.22e+01 angle pdb=" F2 BEF 7 903 " pdb="BE BEF 7 903 " pdb=" F3 BEF 7 903 " ideal model delta sigma weight residual 119.96 109.73 10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N1 ADP 7 901 " pdb=" C2 ADP 7 901 " pdb=" N3 ADP 7 901 " ideal model delta sigma weight residual 120.00 129.29 -9.29 3.00e+00 1.11e-01 9.59e+00 ... (remaining 12867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 4965 23.52 - 47.03: 433 47.03 - 70.55: 97 70.55 - 94.06: 9 94.06 - 117.58: 1 Dihedral angle restraints: 5505 sinusoidal: 2566 harmonic: 2939 Sorted by residual: dihedral pdb=" C5' ADP 7 901 " pdb=" O5' ADP 7 901 " pdb=" PA ADP 7 901 " pdb=" O2A ADP 7 901 " ideal model delta sinusoidal sigma weight residual -60.00 -177.57 117.58 1 2.00e+01 2.50e-03 3.51e+01 dihedral pdb=" O1B ADP 7 901 " pdb=" O3A ADP 7 901 " pdb=" PB ADP 7 901 " pdb=" PA ADP 7 901 " ideal model delta sinusoidal sigma weight residual -60.00 -128.87 68.87 1 2.00e+01 2.50e-03 1.53e+01 dihedral pdb=" CA ASP 7 563 " pdb=" CB ASP 7 563 " pdb=" CG ASP 7 563 " pdb=" OD1 ASP 7 563 " ideal model delta sinusoidal sigma weight residual -30.00 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1047 0.033 - 0.066: 246 0.066 - 0.099: 101 0.099 - 0.132: 52 0.132 - 0.165: 2 Chirality restraints: 1448 Sorted by residual: chirality pdb=" C3' ADP 7 901 " pdb=" C2' ADP 7 901 " pdb=" C4' ADP 7 901 " pdb=" O3' ADP 7 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE 7 580 " pdb=" N ILE 7 580 " pdb=" C ILE 7 580 " pdb=" CB ILE 7 580 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE 7 559 " pdb=" N ILE 7 559 " pdb=" C ILE 7 559 " pdb=" CB ILE 7 559 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 1445 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 7 62 " 0.172 9.50e-02 1.11e+02 7.70e-02 3.83e+00 pdb=" NE ARG 7 62 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG 7 62 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG 7 62 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG 7 62 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE 2 338 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO 2 339 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO 2 339 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO 2 339 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR 7 581 " 0.009 2.00e-02 2.50e+03 9.58e-03 1.84e+00 pdb=" CG TYR 7 581 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR 7 581 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR 7 581 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 7 581 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR 7 581 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR 7 581 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR 7 581 " 0.000 2.00e-02 2.50e+03 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 66 2.57 - 3.15: 7366 3.15 - 3.73: 15099 3.73 - 4.32: 21014 4.32 - 4.90: 33957 Nonbonded interactions: 77502 Sorted by model distance: nonbonded pdb=" O LYS 7 165 " pdb=" OG SER 7 179 " model vdw 1.984 3.040 nonbonded pdb=" OG SER 2 172 " pdb=" OD1 ASP 2 174 " model vdw 2.000 3.040 nonbonded pdb="MG MG 7 902 " pdb=" F1 BEF 7 903 " model vdw 2.009 2.120 nonbonded pdb=" OH TYR 7 319 " pdb=" O ALA 7 344 " model vdw 2.014 3.040 nonbonded pdb=" O PHE 7 378 " pdb=" OG SER 7 382 " model vdw 2.018 3.040 ... (remaining 77497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 93.830 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: 0.400 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 29.560 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 9358 Z= 0.169 Angle : 0.519 10.969 12872 Z= 0.261 Chirality : 0.038 0.165 1448 Planarity : 0.003 0.077 1459 Dihedral : 17.438 117.575 3593 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP W 280 HIS 0.002 0.000 HIS 7 114 PHE 0.009 0.001 PHE 7 482 TYR 0.023 0.001 TYR 7 581 ARG 0.008 0.000 ARG 7 62 *********************** 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 : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7789 (t-100) cc_final: 0.7486 (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: 1.5170 time to fit residues: 307.3570 Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 42 optimal weight: 0.0070 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 173 GLN 2 211 GLN 2 224 GLN 2 352 GLN ** 2 424 HIS ** 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** 7 595 ASN 7 668 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.163489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116548 restraints weight = 12057.379| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.07 r_work: 0.3381 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9358 Z= 0.307 Angle : 0.611 7.043 12872 Z= 0.323 Chirality : 0.042 0.170 1448 Planarity : 0.004 0.033 1459 Dihedral : 18.526 109.329 1632 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.01 % Allowed : 12.72 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 961 helix: 1.46 (0.24), residues: 483 sheet: -0.61 (0.44), residues: 139 loop : -0.46 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 213 HIS 0.011 0.002 HIS 7 286 PHE 0.032 0.002 PHE 2 261 TYR 0.023 0.002 TYR 7 581 ARG 0.006 0.001 ARG 2 426 *********************** 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 155 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7995 (t-100) cc_final: 0.7566 (t-100) REVERT: 2 336 TYR cc_start: 0.9066 (m-80) cc_final: 0.8850 (m-80) REVERT: 2 452 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8808 (ptmt) REVERT: 5 48 GLU cc_start: 0.8516 (pm20) cc_final: 0.8079 (pm20) REVERT: 5 51 ASN cc_start: 0.8425 (t0) cc_final: 0.8063 (m110) REVERT: 5 61 MET cc_start: 0.8766 (mmt) cc_final: 0.8503 (mmp) REVERT: 7 570 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7945 (mt-10) REVERT: 7 590 MET cc_start: 0.8479 (tpt) cc_final: 0.8160 (tpt) REVERT: 7 612 ASP cc_start: 0.8368 (p0) cc_final: 0.8028 (p0) outliers start: 26 outliers final: 8 residues processed: 141 average time/residue: 1.3437 time to fit residues: 204.2006 Evaluate side-chains 120 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 410 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 Chi-restraints excluded: chain W residue 279 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 14 optimal weight: 0.0670 chunk 18 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 0.0770 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 366 ASN ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.163828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117184 restraints weight = 12174.049| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.05 r_work: 0.3379 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9358 Z= 0.244 Angle : 0.572 8.842 12872 Z= 0.296 Chirality : 0.040 0.178 1448 Planarity : 0.004 0.041 1459 Dihedral : 18.631 103.238 1632 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.89 % Allowed : 16.18 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.27), residues: 961 helix: 1.27 (0.24), residues: 485 sheet: -0.70 (0.43), residues: 139 loop : -0.65 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 213 HIS 0.006 0.001 HIS 7 286 PHE 0.021 0.002 PHE 2 261 TYR 0.022 0.001 TYR 7 534 ARG 0.006 0.000 ARG 2 426 *********************** 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 145 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7880 (t-100) cc_final: 0.7466 (t-100) REVERT: 2 261 PHE cc_start: 0.8152 (t80) cc_final: 0.7735 (t80) REVERT: 2 336 TYR cc_start: 0.9069 (m-80) cc_final: 0.8825 (m-80) REVERT: 2 456 LYS cc_start: 0.9352 (ptmt) cc_final: 0.9099 (mmmt) REVERT: 5 48 GLU cc_start: 0.8554 (pm20) cc_final: 0.8105 (pm20) REVERT: 5 63 GLN cc_start: 0.7791 (mt0) cc_final: 0.7438 (tt0) REVERT: 7 287 LEU cc_start: 0.8667 (mt) cc_final: 0.8398 (mt) REVERT: 7 590 MET cc_start: 0.8529 (tpt) cc_final: 0.8248 (tpt) REVERT: 7 612 ASP cc_start: 0.8316 (p0) cc_final: 0.8039 (p0) outliers start: 25 outliers final: 12 residues processed: 131 average time/residue: 1.2830 time to fit residues: 181.1283 Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 438 LYS Chi-restraints excluded: chain 2 residue 450 ASP 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 604 THR Chi-restraints excluded: chain 7 residue 686 SER Chi-restraints excluded: chain W residue 279 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN 2 224 GLN ** 2 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 366 ASN ** 7 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 461 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.160822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113781 restraints weight = 12124.683| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.03 r_work: 0.3337 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9358 Z= 0.387 Angle : 0.620 7.610 12872 Z= 0.320 Chirality : 0.044 0.330 1448 Planarity : 0.004 0.052 1459 Dihedral : 19.019 106.940 1632 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.70 % Allowed : 17.23 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 961 helix: 1.01 (0.24), residues: 483 sheet: -0.91 (0.43), residues: 139 loop : -0.78 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 213 HIS 0.009 0.001 HIS 7 114 PHE 0.018 0.002 PHE 2 268 TYR 0.023 0.002 TYR 7 534 ARG 0.005 0.001 ARG 7 676 *********************** 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 148 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.8008 (t-100) cc_final: 0.7620 (t-100) REVERT: 2 261 PHE cc_start: 0.8319 (t80) cc_final: 0.7959 (t80) REVERT: 2 336 TYR cc_start: 0.9080 (m-80) cc_final: 0.8161 (m-80) REVERT: 2 421 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8900 (mp) REVERT: 2 456 LYS cc_start: 0.9339 (ptmt) cc_final: 0.8990 (mmmt) REVERT: 5 11 GLU cc_start: 0.8092 (tt0) cc_final: 0.7878 (tt0) REVERT: 5 48 GLU cc_start: 0.8491 (pm20) cc_final: 0.8005 (pm20) REVERT: 5 63 GLN cc_start: 0.7886 (mt0) cc_final: 0.7525 (tt0) REVERT: 5 64 ASN cc_start: 0.8389 (m110) cc_final: 0.8059 (m-40) REVERT: 7 70 ASP cc_start: 0.7969 (t0) cc_final: 0.7477 (t0) REVERT: 7 287 LEU cc_start: 0.8754 (mt) cc_final: 0.8513 (mt) REVERT: 7 379 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7033 (mttp) REVERT: 7 570 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7959 (mt-10) REVERT: 7 590 MET cc_start: 0.8581 (tpt) cc_final: 0.8354 (tpt) REVERT: 7 612 ASP cc_start: 0.8464 (p0) cc_final: 0.8158 (p0) REVERT: 7 706 LYS cc_start: 0.7564 (tptt) cc_final: 0.7331 (tptt) outliers start: 32 outliers final: 19 residues processed: 137 average time/residue: 1.3988 time to fit residues: 207.8863 Evaluate side-chains 131 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 2 residue 421 LEU Chi-restraints excluded: chain 2 residue 438 LYS Chi-restraints excluded: chain 2 residue 450 ASP Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 52 VAL 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 379 LYS Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 424 HIS 7 668 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.161185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114318 restraints weight = 12135.940| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.02 r_work: 0.3330 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9358 Z= 0.338 Angle : 0.608 8.145 12872 Z= 0.313 Chirality : 0.042 0.207 1448 Planarity : 0.004 0.055 1459 Dihedral : 19.121 107.569 1632 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.93 % Allowed : 19.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 961 helix: 0.98 (0.24), residues: 484 sheet: -1.06 (0.42), residues: 139 loop : -0.88 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 7 77 HIS 0.009 0.001 HIS 7 114 PHE 0.016 0.002 PHE 2 268 TYR 0.024 0.001 TYR 7 534 ARG 0.004 0.001 ARG 7 676 *********************** 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 148 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7965 (t-100) cc_final: 0.7570 (t-100) REVERT: 2 261 PHE cc_start: 0.8278 (t80) cc_final: 0.7915 (t80) REVERT: 2 421 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8870 (mp) REVERT: 2 456 LYS cc_start: 0.9368 (ptmt) cc_final: 0.9066 (mmmt) REVERT: 5 11 GLU cc_start: 0.8096 (tt0) cc_final: 0.7832 (tt0) REVERT: 5 48 GLU cc_start: 0.8456 (pm20) cc_final: 0.7979 (pm20) REVERT: 5 63 GLN cc_start: 0.7848 (mt0) cc_final: 0.7493 (tt0) REVERT: 5 64 ASN cc_start: 0.8362 (m110) cc_final: 0.8029 (m-40) REVERT: 7 70 ASP cc_start: 0.8009 (t0) cc_final: 0.7415 (t0) REVERT: 7 379 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6894 (mttp) REVERT: 7 590 MET cc_start: 0.8510 (tpt) cc_final: 0.8306 (tpt) REVERT: 7 612 ASP cc_start: 0.8425 (p0) cc_final: 0.8094 (p0) REVERT: 7 707 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7239 (pt0) outliers start: 34 outliers final: 17 residues processed: 139 average time/residue: 1.1035 time to fit residues: 165.6576 Evaluate side-chains 127 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 2 residue 421 LEU 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 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 Chi-restraints excluded: chain 7 residue 707 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 14 optimal weight: 0.1980 chunk 16 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 66 optimal weight: 0.0870 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.163493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116959 restraints weight = 11973.950| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.02 r_work: 0.3390 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9358 Z= 0.211 Angle : 0.565 8.099 12872 Z= 0.290 Chirality : 0.039 0.186 1448 Planarity : 0.004 0.056 1459 Dihedral : 18.944 98.676 1632 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.82 % Allowed : 19.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 961 helix: 1.09 (0.24), residues: 482 sheet: -0.95 (0.42), residues: 139 loop : -0.88 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 7 77 HIS 0.005 0.001 HIS 7 114 PHE 0.014 0.001 PHE 2 367 TYR 0.021 0.001 TYR 7 534 ARG 0.002 0.000 ARG 2 426 *********************** 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 148 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7904 (t-100) cc_final: 0.7390 (t-100) REVERT: 2 261 PHE cc_start: 0.8100 (t80) cc_final: 0.7656 (t80) REVERT: 2 336 TYR cc_start: 0.9054 (m-80) cc_final: 0.8152 (m-80) REVERT: 2 421 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8809 (mp) REVERT: 2 456 LYS cc_start: 0.9366 (ptmt) cc_final: 0.9132 (pttm) REVERT: 5 11 GLU cc_start: 0.8012 (tt0) cc_final: 0.7640 (tt0) REVERT: 5 48 GLU cc_start: 0.8392 (pm20) cc_final: 0.7917 (pm20) REVERT: 5 59 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6690 (tm-30) REVERT: 5 63 GLN cc_start: 0.7778 (mt0) cc_final: 0.7413 (tt0) REVERT: 5 64 ASN cc_start: 0.8365 (m110) cc_final: 0.8005 (m-40) REVERT: 7 70 ASP cc_start: 0.8011 (t0) cc_final: 0.7360 (t0) REVERT: 7 612 ASP cc_start: 0.8401 (p0) cc_final: 0.8100 (p0) REVERT: 7 714 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8387 (mm-40) outliers start: 33 outliers final: 17 residues processed: 139 average time/residue: 1.0558 time to fit residues: 159.2229 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 : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 237 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 2 residue 421 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 139 TYR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.0670 chunk 95 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.0170 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.162792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.115945 restraints weight = 12239.272| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.04 r_work: 0.3357 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9358 Z= 0.250 Angle : 0.587 8.174 12872 Z= 0.299 Chirality : 0.041 0.283 1448 Planarity : 0.004 0.058 1459 Dihedral : 18.961 96.466 1632 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.58 % Allowed : 20.81 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 961 helix: 1.09 (0.24), residues: 485 sheet: -0.94 (0.42), residues: 139 loop : -0.92 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 213 HIS 0.006 0.001 HIS 7 114 PHE 0.026 0.002 PHE 2 433 TYR 0.023 0.001 TYR 7 534 ARG 0.003 0.000 ARG 7 676 *********************** 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 138 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7921 (t-100) cc_final: 0.7418 (t-100) REVERT: 2 336 TYR cc_start: 0.9064 (m-80) cc_final: 0.8100 (m-80) REVERT: 2 421 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8685 (mp) REVERT: 2 456 LYS cc_start: 0.9354 (ptmt) cc_final: 0.9018 (mmmt) REVERT: 5 11 GLU cc_start: 0.7952 (tt0) cc_final: 0.7552 (tt0) REVERT: 5 16 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8110 (mmm) REVERT: 5 48 GLU cc_start: 0.8376 (pm20) cc_final: 0.7915 (pm20) REVERT: 5 63 GLN cc_start: 0.7861 (mt0) cc_final: 0.7510 (tt0) REVERT: 5 64 ASN cc_start: 0.8443 (m110) cc_final: 0.8081 (m-40) REVERT: 7 70 ASP cc_start: 0.8043 (t0) cc_final: 0.7379 (t0) REVERT: 7 379 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6844 (mttp) REVERT: 7 612 ASP cc_start: 0.8428 (p0) cc_final: 0.8134 (p0) REVERT: 7 714 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8436 (mm-40) outliers start: 31 outliers final: 18 residues processed: 129 average time/residue: 1.0526 time to fit residues: 146.7230 Evaluate side-chains 126 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 2 residue 237 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 2 residue 421 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 139 TYR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 285 ILE Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 379 LYS Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 63 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.163457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.116773 restraints weight = 12334.998| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.05 r_work: 0.3367 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9358 Z= 0.233 Angle : 0.599 13.839 12872 Z= 0.300 Chirality : 0.041 0.415 1448 Planarity : 0.004 0.058 1459 Dihedral : 18.954 93.105 1632 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.35 % Allowed : 21.50 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.27), residues: 961 helix: 1.09 (0.24), residues: 485 sheet: -0.93 (0.42), residues: 139 loop : -0.96 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 213 HIS 0.005 0.001 HIS 7 114 PHE 0.047 0.002 PHE 2 261 TYR 0.022 0.001 TYR 7 534 ARG 0.003 0.000 ARG 2 266 *********************** 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 135 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7854 (t-100) cc_final: 0.7281 (t-100) REVERT: 2 336 TYR cc_start: 0.9059 (m-80) cc_final: 0.8104 (m-80) REVERT: 2 421 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8660 (mp) REVERT: 2 456 LYS cc_start: 0.9343 (ptmt) cc_final: 0.9015 (mmmt) REVERT: 5 11 GLU cc_start: 0.7985 (tt0) cc_final: 0.7593 (tt0) REVERT: 5 16 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8159 (mmm) REVERT: 5 48 GLU cc_start: 0.8266 (pm20) cc_final: 0.7820 (pm20) REVERT: 5 59 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6631 (pp20) REVERT: 5 63 GLN cc_start: 0.7889 (mt0) cc_final: 0.7524 (tt0) REVERT: 5 64 ASN cc_start: 0.8428 (m110) cc_final: 0.8078 (m-40) REVERT: 7 52 LYS cc_start: 0.7193 (tppt) cc_final: 0.6173 (ttmt) REVERT: 7 70 ASP cc_start: 0.8053 (t0) cc_final: 0.7367 (t0) REVERT: 7 612 ASP cc_start: 0.8413 (p0) cc_final: 0.8126 (p0) REVERT: 7 714 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8432 (mm-40) outliers start: 29 outliers final: 18 residues processed: 127 average time/residue: 1.2266 time to fit residues: 169.9571 Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 2 residue 421 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 26 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 285 ILE Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 0.0670 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.163782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117526 restraints weight = 12110.898| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.02 r_work: 0.3394 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9358 Z= 0.231 Angle : 0.613 11.448 12872 Z= 0.307 Chirality : 0.040 0.205 1448 Planarity : 0.004 0.059 1459 Dihedral : 18.944 91.319 1632 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.58 % Allowed : 21.16 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 961 helix: 1.06 (0.24), residues: 485 sheet: -0.91 (0.42), residues: 139 loop : -0.98 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 213 HIS 0.005 0.001 HIS 7 114 PHE 0.022 0.002 PHE 2 418 TYR 0.023 0.001 TYR 7 534 ARG 0.003 0.000 ARG 7 360 *********************** 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 138 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7835 (t-100) cc_final: 0.7235 (t-100) REVERT: 2 336 TYR cc_start: 0.9056 (m-80) cc_final: 0.8080 (m-80) REVERT: 2 421 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8652 (mp) REVERT: 2 456 LYS cc_start: 0.9350 (ptmt) cc_final: 0.9012 (mmmt) REVERT: 5 11 GLU cc_start: 0.7955 (tt0) cc_final: 0.7360 (tt0) REVERT: 5 16 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8152 (mmm) REVERT: 5 48 GLU cc_start: 0.8201 (pm20) cc_final: 0.7746 (pm20) REVERT: 5 63 GLN cc_start: 0.7753 (mt0) cc_final: 0.7425 (tt0) REVERT: 5 64 ASN cc_start: 0.8387 (m110) cc_final: 0.8065 (m-40) REVERT: 7 54 ASP cc_start: 0.7202 (m-30) cc_final: 0.6777 (m-30) REVERT: 7 70 ASP cc_start: 0.8050 (t0) cc_final: 0.7373 (t0) REVERT: 7 379 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6817 (mttp) REVERT: 7 612 ASP cc_start: 0.8417 (p0) cc_final: 0.8121 (p0) REVERT: 7 714 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8428 (mm-40) outliers start: 31 outliers final: 16 residues processed: 128 average time/residue: 1.0136 time to fit residues: 140.8463 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 : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 2 residue 421 LEU Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 26 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 285 ILE Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 379 LYS Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 0.2980 chunk 91 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.162537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.115945 restraints weight = 12307.959| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.04 r_work: 0.3352 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9358 Z= 0.285 Angle : 0.639 11.832 12872 Z= 0.321 Chirality : 0.042 0.271 1448 Planarity : 0.004 0.060 1459 Dihedral : 19.072 94.511 1632 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.77 % Allowed : 22.20 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 961 helix: 0.97 (0.24), residues: 487 sheet: -0.97 (0.42), residues: 139 loop : -0.95 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 213 HIS 0.007 0.001 HIS 7 114 PHE 0.024 0.002 PHE 2 261 TYR 0.022 0.001 TYR 7 534 ARG 0.003 0.000 ARG 7 360 ********************** 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 129 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.497 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7925 (t-100) cc_final: 0.7362 (t-100) REVERT: 2 336 TYR cc_start: 0.9061 (m-80) cc_final: 0.8110 (m-80) REVERT: 2 421 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8769 (mm) REVERT: 2 456 LYS cc_start: 0.9354 (ptmt) cc_final: 0.9016 (mmmt) REVERT: 5 11 GLU cc_start: 0.7955 (tt0) cc_final: 0.7370 (tt0) REVERT: 5 48 GLU cc_start: 0.8192 (pm20) cc_final: 0.7750 (pm20) REVERT: 5 63 GLN cc_start: 0.7837 (mt0) cc_final: 0.7474 (tt0) REVERT: 5 64 ASN cc_start: 0.8437 (m110) cc_final: 0.8143 (m-40) REVERT: 7 52 LYS cc_start: 0.7104 (tppt) cc_final: 0.6091 (ttmt) REVERT: 7 70 ASP cc_start: 0.8094 (t0) cc_final: 0.7440 (t0) REVERT: 7 379 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6883 (mttp) REVERT: 7 612 ASP cc_start: 0.8401 (p0) cc_final: 0.8113 (p0) REVERT: 7 714 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8434 (mm-40) outliers start: 24 outliers final: 17 residues processed: 123 average time/residue: 1.3346 time to fit residues: 181.0268 Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 2 residue 421 LEU Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 26 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 285 ILE Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 379 LYS Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 677 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.161490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114641 restraints weight = 12128.534| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.02 r_work: 0.3333 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 9358 Z= 0.342 Angle : 0.667 11.483 12872 Z= 0.333 Chirality : 0.043 0.283 1448 Planarity : 0.004 0.061 1459 Dihedral : 19.246 99.488 1632 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.24 % Allowed : 21.85 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 961 helix: 0.85 (0.24), residues: 488 sheet: -0.97 (0.41), residues: 144 loop : -1.03 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 213 HIS 0.008 0.001 HIS 7 114 PHE 0.025 0.002 PHE 2 261 TYR 0.023 0.002 TYR 7 534 ARG 0.006 0.000 ARG 7 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8291.70 seconds wall clock time: 147 minutes 45.93 seconds (8865.93 seconds total)