Starting phenix.real_space_refine on Thu Feb 13 17:31:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nvv_12614/02_2025/7nvv_12614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvv_12614/02_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_12614/02_2025/7nvv_12614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvv_12614/02_2025/7nvv_12614.map" model { file = "/net/cci-nas-00/data/ceres_data/7nvv_12614/02_2025/7nvv_12614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvv_12614/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.04, per 1000 atoms: 0.78 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: 2.57 Conformation dependent library (CDL) restraints added in 858.7 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: 3.64 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: 4.15 Time building geometry restraints manager: 2.85 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: 6.780 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.670 Find NCS groups from input model: 0.100 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.620 ------------------------------------------------------------------------------- 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 : 0.931 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: 1.4030 time to fit residues: 284.4203 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 : 0.969 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116548 restraints weight = 12057.248| |-----------------------------------------------------------------------------| 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 7.042 12872 Z= 0.323 Chirality : 0.042 0.171 1448 Planarity : 0.004 0.033 1459 Dihedral : 18.526 109.331 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 : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7997 (t-100) cc_final: 0.7568 (t-100) REVERT: 2 336 TYR cc_start: 0.9065 (m-80) cc_final: 0.8850 (m-80) REVERT: 2 452 LYS cc_start: 0.9081 (ttmt) cc_final: 0.8806 (ptmt) REVERT: 5 48 GLU cc_start: 0.8516 (pm20) cc_final: 0.8080 (pm20) REVERT: 5 51 ASN cc_start: 0.8424 (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: 0.8465 (mm-30) cc_final: 0.7945 (mt-10) REVERT: 7 590 MET cc_start: 0.8480 (tpt) cc_final: 0.8162 (tpt) REVERT: 7 612 ASP cc_start: 0.8369 (p0) cc_final: 0.8029 (p0) outliers start: 26 outliers final: 8 residues processed: 141 average time/residue: 1.1750 time to fit residues: 178.1412 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 : 1.067 ------------------------------------------------------------------------------- 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: 0.9990 chunk 95 optimal weight: 0.9990 chunk 14 optimal weight: 0.0670 chunk 18 optimal weight: 0.2980 chunk 53 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 3 ASN 5 64 ASN 7 366 ASN ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.164606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118019 restraints weight = 12175.541| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.06 r_work: 0.3390 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9358 Z= 0.220 Angle : 0.568 8.162 12872 Z= 0.295 Chirality : 0.040 0.177 1448 Planarity : 0.004 0.039 1459 Dihedral : 18.557 102.747 1632 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.01 % Allowed : 15.84 % Favored : 81.16 % 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: 0.46 (0.27), residues: 961 helix: 1.30 (0.24), residues: 485 sheet: -0.66 (0.43), residues: 139 loop : -0.62 (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 0.005 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 147 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7877 (t-100) cc_final: 0.7460 (t-100) REVERT: 2 234 LEU cc_start: 0.9471 (tp) cc_final: 0.9113 (pp) REVERT: 2 261 PHE cc_start: 0.8184 (t80) cc_final: 0.7759 (t80) REVERT: 2 341 MET cc_start: 0.8792 (tmm) cc_final: 0.8586 (tmm) REVERT: 2 456 LYS cc_start: 0.9349 (ptmt) cc_final: 0.9037 (mmmt) REVERT: 5 11 GLU cc_start: 0.7946 (tt0) cc_final: 0.7423 (mt-10) REVERT: 5 48 GLU cc_start: 0.8550 (pm20) cc_final: 0.8108 (pm20) REVERT: 5 61 MET cc_start: 0.8727 (mmt) cc_final: 0.8476 (mmp) REVERT: 5 63 GLN cc_start: 0.7805 (mt0) cc_final: 0.7449 (tt0) REVERT: 7 287 LEU cc_start: 0.8670 (mt) cc_final: 0.8392 (mt) REVERT: 7 570 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7998 (mt-10) REVERT: 7 590 MET cc_start: 0.8525 (tpt) cc_final: 0.8233 (tpt) REVERT: 7 612 ASP cc_start: 0.8348 (p0) cc_final: 0.7987 (p0) REVERT: 7 636 GLU cc_start: 0.8540 (tp30) cc_final: 0.8285 (tp30) outliers start: 26 outliers final: 12 residues processed: 132 average time/residue: 1.1277 time to fit residues: 160.9481 Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 438 LYS Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 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 197 CYS 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: 0.5980 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 5 64 ASN 7 366 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.162448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115803 restraints weight = 12123.016| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.04 r_work: 0.3352 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9358 Z= 0.308 Angle : 0.585 7.923 12872 Z= 0.302 Chirality : 0.042 0.264 1448 Planarity : 0.004 0.047 1459 Dihedral : 18.809 101.011 1632 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.47 % Allowed : 16.88 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.24 (0.26), residues: 961 helix: 1.10 (0.24), residues: 484 sheet: -0.74 (0.43), residues: 139 loop : -0.70 (0.30), residues: 338 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 0.015 0.002 PHE 7 270 TYR 0.021 0.001 TYR 7 534 ARG 0.004 0.001 ARG 7 74 *********************** 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: 30 poor density : 118 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7961 (t-100) cc_final: 0.7524 (t-100) REVERT: 2 261 PHE cc_start: 0.8313 (t80) cc_final: 0.8063 (t80) REVERT: 2 336 TYR cc_start: 0.9119 (m-80) cc_final: 0.8150 (m-80) REVERT: 2 421 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8914 (mp) REVERT: 2 456 LYS cc_start: 0.9355 (ptmt) cc_final: 0.9068 (mmmt) REVERT: 5 11 GLU cc_start: 0.8043 (tt0) cc_final: 0.7780 (tt0) REVERT: 5 48 GLU cc_start: 0.8499 (pm20) cc_final: 0.8054 (pm20) REVERT: 5 59 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6619 (tm-30) REVERT: 5 63 GLN cc_start: 0.7804 (mt0) cc_final: 0.7435 (tt0) REVERT: 5 64 ASN cc_start: 0.8275 (m110) cc_final: 0.7970 (m-40) REVERT: 7 70 ASP cc_start: 0.7961 (t0) cc_final: 0.7448 (t0) REVERT: 7 287 LEU cc_start: 0.8666 (mt) cc_final: 0.8386 (mt) REVERT: 7 570 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7941 (mt-10) REVERT: 7 590 MET cc_start: 0.8522 (tpt) cc_final: 0.8253 (tpt) REVERT: 7 612 ASP cc_start: 0.8394 (p0) cc_final: 0.8094 (p0) REVERT: 7 636 GLU cc_start: 0.8580 (tp30) cc_final: 0.8351 (tp30) outliers start: 30 outliers final: 15 residues processed: 135 average time/residue: 1.1223 time to fit residues: 163.1232 Evaluate side-chains 127 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 265 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 82 optimal weight: 0.0570 chunk 61 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 0.0980 overall best weight: 0.2098 ------------------------------------------------------------------------------- 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** 7 668 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.165173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119183 restraints weight = 12147.390| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.03 r_work: 0.3410 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9358 Z= 0.183 Angle : 0.556 8.472 12872 Z= 0.284 Chirality : 0.039 0.275 1448 Planarity : 0.004 0.048 1459 Dihedral : 18.720 92.189 1632 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.12 % Allowed : 18.50 % Favored : 78.38 % 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: 0.28 (0.27), residues: 961 helix: 1.20 (0.24), residues: 480 sheet: -0.73 (0.43), residues: 139 loop : -0.78 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 7 77 HIS 0.004 0.001 HIS 7 286 PHE 0.013 0.001 PHE 2 367 TYR 0.022 0.001 TYR 7 534 ARG 0.003 0.000 ARG 2 426 *********************** 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 146 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7792 (t-100) cc_final: 0.7304 (t-100) REVERT: 2 261 PHE cc_start: 0.8338 (t80) cc_final: 0.7874 (t80) REVERT: 2 336 TYR cc_start: 0.9097 (m-80) cc_final: 0.8091 (m-80) REVERT: 2 341 MET cc_start: 0.8802 (tmm) cc_final: 0.8559 (tmm) REVERT: 2 421 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8819 (mp) REVERT: 2 456 LYS cc_start: 0.9349 (ptmt) cc_final: 0.9065 (mmmt) REVERT: 5 11 GLU cc_start: 0.8032 (tt0) cc_final: 0.7718 (tt0) REVERT: 5 48 GLU cc_start: 0.8460 (pm20) cc_final: 0.8007 (pm20) REVERT: 5 63 GLN cc_start: 0.7814 (mt0) cc_final: 0.7491 (tt0) REVERT: 5 64 ASN cc_start: 0.8238 (m110) cc_final: 0.7887 (m-40) REVERT: 7 54 ASP cc_start: 0.7261 (m-30) cc_final: 0.6915 (m-30) REVERT: 7 70 ASP cc_start: 0.8021 (t0) cc_final: 0.7443 (t0) REVERT: 7 287 LEU cc_start: 0.8674 (mt) cc_final: 0.8396 (mt) REVERT: 7 570 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7972 (mt-10) REVERT: 7 590 MET cc_start: 0.8538 (tpt) cc_final: 0.8329 (tpt) REVERT: 7 612 ASP cc_start: 0.8362 (p0) cc_final: 0.8004 (p0) REVERT: 7 636 GLU cc_start: 0.8561 (tp30) cc_final: 0.8274 (tp30) outliers start: 27 outliers final: 12 residues processed: 136 average time/residue: 1.1729 time to fit residues: 173.2250 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 : 0.925 ------------------------------------------------------------------------------- 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 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 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 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: 0.3980 chunk 23 optimal weight: 0.0060 chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 66 optimal weight: 0.0970 overall best weight: 0.1794 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.165616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.119575 restraints weight = 11984.321| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.03 r_work: 0.3415 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9358 Z= 0.180 Angle : 0.552 7.993 12872 Z= 0.281 Chirality : 0.039 0.172 1448 Planarity : 0.004 0.051 1459 Dihedral : 18.668 87.252 1632 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.54 % Allowed : 20.23 % Favored : 77.23 % 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: 0.30 (0.27), residues: 961 helix: 1.24 (0.24), residues: 480 sheet: -0.69 (0.43), residues: 139 loop : -0.82 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 7 77 HIS 0.003 0.001 HIS 5 42 PHE 0.020 0.001 PHE 2 433 TYR 0.022 0.001 TYR 7 534 ARG 0.002 0.000 ARG 7 62 *********************** 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 136 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7788 (t-100) cc_final: 0.7180 (t-100) REVERT: 2 261 PHE cc_start: 0.8149 (t80) cc_final: 0.7733 (t80) REVERT: 2 336 TYR cc_start: 0.9076 (m-80) cc_final: 0.8059 (m-80) REVERT: 2 421 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8766 (mp) REVERT: 2 456 LYS cc_start: 0.9366 (ptmt) cc_final: 0.9074 (mmmt) REVERT: 5 11 GLU cc_start: 0.8001 (tt0) cc_final: 0.7656 (tt0) REVERT: 5 16 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8152 (mmm) REVERT: 5 48 GLU cc_start: 0.8477 (pm20) cc_final: 0.8027 (pm20) REVERT: 5 63 GLN cc_start: 0.7818 (mt0) cc_final: 0.7475 (tt0) REVERT: 5 64 ASN cc_start: 0.8323 (m110) cc_final: 0.7943 (m-40) REVERT: 7 54 ASP cc_start: 0.7195 (m-30) cc_final: 0.6850 (m-30) REVERT: 7 70 ASP cc_start: 0.7965 (t0) cc_final: 0.7395 (t0) REVERT: 7 287 LEU cc_start: 0.8672 (mt) cc_final: 0.8395 (mt) REVERT: 7 570 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8040 (mt-10) REVERT: 7 590 MET cc_start: 0.8532 (tpt) cc_final: 0.8244 (tpt) REVERT: 7 612 ASP cc_start: 0.8360 (p0) cc_final: 0.7944 (p0) REVERT: 7 636 GLU cc_start: 0.8554 (tp30) cc_final: 0.8287 (tp30) outliers start: 22 outliers final: 11 residues processed: 129 average time/residue: 1.0987 time to fit residues: 153.3882 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 : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.0870 chunk 88 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.0770 overall best weight: 0.2916 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.165115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118829 restraints weight = 12216.847| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.05 r_work: 0.3398 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9358 Z= 0.205 Angle : 0.567 9.525 12872 Z= 0.286 Chirality : 0.040 0.399 1448 Planarity : 0.004 0.052 1459 Dihedral : 18.740 86.750 1632 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.24 % Allowed : 19.54 % Favored : 77.23 % 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: 0.25 (0.27), residues: 961 helix: 1.19 (0.24), residues: 481 sheet: -0.73 (0.43), residues: 139 loop : -0.83 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 280 HIS 0.004 0.001 HIS 7 114 PHE 0.017 0.001 PHE 2 433 TYR 0.022 0.001 TYR 7 534 ARG 0.002 0.000 ARG 2 453 *********************** 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 140 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7795 (t-100) cc_final: 0.7178 (t-100) REVERT: 2 261 PHE cc_start: 0.8269 (t80) cc_final: 0.7994 (t80) REVERT: 2 336 TYR cc_start: 0.9071 (m-80) cc_final: 0.8130 (m-80) REVERT: 2 421 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8713 (mp) REVERT: 2 456 LYS cc_start: 0.9360 (ptmt) cc_final: 0.9020 (mmmt) REVERT: 5 11 GLU cc_start: 0.7963 (tt0) cc_final: 0.7368 (tt0) REVERT: 5 16 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8150 (mmm) REVERT: 5 48 GLU cc_start: 0.8379 (pm20) cc_final: 0.7921 (pm20) REVERT: 5 63 GLN cc_start: 0.7770 (mt0) cc_final: 0.7449 (tt0) REVERT: 5 64 ASN cc_start: 0.8348 (m110) cc_final: 0.7989 (m-40) REVERT: 7 54 ASP cc_start: 0.7176 (m-30) cc_final: 0.6835 (m-30) REVERT: 7 70 ASP cc_start: 0.8010 (t0) cc_final: 0.7394 (t0) REVERT: 7 287 LEU cc_start: 0.8682 (mt) cc_final: 0.8427 (mt) REVERT: 7 570 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8100 (mt-10) REVERT: 7 590 MET cc_start: 0.8550 (tpt) cc_final: 0.8284 (tpt) REVERT: 7 612 ASP cc_start: 0.8366 (p0) cc_final: 0.7959 (p0) REVERT: 7 636 GLU cc_start: 0.8573 (tp30) cc_final: 0.8338 (tp30) outliers start: 28 outliers final: 13 residues processed: 130 average time/residue: 1.0901 time to fit residues: 152.9925 Evaluate side-chains 126 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 309 ASP 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: 0.8980 chunk 92 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 63 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 35 optimal weight: 0.0010 chunk 57 optimal weight: 0.2980 overall best weight: 0.2586 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.165560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.119618 restraints weight = 12351.268| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.05 r_work: 0.3408 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9358 Z= 0.197 Angle : 0.570 10.520 12872 Z= 0.287 Chirality : 0.039 0.251 1448 Planarity : 0.004 0.053 1459 Dihedral : 18.751 85.877 1632 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.01 % Allowed : 20.23 % 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 (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: 0.28 (0.27), residues: 961 helix: 1.19 (0.24), residues: 484 sheet: -0.73 (0.43), residues: 139 loop : -0.79 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 280 HIS 0.004 0.001 HIS 5 42 PHE 0.036 0.002 PHE 2 162 TYR 0.023 0.001 TYR 7 534 ARG 0.004 0.000 ARG 7 360 *********************** 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 138 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7802 (t-100) cc_final: 0.7174 (t-100) REVERT: 2 261 PHE cc_start: 0.8358 (t80) cc_final: 0.8015 (t80) REVERT: 2 421 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8649 (mp) REVERT: 2 456 LYS cc_start: 0.9385 (ptmt) cc_final: 0.9033 (mmmt) REVERT: 5 11 GLU cc_start: 0.7941 (tt0) cc_final: 0.7366 (tt0) REVERT: 5 16 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8145 (mmm) REVERT: 5 48 GLU cc_start: 0.8334 (pm20) cc_final: 0.7860 (pm20) REVERT: 5 63 GLN cc_start: 0.7799 (mt0) cc_final: 0.7445 (tt0) REVERT: 5 64 ASN cc_start: 0.8392 (m110) cc_final: 0.8005 (m-40) REVERT: 7 52 LYS cc_start: 0.7184 (tppt) cc_final: 0.6213 (ttmt) REVERT: 7 54 ASP cc_start: 0.7119 (m-30) cc_final: 0.6793 (m-30) REVERT: 7 70 ASP cc_start: 0.8022 (t0) cc_final: 0.7414 (t0) REVERT: 7 287 LEU cc_start: 0.8675 (mt) cc_final: 0.8416 (mt) REVERT: 7 570 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8092 (mt-10) REVERT: 7 590 MET cc_start: 0.8538 (tpt) cc_final: 0.8267 (tpt) REVERT: 7 612 ASP cc_start: 0.8358 (p0) cc_final: 0.7931 (p0) REVERT: 7 636 GLU cc_start: 0.8581 (tp30) cc_final: 0.8323 (tp30) outliers start: 26 outliers final: 13 residues processed: 128 average time/residue: 1.0462 time to fit residues: 144.9515 Evaluate side-chains 127 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 407 VAL Chi-restraints excluded: chain 2 residue 421 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 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 309 ASP Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 604 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 98 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 40 optimal weight: 0.4980 chunk 21 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.0370 overall best weight: 0.2458 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.165776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120068 restraints weight = 12132.398| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.02 r_work: 0.3415 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9358 Z= 0.196 Angle : 0.578 11.662 12872 Z= 0.289 Chirality : 0.040 0.348 1448 Planarity : 0.004 0.053 1459 Dihedral : 18.755 84.829 1632 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.12 % Allowed : 20.46 % 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 (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: 0.19 (0.27), residues: 961 helix: 1.11 (0.24), residues: 484 sheet: -0.66 (0.42), residues: 144 loop : -0.87 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 2 213 HIS 0.003 0.001 HIS 5 42 PHE 0.020 0.001 PHE 2 418 TYR 0.022 0.001 TYR 7 534 ARG 0.005 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 140 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7745 (t-100) cc_final: 0.7098 (t-100) REVERT: 2 261 PHE cc_start: 0.8408 (t80) cc_final: 0.7952 (t80) REVERT: 2 336 TYR cc_start: 0.8993 (m-80) cc_final: 0.8105 (m-80) REVERT: 2 421 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8643 (mp) REVERT: 2 440 LEU cc_start: 0.8919 (pp) cc_final: 0.8704 (mt) REVERT: 2 456 LYS cc_start: 0.9372 (ptmt) cc_final: 0.9034 (mmmt) REVERT: 5 11 GLU cc_start: 0.7922 (tt0) cc_final: 0.7351 (tt0) REVERT: 5 16 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8132 (mmm) REVERT: 5 48 GLU cc_start: 0.8311 (pm20) cc_final: 0.7822 (pm20) REVERT: 5 63 GLN cc_start: 0.7805 (mt0) cc_final: 0.7403 (tt0) REVERT: 5 64 ASN cc_start: 0.8355 (m110) cc_final: 0.7988 (m-40) REVERT: 7 54 ASP cc_start: 0.7259 (m-30) cc_final: 0.6915 (m-30) REVERT: 7 70 ASP cc_start: 0.8041 (t0) cc_final: 0.7425 (t0) REVERT: 7 287 LEU cc_start: 0.8667 (mt) cc_final: 0.8399 (mt) REVERT: 7 570 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8090 (mt-10) REVERT: 7 590 MET cc_start: 0.8531 (tpt) cc_final: 0.8260 (tpt) REVERT: 7 612 ASP cc_start: 0.8351 (p0) cc_final: 0.7924 (p0) outliers start: 27 outliers final: 15 residues processed: 131 average time/residue: 1.1094 time to fit residues: 156.6987 Evaluate side-chains 128 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 407 VAL Chi-restraints excluded: chain 2 residue 421 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 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 309 ASP 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: 0.0870 chunk 91 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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** 7 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.163930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.117100 restraints weight = 12270.798| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.06 r_work: 0.3372 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9358 Z= 0.263 Angle : 0.621 12.002 12872 Z= 0.309 Chirality : 0.041 0.366 1448 Planarity : 0.004 0.054 1459 Dihedral : 18.940 89.821 1632 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.01 % Allowed : 20.69 % 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 (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: 0.10 (0.26), residues: 961 helix: 1.06 (0.24), residues: 485 sheet: -0.70 (0.42), residues: 144 loop : -0.96 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 7 511 HIS 0.005 0.001 HIS 7 114 PHE 0.037 0.002 PHE 2 162 TYR 0.023 0.001 TYR 7 534 ARG 0.005 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 139 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7797 (t-100) cc_final: 0.7146 (t-100) REVERT: 2 261 PHE cc_start: 0.8477 (t80) cc_final: 0.8061 (t80) REVERT: 2 336 TYR cc_start: 0.9034 (m-80) cc_final: 0.8197 (m-80) REVERT: 2 421 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8744 (mm) REVERT: 2 456 LYS cc_start: 0.9373 (ptmt) cc_final: 0.9031 (mmmt) REVERT: 5 11 GLU cc_start: 0.7944 (tt0) cc_final: 0.7499 (tt0) REVERT: 5 16 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8130 (mmm) REVERT: 5 48 GLU cc_start: 0.8296 (pm20) cc_final: 0.7841 (pm20) REVERT: 5 63 GLN cc_start: 0.7839 (mt0) cc_final: 0.7414 (tt0) REVERT: 5 64 ASN cc_start: 0.8401 (m110) cc_final: 0.8062 (m-40) REVERT: 7 52 LYS cc_start: 0.7156 (tppt) cc_final: 0.6156 (ttmt) REVERT: 7 54 ASP cc_start: 0.7190 (m-30) cc_final: 0.6818 (m-30) REVERT: 7 70 ASP cc_start: 0.8067 (t0) cc_final: 0.7415 (t0) REVERT: 7 287 LEU cc_start: 0.8653 (mt) cc_final: 0.8401 (mt) REVERT: 7 449 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8627 (tttt) REVERT: 7 570 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8040 (mt-10) REVERT: 7 590 MET cc_start: 0.8529 (tpt) cc_final: 0.8256 (tpt) REVERT: 7 612 ASP cc_start: 0.8383 (p0) cc_final: 0.7990 (p0) outliers start: 26 outliers final: 14 residues processed: 129 average time/residue: 1.0761 time to fit residues: 150.2512 Evaluate side-chains 126 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 407 VAL Chi-restraints excluded: chain 2 residue 421 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 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 309 ASP 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: 0.5980 chunk 37 optimal weight: 0.0270 chunk 79 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 83 optimal weight: 0.1980 chunk 77 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 overall best weight: 0.3238 ------------------------------------------------------------------------------- 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** 7 711 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.164615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.118855 restraints weight = 12130.204| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.96 r_work: 0.3400 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9358 Z= 0.223 Angle : 0.621 11.773 12872 Z= 0.306 Chirality : 0.041 0.337 1448 Planarity : 0.004 0.053 1459 Dihedral : 18.920 88.879 1632 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.66 % Allowed : 20.81 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.27), residues: 961 helix: 1.02 (0.24), residues: 485 sheet: -0.68 (0.42), residues: 144 loop : -0.97 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 213 HIS 0.004 0.001 HIS 7 114 PHE 0.020 0.002 PHE 2 418 TYR 0.021 0.001 TYR 7 534 ARG 0.004 0.000 ARG 7 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7608.77 seconds wall clock time: 135 minutes 5.81 seconds (8105.81 seconds total)