Starting phenix.real_space_refine on Fri Oct 23 07:53:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wws_66319/10_2026/9wws_66319.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wws_66319/10_2026/9wws_66319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wws_66319/10_2026/9wws_66319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wws_66319/10_2026/9wws_66319.map" model { file = "/net/cci-nas-00/data/ceres_data/9wws_66319/10_2026/9wws_66319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wws_66319/10_2026/9wws_66319.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 56 5.16 5 C 5812 2.51 5 N 1412 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8883 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "D" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "A" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3351 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 434} Chain breaks: 1 Chain: "B" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3423 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 445} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "A" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'NAP': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 182 Unusual residues: {'NAP': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Time building chain proxies: 2.08, per 1000 atoms: 0.23 Number of scatterers: 8883 At special positions: 0 Unit cell: (104.832, 69.888, 99.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 14 15.00 O 1589 8.00 N 1412 7.00 C 5812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 294.3 milliseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 2 sheets defined 72.9% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 404 through 418 removed outlier: 3.526A pdb=" N ILE C 410 " --> pdb=" O MET C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 445 removed outlier: 3.588A pdb=" N ASN C 444 " --> pdb=" O TYR C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 449 through 462 Processing helix chain 'C' and resid 463 through 472 removed outlier: 4.058A pdb=" N GLY C 467 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 508 removed outlier: 3.573A pdb=" N ASN C 492 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG C 508 " --> pdb=" O LEU C 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 419 removed outlier: 3.955A pdb=" N VAL D 419 " --> pdb=" O TRP D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 445 removed outlier: 3.501A pdb=" N ASN D 444 " --> pdb=" O TYR D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 449 through 461 Processing helix chain 'D' and resid 464 through 472 removed outlier: 3.821A pdb=" N ALA D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 475 No H-bonds generated for 'chain 'D' and resid 473 through 475' Processing helix chain 'D' and resid 476 through 505 removed outlier: 3.608A pdb=" N PHE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 29 through 50 Processing helix chain 'A' and resid 56 through 77 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 108 Processing helix chain 'A' and resid 114 through 146 removed outlier: 3.908A pdb=" N VAL A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 removed outlier: 3.574A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 208 removed outlier: 5.460A pdb=" N MET A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 237 Processing helix chain 'A' and resid 238 through 263 Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.794A pdb=" N ALA A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.797A pdb=" N VAL A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 413 through 417 removed outlier: 3.631A pdb=" N LYS A 416 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 450 through 462 Processing helix chain 'B' and resid 2 through 23 Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 29 through 50 Processing helix chain 'B' and resid 56 through 76 Processing helix chain 'B' and resid 82 through 108 Processing helix chain 'B' and resid 114 through 148 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 183 through 208 Processing helix chain 'B' and resid 213 through 236 removed outlier: 3.760A pdb=" N SER B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 263 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.513A pdb=" N ALA B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 320 removed outlier: 3.879A pdb=" N ALA B 318 " --> pdb=" O GLY B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.619A pdb=" N VAL B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.626A pdb=" N LYS B 416 " --> pdb=" O GLU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 451 through 461 Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 371 removed outlier: 8.131A pdb=" N LEU A 370 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N PHE A 342 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 420 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU A 447 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL A 422 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 369 through 370 removed outlier: 5.662A pdb=" N PHE B 342 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N PHE B 423 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 387 " --> pdb=" O PHE B 423 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1463 1.32 - 1.45: 2208 1.45 - 1.57: 5253 1.57 - 1.70: 26 1.70 - 1.82: 106 Bond restraints: 9056 Sorted by residual: bond pdb=" O2B NAP B 501 " pdb=" P2B NAP B 501 " ideal model delta sigma weight residual 1.736 1.612 0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.429 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" C11 PC1 D 601 " pdb=" O13 PC1 D 601 " ideal model delta sigma weight residual 1.407 1.459 -0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" C11 PC1 B 504 " pdb=" O13 PC1 B 504 " ideal model delta sigma weight residual 1.407 1.457 -0.050 2.00e-02 2.50e+03 6.13e+00 ... (remaining 9051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 11984 2.37 - 4.73: 240 4.73 - 7.10: 36 7.10 - 9.46: 6 9.46 - 11.83: 1 Bond angle restraints: 12267 Sorted by residual: angle pdb=" N ASP B 381 " pdb=" CA ASP B 381 " pdb=" C ASP B 381 " ideal model delta sigma weight residual 113.30 105.85 7.45 1.34e+00 5.57e-01 3.09e+01 angle pdb=" N ILE A 120 " pdb=" CA ILE A 120 " pdb=" C ILE A 120 " ideal model delta sigma weight residual 111.62 107.44 4.18 7.90e-01 1.60e+00 2.79e+01 angle pdb=" N LEU A 191 " pdb=" CA LEU A 191 " pdb=" C LEU A 191 " ideal model delta sigma weight residual 113.18 106.60 6.58 1.33e+00 5.65e-01 2.45e+01 angle pdb=" N ASN A 119 " pdb=" CA ASN A 119 " pdb=" C ASN A 119 " ideal model delta sigma weight residual 113.21 108.52 4.69 1.15e+00 7.56e-01 1.67e+01 angle pdb=" CB MET B 156 " pdb=" CG MET B 156 " pdb=" SD MET B 156 " ideal model delta sigma weight residual 112.70 124.53 -11.83 3.00e+00 1.11e-01 1.55e+01 ... (remaining 12262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 4513 17.36 - 34.72: 640 34.72 - 52.08: 214 52.08 - 69.43: 58 69.43 - 86.79: 32 Dihedral angle restraints: 5457 sinusoidal: 2271 harmonic: 3186 Sorted by residual: dihedral pdb=" CA ALA A 190 " pdb=" C ALA A 190 " pdb=" N LEU A 191 " pdb=" CA LEU A 191 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ARG D 508 " pdb=" C ARG D 508 " pdb=" N LYS D 509 " pdb=" CA LYS D 509 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLY A 144 " pdb=" C GLY A 144 " pdb=" N LYS A 145 " pdb=" CA LYS A 145 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 5454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1081 0.048 - 0.095: 288 0.095 - 0.143: 49 0.143 - 0.191: 9 0.191 - 0.238: 5 Chirality restraints: 1432 Sorted by residual: chirality pdb=" C2 PC1 B 503 " pdb=" C1 PC1 B 503 " pdb=" C3 PC1 B 503 " pdb=" O21 PC1 B 503 " both_signs ideal model delta sigma weight residual False -2.49 -2.25 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3B NAP A 501 " pdb=" C2B NAP A 501 " pdb=" C4B NAP A 501 " pdb=" O3B NAP A 501 " both_signs ideal model delta sigma weight residual False -2.52 -2.74 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C3B NAP B 501 " pdb=" C2B NAP B 501 " pdb=" C4B NAP B 501 " pdb=" O3B NAP B 501 " both_signs ideal model delta sigma weight residual False -2.52 -2.73 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1429 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP B 501 " 0.044 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" C2N NAP B 501 " -0.057 2.00e-02 2.50e+03 pdb=" C3N NAP B 501 " -0.006 2.00e-02 2.50e+03 pdb=" C4N NAP B 501 " 0.027 2.00e-02 2.50e+03 pdb=" C5N NAP B 501 " -0.002 2.00e-02 2.50e+03 pdb=" C6N NAP B 501 " -0.017 2.00e-02 2.50e+03 pdb=" C7N NAP B 501 " 0.021 2.00e-02 2.50e+03 pdb=" N1N NAP B 501 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 117 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C LEU A 117 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU A 117 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 118 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 381 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ASP B 381 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP B 381 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 382 " -0.017 2.00e-02 2.50e+03 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 199 2.68 - 3.23: 8717 3.23 - 3.79: 14667 3.79 - 4.34: 19897 4.34 - 4.90: 33124 Nonbonded interactions: 76604 Sorted by model distance: nonbonded pdb=" O GLN C 474 " pdb=" OG SER C 479 " model vdw 2.121 3.040 nonbonded pdb=" O TRP D 415 " pdb=" OG SER D 418 " model vdw 2.172 3.040 nonbonded pdb=" O ALA C 468 " pdb=" OG SER C 482 " model vdw 2.176 3.040 nonbonded pdb=" N GLN B 418 " pdb=" OE1 GLN B 418 " model vdw 2.220 3.120 nonbonded pdb=" O VAL D 486 " pdb=" OG SER D 490 " model vdw 2.230 3.040 ... (remaining 76599 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 278 or resid 290 through 501 or (resid 502 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or name \ C2D or name C2E or name C2F or name C2G or name C2H or name C2I or name C3 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C3A or name C3B or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or \ (resid 503 and (name N or name C1 or name C11 or name C12 or name C13 or name C1 \ 4 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27 or name C28 or name C29 or name C2A or name C2B or \ name C2C or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 \ or name C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )))) } ncs_group { reference = (chain 'C' and (resid 403 through 510 or (resid 601 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name C3A or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'D' and (resid 403 through 510 or (resid 601 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name C3A or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) } 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: 4.660 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.340 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 9057 Z= 0.279 Angle : 0.804 11.828 12267 Z= 0.427 Chirality : 0.045 0.238 1432 Planarity : 0.005 0.069 1482 Dihedral : 19.356 86.793 3417 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.83 % Favored : 94.64 % Rotamer: Outliers : 3.62 % Allowed : 30.43 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1119 helix: 1.61 (0.19), residues: 761 sheet: -2.25 (0.67), residues: 53 loop : -1.51 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.012 0.001 TYR D 440 PHE 0.038 0.001 PHE A 126 TRP 0.008 0.001 TRP B 203 HIS 0.006 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.28 ( 9056) covalent geometry : angle 0.80372 / 0.43 (12267) hydrogen bonds : bond 0.12749 / 8.37 ( 609) hydrogen bonds : angle 4.89554 / 3.57 ( 1782) Misc. bond : bond 0.00696 / 0.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7878 (ptp) cc_final: 0.7675 (ptp) REVERT: A 182 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8094 (p0) REVERT: B 302 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7927 (tt) outliers start: 32 outliers final: 26 residues processed: 152 average time/residue: 0.4293 time to fit residues: 70.8583 Evaluate side-chains 144 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 383 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS B 339 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099504 restraints weight = 10031.917| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.81 r_work: 0.3034 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9057 Z= 0.162 Angle : 0.583 7.630 12267 Z= 0.296 Chirality : 0.042 0.179 1432 Planarity : 0.005 0.065 1482 Dihedral : 14.373 87.272 1663 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.11 % Favored : 95.35 % Rotamer: Outliers : 4.41 % Allowed : 26.13 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1119 helix: 1.70 (0.19), residues: 760 sheet: -1.80 (0.70), residues: 52 loop : -1.18 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 180 TYR 0.013 0.001 TYR A 366 PHE 0.026 0.001 PHE A 126 TRP 0.008 0.001 TRP D 443 HIS 0.005 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9056) covalent geometry : angle 0.58328 / 0.30 (12267) hydrogen bonds : bond 0.04422 / 3.04 ( 609) hydrogen bonds : angle 4.10620 / 3.06 ( 1782) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8360 (m-40) cc_final: 0.8071 (m110) REVERT: B 302 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7566 (tt) REVERT: B 381 ASP cc_start: 0.7292 (m-30) cc_final: 0.7070 (t0) REVERT: B 403 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7923 (ptpp) REVERT: B 435 GLN cc_start: 0.6669 (mm-40) cc_final: 0.6261 (mt0) outliers start: 39 outliers final: 14 residues processed: 159 average time/residue: 0.4003 time to fit residues: 69.4629 Evaluate side-chains 136 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 444 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [81, 35, 36, 19, 52, 74, 50, 28, 77, 13, 29] chunk 81 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 419 ASN B 339 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.102902 restraints weight = 10347.244| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.93 r_work: 0.3079 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9057 Z= 0.123 Angle : 0.529 7.001 12267 Z= 0.270 Chirality : 0.041 0.178 1432 Planarity : 0.005 0.062 1482 Dihedral : 13.359 80.082 1635 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.65 % Favored : 94.91 % Rotamer: Outliers : 4.52 % Allowed : 25.68 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.26), residues: 1119 helix: 1.87 (0.19), residues: 764 sheet: -1.99 (0.69), residues: 51 loop : -1.16 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 180 TYR 0.010 0.001 TYR A 366 PHE 0.009 0.001 PHE A 126 TRP 0.006 0.001 TRP C 443 HIS 0.004 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9056) covalent geometry : angle 0.52906 / 0.27 (12267) hydrogen bonds : bond 0.03958 / 2.71 ( 609) hydrogen bonds : angle 3.91063 / 2.91 ( 1782) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8402 (m-40) cc_final: 0.8070 (m110) REVERT: A 328 GLU cc_start: 0.7208 (tt0) cc_final: 0.6999 (tt0) REVERT: A 383 ASP cc_start: 0.8257 (m-30) cc_final: 0.7820 (m-30) REVERT: A 401 ASP cc_start: 0.7756 (t0) cc_final: 0.7468 (t0) REVERT: A 443 ASN cc_start: 0.7364 (m-40) cc_final: 0.6860 (m-40) REVERT: B 165 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7227 (mm) REVERT: B 317 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7989 (ttp) REVERT: B 381 ASP cc_start: 0.7230 (m-30) cc_final: 0.7021 (t0) REVERT: B 418 GLN cc_start: 0.7425 (mp10) cc_final: 0.6877 (tt0) outliers start: 40 outliers final: 20 residues processed: 162 average time/residue: 0.4352 time to fit residues: 76.1719 Evaluate side-chains 145 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 444 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [62, 95, 61, 96, 97, 42, 66, 75, 23, 80, 41] chunk 62 optimal weight: 0.0970 chunk 95 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 458 ASN ** D 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN B 339 ASN ** B 436 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 = 0.3582 r_free = 0.3582 target = 0.133850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.100744 restraints weight = 10472.118| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.96 r_work: 0.3054 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9057 Z= 0.141 Angle : 0.545 11.577 12267 Z= 0.275 Chirality : 0.041 0.186 1432 Planarity : 0.005 0.059 1482 Dihedral : 13.152 76.594 1627 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.65 % Favored : 94.91 % Rotamer: Outliers : 4.52 % Allowed : 25.68 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.26), residues: 1119 helix: 1.88 (0.19), residues: 764 sheet: -2.03 (0.65), residues: 58 loop : -1.02 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 180 TYR 0.012 0.001 TYR A 366 PHE 0.009 0.001 PHE B 423 TRP 0.006 0.001 TRP D 443 HIS 0.004 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9056) covalent geometry : angle 0.54488 / 0.27 (12267) hydrogen bonds : bond 0.04110 / 2.83 ( 609) hydrogen bonds : angle 3.91163 / 2.91 ( 1782) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7566 (mt-10) cc_final: 0.6982 (tp30) REVERT: A 119 ASN cc_start: 0.8469 (m-40) cc_final: 0.8151 (m110) REVERT: A 383 ASP cc_start: 0.8236 (m-30) cc_final: 0.7795 (m-30) REVERT: A 401 ASP cc_start: 0.7770 (t0) cc_final: 0.7505 (t0) REVERT: A 425 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7071 (mtm180) REVERT: A 443 ASN cc_start: 0.7377 (m-40) cc_final: 0.6913 (m-40) REVERT: B 165 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7181 (mm) REVERT: B 317 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8155 (ttp) REVERT: B 381 ASP cc_start: 0.7293 (m-30) cc_final: 0.7009 (t0) REVERT: B 435 GLN cc_start: 0.6616 (mm-40) cc_final: 0.6211 (mt0) outliers start: 40 outliers final: 20 residues processed: 157 average time/residue: 0.4344 time to fit residues: 73.7539 Evaluate side-chains 147 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 444 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [69, 44, 0, 91, 81, 23, 76, 95, 79, 72, 8] chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 0.0470 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 492 ASN ** D 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN B 339 ASN ** B 436 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 = 0.3595 r_free = 0.3595 target = 0.135075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102025 restraints weight = 10440.199| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.95 r_work: 0.3058 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9057 Z= 0.118 Angle : 0.519 8.745 12267 Z= 0.262 Chirality : 0.041 0.186 1432 Planarity : 0.005 0.059 1482 Dihedral : 12.825 78.193 1624 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.56 % Favored : 95.00 % Rotamer: Outliers : 3.85 % Allowed : 26.24 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.26), residues: 1119 helix: 1.96 (0.19), residues: 772 sheet: -1.76 (0.70), residues: 53 loop : -1.11 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 292 TYR 0.010 0.001 TYR A 366 PHE 0.007 0.001 PHE A 126 TRP 0.006 0.001 TRP D 443 HIS 0.003 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9056) covalent geometry : angle 0.51871 / 0.26 (12267) hydrogen bonds : bond 0.03820 / 2.63 ( 609) hydrogen bonds : angle 3.81196 / 2.83 ( 1782) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6830 (tp30) REVERT: A 119 ASN cc_start: 0.8597 (m-40) cc_final: 0.8280 (m110) REVERT: A 383 ASP cc_start: 0.8318 (m-30) cc_final: 0.7837 (m-30) REVERT: A 401 ASP cc_start: 0.7777 (t0) cc_final: 0.7550 (t0) REVERT: A 443 ASN cc_start: 0.7316 (m-40) cc_final: 0.6894 (m-40) REVERT: B 165 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7148 (mm) REVERT: B 331 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: B 381 ASP cc_start: 0.7427 (m-30) cc_final: 0.7069 (t0) REVERT: B 403 LYS cc_start: 0.8575 (mtpp) cc_final: 0.7883 (ptpp) REVERT: B 418 GLN cc_start: 0.7514 (mp10) cc_final: 0.7029 (mt0) outliers start: 34 outliers final: 17 residues processed: 150 average time/residue: 0.4254 time to fit residues: 69.0543 Evaluate side-chains 141 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 444 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [69, 87, 51, 47, 32, 4, 55, 13, 61, 39, 1] chunk 69 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 501 GLN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN B 339 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.132775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099556 restraints weight = 10388.473| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.95 r_work: 0.3036 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9057 Z= 0.156 Angle : 0.546 7.766 12267 Z= 0.277 Chirality : 0.042 0.191 1432 Planarity : 0.005 0.057 1482 Dihedral : 13.034 81.077 1619 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.65 % Favored : 94.91 % Rotamer: Outliers : 3.85 % Allowed : 27.15 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.26), residues: 1119 helix: 1.82 (0.19), residues: 771 sheet: -1.36 (0.74), residues: 49 loop : -1.06 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 508 TYR 0.013 0.001 TYR A 366 PHE 0.011 0.001 PHE B 423 TRP 0.006 0.001 TRP A 203 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9056) covalent geometry : angle 0.54581 / 0.28 (12267) hydrogen bonds : bond 0.04187 / 2.88 ( 609) hydrogen bonds : angle 3.92144 / 2.91 ( 1782) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6895 (tp30) REVERT: A 119 ASN cc_start: 0.8674 (m-40) cc_final: 0.8322 (m110) REVERT: A 266 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8353 (p) REVERT: A 383 ASP cc_start: 0.8315 (m-30) cc_final: 0.7830 (m-30) REVERT: A 387 VAL cc_start: 0.8026 (t) cc_final: 0.7819 (m) REVERT: A 401 ASP cc_start: 0.7795 (t0) cc_final: 0.7536 (t0) REVERT: A 443 ASN cc_start: 0.7382 (m-40) cc_final: 0.6907 (m-40) REVERT: B 165 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7111 (mm) REVERT: B 381 ASP cc_start: 0.7457 (m-30) cc_final: 0.7061 (t0) REVERT: B 392 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8069 (t0) REVERT: B 418 GLN cc_start: 0.7496 (mp10) cc_final: 0.7038 (mt0) outliers start: 34 outliers final: 19 residues processed: 145 average time/residue: 0.4136 time to fit residues: 65.3861 Evaluate side-chains 142 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 444 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [64, 97, 22, 30, 85, 43, 109, 83, 35, 47, 92] chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098006 restraints weight = 10490.935| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.95 r_work: 0.3004 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9057 Z= 0.177 Angle : 0.570 10.205 12267 Z= 0.287 Chirality : 0.043 0.195 1432 Planarity : 0.005 0.058 1482 Dihedral : 13.455 83.182 1619 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.74 % Favored : 94.82 % Rotamer: Outliers : 3.85 % Allowed : 27.15 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.26), residues: 1119 helix: 1.66 (0.19), residues: 777 sheet: -1.37 (0.72), residues: 48 loop : -1.08 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 508 TYR 0.014 0.001 TYR A 366 PHE 0.012 0.001 PHE B 423 TRP 0.008 0.001 TRP C 415 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 9056) covalent geometry : angle 0.56993 / 0.29 (12267) hydrogen bonds : bond 0.04389 / 3.02 ( 609) hydrogen bonds : angle 4.01916 / 2.99 ( 1782) Misc. bond : bond 0.00049 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6942 (tp30) REVERT: A 119 ASN cc_start: 0.8780 (m-40) cc_final: 0.8410 (m110) REVERT: A 383 ASP cc_start: 0.8363 (m-30) cc_final: 0.7870 (m-30) REVERT: A 387 VAL cc_start: 0.8117 (t) cc_final: 0.7904 (m) REVERT: A 401 ASP cc_start: 0.7835 (t0) cc_final: 0.7565 (t0) REVERT: A 443 ASN cc_start: 0.7511 (m-40) cc_final: 0.6979 (m-40) REVERT: B 92 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8807 (p) REVERT: B 165 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7192 (mm) REVERT: B 381 ASP cc_start: 0.7537 (m-30) cc_final: 0.7150 (t0) REVERT: B 392 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8098 (t0) REVERT: B 418 GLN cc_start: 0.7558 (mp10) cc_final: 0.7078 (mt0) outliers start: 34 outliers final: 18 residues processed: 145 average time/residue: 0.4216 time to fit residues: 66.4517 Evaluate side-chains 143 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 444 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [53, 91, 69, 24, 39, 18, 6, 72, 79, 9, 25] chunk 53 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 436 ASN ** 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 = 0.3572 r_free = 0.3572 target = 0.133184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100161 restraints weight = 10465.436| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.95 r_work: 0.3045 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9057 Z= 0.134 Angle : 0.540 11.160 12267 Z= 0.272 Chirality : 0.041 0.188 1432 Planarity : 0.005 0.058 1482 Dihedral : 13.115 85.386 1619 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.38 % Favored : 95.17 % Rotamer: Outliers : 3.73 % Allowed : 27.15 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.26), residues: 1119 helix: 1.85 (0.19), residues: 769 sheet: -1.83 (0.69), residues: 53 loop : -0.96 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 292 TYR 0.012 0.001 TYR A 366 PHE 0.008 0.001 PHE B 423 TRP 0.007 0.001 TRP C 415 HIS 0.003 0.001 HIS C 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9056) covalent geometry : angle 0.53951 / 0.27 (12267) hydrogen bonds : bond 0.04011 / 2.76 ( 609) hydrogen bonds : angle 3.86589 / 2.88 ( 1782) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6818 (tp30) REVERT: A 119 ASN cc_start: 0.8745 (m-40) cc_final: 0.8340 (m110) REVERT: A 255 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 266 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 301 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7620 (mm-30) REVERT: A 383 ASP cc_start: 0.8309 (m-30) cc_final: 0.7799 (m-30) REVERT: A 401 ASP cc_start: 0.7800 (t0) cc_final: 0.7552 (t0) REVERT: A 425 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7019 (mtm180) REVERT: A 443 ASN cc_start: 0.7339 (m-40) cc_final: 0.6865 (m-40) REVERT: B 165 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7102 (mm) REVERT: B 381 ASP cc_start: 0.7480 (m-30) cc_final: 0.7000 (t0) REVERT: B 392 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8061 (t0) REVERT: B 418 GLN cc_start: 0.7478 (mp10) cc_final: 0.6990 (mt0) outliers start: 33 outliers final: 18 residues processed: 149 average time/residue: 0.4246 time to fit residues: 68.7728 Evaluate side-chains 146 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 444 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [103, 37, 22, 72, 95, 107, 55, 44, 26, 51, 105] chunk 103 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 95 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS B 339 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102807 restraints weight = 10339.893| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.94 r_work: 0.3079 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9057 Z= 0.113 Angle : 0.524 11.698 12267 Z= 0.265 Chirality : 0.040 0.175 1432 Planarity : 0.004 0.058 1482 Dihedral : 12.578 89.769 1619 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.20 % Favored : 95.44 % Rotamer: Outliers : 2.71 % Allowed : 27.71 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.26), residues: 1119 helix: 2.00 (0.19), residues: 772 sheet: -1.76 (0.70), residues: 53 loop : -0.89 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 292 TYR 0.009 0.001 TYR A 366 PHE 0.007 0.001 PHE B 423 TRP 0.009 0.001 TRP B 203 HIS 0.004 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9056) covalent geometry : angle 0.52440 / 0.26 (12267) hydrogen bonds : bond 0.03714 / 2.55 ( 609) hydrogen bonds : angle 3.74154 / 2.79 ( 1782) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6701 (tp30) REVERT: A 119 ASN cc_start: 0.8686 (m-40) cc_final: 0.8333 (m-40) REVERT: A 255 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8070 (mp) REVERT: A 266 SER cc_start: 0.8691 (m) cc_final: 0.8391 (p) REVERT: A 383 ASP cc_start: 0.8280 (m-30) cc_final: 0.7750 (m-30) REVERT: A 425 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7018 (mtm180) REVERT: A 443 ASN cc_start: 0.7208 (m-40) cc_final: 0.6770 (m-40) REVERT: B 165 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7078 (mm) REVERT: B 381 ASP cc_start: 0.7360 (m-30) cc_final: 0.6919 (t0) REVERT: B 418 GLN cc_start: 0.7455 (mp10) cc_final: 0.6901 (mt0) outliers start: 24 outliers final: 16 residues processed: 145 average time/residue: 0.4320 time to fit residues: 67.9707 Evaluate side-chains 138 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [55, 33, 43, 30, 14, 84, 74, 101, 87, 25, 0] chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 436 ASN ** 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 = 0.3583 r_free = 0.3583 target = 0.134064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101263 restraints weight = 10362.810| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.94 r_work: 0.3047 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9057 Z= 0.135 Angle : 0.550 12.281 12267 Z= 0.276 Chirality : 0.041 0.163 1432 Planarity : 0.004 0.057 1482 Dihedral : 12.616 86.899 1619 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.56 % Favored : 95.08 % Rotamer: Outliers : 2.60 % Allowed : 28.05 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.26), residues: 1119 helix: 1.93 (0.19), residues: 771 sheet: -1.77 (0.71), residues: 53 loop : -0.87 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 160 TYR 0.012 0.001 TYR A 366 PHE 0.011 0.001 PHE B 423 TRP 0.017 0.001 TRP B 203 HIS 0.003 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9056) covalent geometry : angle 0.54954 / 0.28 (12267) hydrogen bonds : bond 0.03978 / 2.74 ( 609) hydrogen bonds : angle 3.81856 / 2.85 ( 1782) Misc. bond : bond 0.00046 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6835 (tp30) REVERT: A 119 ASN cc_start: 0.8771 (m-40) cc_final: 0.8335 (m110) REVERT: A 266 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8488 (p) REVERT: A 301 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7657 (mm-30) REVERT: A 383 ASP cc_start: 0.8350 (m-30) cc_final: 0.7861 (m-30) REVERT: A 443 ASN cc_start: 0.7325 (m-40) cc_final: 0.6859 (m-40) REVERT: B 156 MET cc_start: 0.7718 (mmm) cc_final: 0.7238 (tpp) REVERT: B 165 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7164 (mm) REVERT: B 381 ASP cc_start: 0.7411 (m-30) cc_final: 0.6968 (t0) REVERT: B 392 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8098 (t0) REVERT: B 418 GLN cc_start: 0.7522 (mp10) cc_final: 0.6977 (mt0) outliers start: 23 outliers final: 16 residues processed: 136 average time/residue: 0.4474 time to fit residues: 65.8713 Evaluate side-chains 138 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [22, 79, 20, 25, 54, 85, 11, 101, 48, 80, 77] chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 436 ASN ** 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 = 0.3564 r_free = 0.3564 target = 0.132444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099373 restraints weight = 10371.817| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.95 r_work: 0.3037 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9057 Z= 0.158 Angle : 0.572 12.020 12267 Z= 0.288 Chirality : 0.042 0.173 1432 Planarity : 0.005 0.057 1482 Dihedral : 12.876 86.354 1619 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.47 % Favored : 95.17 % Rotamer: Outliers : 2.60 % Allowed : 27.94 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.26), residues: 1119 helix: 1.77 (0.19), residues: 777 sheet: -1.31 (0.75), residues: 48 loop : -0.98 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 336 TYR 0.014 0.001 TYR A 366 PHE 0.012 0.001 PHE B 423 TRP 0.018 0.001 TRP B 203 HIS 0.003 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9056) covalent geometry : angle 0.57184 / 0.29 (12267) hydrogen bonds : bond 0.04194 / 2.88 ( 609) hydrogen bonds : angle 3.91323 / 2.93 ( 1782) Misc. bond : bond 0.00054 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2818.34 seconds wall clock time: 48 minutes 49.07 seconds (2929.07 seconds total)