Starting phenix.real_space_refine on Fri Mar 15 07:39:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/03_2024/8c80_16467_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/03_2024/8c80_16467.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/03_2024/8c80_16467_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/03_2024/8c80_16467_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/03_2024/8c80_16467_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/03_2024/8c80_16467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/03_2024/8c80_16467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/03_2024/8c80_16467_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/03_2024/8c80_16467_updated.pdb" } resolution = 3.4 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= -0.000 sd= 0.019 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 1 5.49 5 S 55 5.16 5 C 7088 2.51 5 N 1795 2.21 5 O 2029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10968 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1502 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain: "B" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4214 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "C" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "D" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 626 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'ERG': 2, 'Z8A': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'ERG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PLP': 1, 'Q7G': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.28, per 1000 atoms: 0.57 Number of scatterers: 10968 At special positions: 0 Unit cell: (90.552, 108.108, 126.588, 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 55 16.00 P 1 15.00 O 2029 8.00 N 1795 7.00 C 7088 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 - 3.50 Amino acid : False - 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: 4.36 Conformation dependent library (CDL) restraints added in 1.9 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2542 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 9 sheets defined 43.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 108 through 128 Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 159 through 178 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.539A pdb=" N PHE A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 removed outlier: 3.703A pdb=" N TYR B 24 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 31 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 34 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 Processing helix chain 'B' and resid 54 through 72 removed outlier: 3.508A pdb=" N LEU B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 116 through 119 No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 190 through 203 Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 218 through 225 Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 261 through 278 Processing helix chain 'B' and resid 303 through 313 Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 343 through 346 No H-bonds generated for 'chain 'B' and resid 343 through 346' Processing helix chain 'B' and resid 369 through 378 removed outlier: 4.046A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 390 through 405 Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 451 through 458 removed outlier: 3.725A pdb=" N SER B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 475 Processing helix chain 'B' and resid 483 through 502 Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 535 through 554 removed outlier: 3.537A pdb=" N CYS B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 25 No H-bonds generated for 'chain 'C' and resid 22 through 25' Processing helix chain 'C' and resid 58 through 85 removed outlier: 3.559A pdb=" N VAL C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.833A pdb=" N ASP C 120 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS C 121 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.593A pdb=" N VAL C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.567A pdb=" N GLY C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 285 removed outlier: 3.734A pdb=" N VAL C 284 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 323 removed outlier: 3.570A pdb=" N GLU C 319 " --> pdb=" O PRO C 315 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 379 through 388 removed outlier: 3.857A pdb=" N LEU C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 394 No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 423 through 426 No H-bonds generated for 'chain 'C' and resid 423 through 426' Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 463 through 475 Proline residue: C 467 - end of helix removed outlier: 3.923A pdb=" N MET C 473 " --> pdb=" O PHE C 469 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 475 " --> pdb=" O ARG C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 487 No H-bonds generated for 'chain 'C' and resid 485 through 487' Processing helix chain 'C' and resid 505 through 522 Processing helix chain 'C' and resid 542 through 552 Proline residue: C 550 - end of helix Processing helix chain 'D' and resid 14 through 21 removed outlier: 3.993A pdb=" N LYS D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 4.151A pdb=" N GLU D 33 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL D 34 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 41 " --> pdb=" O LYS D 37 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYR D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS D 45 " --> pdb=" O THR D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 75 removed outlier: 3.612A pdb=" N LEU D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 55 through 57 Processing sheet with id= B, first strand: chain 'B' and resid 135 through 137 removed outlier: 3.544A pdb=" N GLU B 142 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.587A pdb=" N GLY B 367 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 252 through 256 removed outlier: 3.537A pdb=" N ALA B 234 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLU B 291 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG B 316 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR B 290 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE B 318 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE B 349 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 434 through 436 removed outlier: 3.558A pdb=" N ILE B 435 " --> pdb=" O GLN B 448 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 133 through 137 removed outlier: 3.523A pdb=" N CYS C 136 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 155 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 139 through 142 removed outlier: 4.093A pdb=" N TYR C 147 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 218 through 222 removed outlier: 3.536A pdb=" N ASP C 218 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY C 373 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 359 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU C 242 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N CYS C 300 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 244 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 263 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N SER C 245 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG C 265 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 455 through 460 removed outlier: 3.587A pdb=" N SER C 493 " --> pdb=" O LEU C 460 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1110 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: 3.11 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2964 1.33 - 1.45: 2008 1.45 - 1.57: 6179 1.57 - 1.69: 4 1.69 - 1.81: 83 Bond restraints: 11238 Sorted by residual: bond pdb=" C04 Q7G C 602 " pdb=" C05 Q7G C 602 " ideal model delta sigma weight residual 1.836 1.531 0.305 2.00e-02 2.50e+03 2.33e+02 bond pdb=" C13 Q7G C 602 " pdb=" C14 Q7G C 602 " ideal model delta sigma weight residual 1.599 1.323 0.276 2.00e-02 2.50e+03 1.91e+02 bond pdb=" C07 Q7G C 602 " pdb=" C15 Q7G C 602 " ideal model delta sigma weight residual 1.779 1.524 0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C07 Q7G C 602 " pdb=" C08 Q7G C 602 " ideal model delta sigma weight residual 1.323 1.535 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C03 Q7G C 602 " pdb=" C04 Q7G C 602 " ideal model delta sigma weight residual 1.332 1.537 -0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 11233 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.05: 335 106.05 - 113.04: 6156 113.04 - 120.03: 3954 120.03 - 127.02: 4705 127.02 - 134.02: 123 Bond angle restraints: 15273 Sorted by residual: angle pdb=" N LEU D 28 " pdb=" CA LEU D 28 " pdb=" C LEU D 28 " ideal model delta sigma weight residual 113.16 100.40 12.76 1.24e+00 6.50e-01 1.06e+02 angle pdb=" N THR A 194 " pdb=" CA THR A 194 " pdb=" C THR A 194 " ideal model delta sigma weight residual 110.97 120.01 -9.04 1.09e+00 8.42e-01 6.88e+01 angle pdb=" C ILE D 31 " pdb=" N GLU D 32 " pdb=" CA GLU D 32 " ideal model delta sigma weight residual 120.38 111.58 8.80 1.37e+00 5.33e-01 4.12e+01 angle pdb=" C THR D 30 " pdb=" N ILE D 31 " pdb=" CA ILE D 31 " ideal model delta sigma weight residual 122.66 116.60 6.06 9.70e-01 1.06e+00 3.90e+01 angle pdb=" N ILE D 31 " pdb=" CA ILE D 31 " pdb=" C ILE D 31 " ideal model delta sigma weight residual 111.90 107.04 4.86 8.10e-01 1.52e+00 3.60e+01 ... (remaining 15268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 6508 22.98 - 45.96: 305 45.96 - 68.94: 47 68.94 - 91.92: 10 91.92 - 114.90: 17 Dihedral angle restraints: 6887 sinusoidal: 2937 harmonic: 3950 Sorted by residual: dihedral pdb=" C5A PLP C 601 " pdb=" O4P PLP C 601 " pdb=" P PLP C 601 " pdb=" O1P PLP C 601 " ideal model delta sinusoidal sigma weight residual 76.43 174.49 -98.06 1 2.00e+01 2.50e-03 2.74e+01 dihedral pdb=" CA CYS C 121 " pdb=" C CYS C 121 " pdb=" N PHE C 122 " pdb=" CA PHE C 122 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C3 Q7G C 602 " pdb=" C1 Q7G C 602 " pdb=" C2 Q7G C 602 " pdb=" O5 Q7G C 602 " ideal model delta sinusoidal sigma weight residual -52.95 61.95 -114.90 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 6884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1714 0.152 - 0.304: 23 0.304 - 0.456: 2 0.456 - 0.608: 0 0.608 - 0.761: 1 Chirality restraints: 1740 Sorted by residual: chirality pdb=" C02 Q7G C 602 " pdb=" C03 Q7G C 602 " pdb=" C06 Q7G C 602 " pdb=" C10 Q7G C 602 " both_signs ideal model delta sigma weight residual False 2.14 2.90 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" CA LEU D 28 " pdb=" N LEU D 28 " pdb=" C LEU D 28 " pdb=" CB LEU D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C74 Q7G C 602 " pdb=" C03 Q7G C 602 " pdb=" C73 Q7G C 602 " pdb=" C75 Q7G C 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.43 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 1737 not shown) Planarity restraints: 1904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG A 301 " -0.097 2.00e-02 2.50e+03 9.78e-02 9.56e+01 pdb=" C22 ERG A 301 " 0.096 2.00e-02 2.50e+03 pdb=" C23 ERG A 301 " 0.099 2.00e-02 2.50e+03 pdb=" C24 ERG A 301 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 Q7G C 602 " 0.018 2.00e-02 2.50e+03 6.86e-02 5.88e+01 pdb=" C13 Q7G C 602 " 0.011 2.00e-02 2.50e+03 pdb=" C14 Q7G C 602 " 0.113 2.00e-02 2.50e+03 pdb=" C15 Q7G C 602 " -0.083 2.00e-02 2.50e+03 pdb=" C16 Q7G C 602 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG A 303 " -0.052 2.00e-02 2.50e+03 5.20e-02 2.71e+01 pdb=" C22 ERG A 303 " 0.052 2.00e-02 2.50e+03 pdb=" C23 ERG A 303 " 0.052 2.00e-02 2.50e+03 pdb=" C24 ERG A 303 " -0.052 2.00e-02 2.50e+03 ... (remaining 1901 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 46 2.56 - 3.15: 8599 3.15 - 3.73: 15034 3.73 - 4.32: 20395 4.32 - 4.90: 35273 Nonbonded interactions: 79347 Sorted by model distance: nonbonded pdb=" CD1 PHE B 185 " pdb=" CD1 TYR B 186 " model vdw 1.975 3.640 nonbonded pdb=" CD1 PHE B 185 " pdb=" N TYR B 186 " model vdw 2.182 3.420 nonbonded pdb=" OH TYR B 460 " pdb=" OE1 GLU B 488 " model vdw 2.215 2.440 nonbonded pdb=" O ALA B 183 " pdb=" ND2 ASN B 188 " model vdw 2.262 2.520 nonbonded pdb=" O ASN A 74 " pdb=" OG1 THR A 78 " model vdw 2.273 2.440 ... (remaining 79342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.870 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: 16.800 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 32.550 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 : 0.009 0.305 11238 Z= 0.549 Angle : 0.865 12.756 15273 Z= 0.492 Chirality : 0.057 0.761 1740 Planarity : 0.006 0.098 1904 Dihedral : 14.757 114.900 4345 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.75 % Allowed : 5.02 % Favored : 94.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.20), residues: 1342 helix: -0.34 (0.19), residues: 595 sheet: 0.32 (0.51), residues: 113 loop : -1.86 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 102 HIS 0.010 0.001 HIS A 206 PHE 0.013 0.001 PHE C 109 TYR 0.028 0.002 TYR B 186 ARG 0.004 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 233 time to evaluate : 1.261 Fit side-chains REVERT: A 82 GLN cc_start: 0.8846 (mm110) cc_final: 0.8629 (mm-40) REVERT: B 274 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7826 (tp-100) REVERT: B 373 LEU cc_start: 0.9189 (tp) cc_final: 0.8924 (tt) REVERT: B 547 GLN cc_start: 0.7334 (tp40) cc_final: 0.7081 (tm-30) REVERT: C 23 GLN cc_start: 0.8608 (tp40) cc_final: 0.8380 (tp40) REVERT: D 7 SER cc_start: 0.8750 (t) cc_final: 0.8382 (p) outliers start: 9 outliers final: 2 residues processed: 240 average time/residue: 0.2551 time to fit residues: 83.8278 Evaluate side-chains 114 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 180 HIS A 220 GLN B 50 HIS C 90 HIS C 142 HIS C 145 ASN C 229 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11238 Z= 0.268 Angle : 0.679 10.637 15273 Z= 0.335 Chirality : 0.047 0.249 1740 Planarity : 0.004 0.043 1904 Dihedral : 11.332 118.362 1770 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.18 % Allowed : 10.63 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1342 helix: 0.87 (0.21), residues: 604 sheet: 0.73 (0.45), residues: 124 loop : -1.72 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 188 HIS 0.007 0.001 HIS C 90 PHE 0.025 0.002 PHE C 106 TYR 0.030 0.002 TYR B 186 ARG 0.007 0.001 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 1.423 Fit side-chains REVERT: B 274 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7731 (tp-100) REVERT: C 292 ARG cc_start: 0.7572 (mtp85) cc_final: 0.7088 (mtp85) REVERT: C 499 MET cc_start: 0.7909 (mmm) cc_final: 0.7450 (mmm) REVERT: D 7 SER cc_start: 0.8737 (t) cc_final: 0.8426 (p) outliers start: 38 outliers final: 26 residues processed: 151 average time/residue: 0.2543 time to fit residues: 54.3353 Evaluate side-chains 127 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 82 optimal weight: 0.0020 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN C 90 HIS C 229 ASN C 291 ASN D 60 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11238 Z= 0.243 Angle : 0.596 9.362 15273 Z= 0.296 Chirality : 0.043 0.226 1740 Planarity : 0.004 0.043 1904 Dihedral : 10.528 114.638 1767 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.18 % Allowed : 13.05 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.00 (0.23), residues: 1342 helix: 1.49 (0.22), residues: 584 sheet: 0.41 (0.43), residues: 142 loop : -1.65 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.007 0.001 HIS C 90 PHE 0.016 0.001 PHE D 62 TYR 0.017 0.001 TYR C 510 ARG 0.003 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 110 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 178 TYR cc_start: 0.5851 (t80) cc_final: 0.5600 (t80) REVERT: B 274 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7751 (tp-100) REVERT: C 272 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7889 (mmt) REVERT: C 292 ARG cc_start: 0.7663 (mtp85) cc_final: 0.7160 (mtp85) REVERT: C 405 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: C 424 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: D 7 SER cc_start: 0.8739 (t) cc_final: 0.8448 (p) outliers start: 38 outliers final: 25 residues processed: 135 average time/residue: 0.2223 time to fit residues: 43.5918 Evaluate side-chains 130 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 552 CYS Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 HIS C 23 GLN C 379 GLN D 60 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11238 Z= 0.407 Angle : 0.701 10.468 15273 Z= 0.357 Chirality : 0.048 0.206 1740 Planarity : 0.005 0.048 1904 Dihedral : 10.182 111.870 1767 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.85 % Allowed : 13.22 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.22), residues: 1342 helix: 1.28 (0.22), residues: 572 sheet: 0.22 (0.51), residues: 109 loop : -1.84 (0.21), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 188 HIS 0.006 0.001 HIS C 76 PHE 0.024 0.002 PHE B 318 TYR 0.022 0.002 TYR C 510 ARG 0.003 0.001 ARG C 476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 106 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7997 (mm-40) REVERT: A 143 ASP cc_start: 0.8540 (t0) cc_final: 0.8297 (t0) REVERT: A 178 TYR cc_start: 0.6209 (t80) cc_final: 0.5917 (t80) REVERT: B 26 TRP cc_start: 0.4673 (t-100) cc_final: 0.4341 (m100) REVERT: C 292 ARG cc_start: 0.7782 (mtp85) cc_final: 0.7288 (mtp85) REVERT: C 405 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: C 424 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: D 37 LYS cc_start: 0.7851 (tttm) cc_final: 0.7367 (tppt) outliers start: 46 outliers final: 30 residues processed: 142 average time/residue: 0.2266 time to fit residues: 46.3349 Evaluate side-chains 128 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 0.0020 chunk 32 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 138 ASN D 60 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11238 Z= 0.152 Angle : 0.538 9.686 15273 Z= 0.265 Chirality : 0.042 0.213 1740 Planarity : 0.004 0.042 1904 Dihedral : 9.434 112.329 1767 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.43 % Allowed : 15.31 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1342 helix: 1.73 (0.22), residues: 569 sheet: 0.10 (0.47), residues: 132 loop : -1.70 (0.21), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 110 HIS 0.005 0.001 HIS D 60 PHE 0.015 0.001 PHE C 329 TYR 0.016 0.001 TYR B 66 ARG 0.002 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.191 Fit side-chains REVERT: A 70 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7738 (mm-40) REVERT: A 178 TYR cc_start: 0.6041 (t80) cc_final: 0.5732 (t80) REVERT: B 280 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8587 (tt) REVERT: B 424 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6763 (t80) REVERT: C 146 GLU cc_start: 0.8520 (tp30) cc_final: 0.8113 (mt-10) REVERT: C 292 ARG cc_start: 0.7673 (mtp85) cc_final: 0.7169 (mtp85) REVERT: C 424 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8398 (tt0) outliers start: 29 outliers final: 21 residues processed: 131 average time/residue: 0.2252 time to fit residues: 43.3585 Evaluate side-chains 124 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 0.2980 chunk 115 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11238 Z= 0.152 Angle : 0.516 8.768 15273 Z= 0.254 Chirality : 0.041 0.257 1740 Planarity : 0.004 0.039 1904 Dihedral : 8.835 112.707 1767 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.68 % Allowed : 15.40 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1342 helix: 1.89 (0.22), residues: 577 sheet: 0.27 (0.48), residues: 132 loop : -1.60 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.004 0.001 HIS D 60 PHE 0.014 0.001 PHE C 329 TYR 0.016 0.001 TYR B 66 ARG 0.002 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 1.323 Fit side-chains REVERT: A 178 TYR cc_start: 0.6034 (t80) cc_final: 0.5710 (t80) REVERT: B 280 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 424 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6887 (t80) REVERT: C 85 PHE cc_start: 0.7596 (m-10) cc_final: 0.7396 (m-10) REVERT: C 117 ARG cc_start: 0.7991 (mpt180) cc_final: 0.7439 (mmm-85) REVERT: C 146 GLU cc_start: 0.8512 (tp30) cc_final: 0.8153 (mt-10) REVERT: C 292 ARG cc_start: 0.7636 (mtp85) cc_final: 0.7141 (mtp85) REVERT: D 5 LYS cc_start: 0.7662 (mmmt) cc_final: 0.7130 (mmtp) outliers start: 32 outliers final: 21 residues processed: 133 average time/residue: 0.2220 time to fit residues: 42.5790 Evaluate side-chains 128 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 502 ASN C 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 11238 Z= 0.486 Angle : 0.706 10.479 15273 Z= 0.363 Chirality : 0.048 0.254 1740 Planarity : 0.005 0.040 1904 Dihedral : 9.032 109.982 1767 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.68 % Allowed : 15.40 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.22), residues: 1342 helix: 1.39 (0.22), residues: 575 sheet: 0.03 (0.44), residues: 133 loop : -1.93 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 110 HIS 0.005 0.001 HIS C 203 PHE 0.025 0.002 PHE B 318 TYR 0.022 0.002 TYR C 510 ARG 0.004 0.001 ARG C 434 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 101 time to evaluate : 1.378 Fit side-chains REVERT: A 70 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7754 (mm-40) REVERT: A 178 TYR cc_start: 0.6395 (t80) cc_final: 0.6053 (t80) REVERT: B 25 LEU cc_start: 0.7263 (mt) cc_final: 0.7021 (tp) REVERT: B 280 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8677 (tt) REVERT: C 117 ARG cc_start: 0.8158 (mpt180) cc_final: 0.7533 (mmm-85) REVERT: C 146 GLU cc_start: 0.8549 (tp30) cc_final: 0.8266 (mt-10) REVERT: C 292 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7318 (mtp85) REVERT: D 5 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7147 (mmtp) outliers start: 44 outliers final: 35 residues processed: 131 average time/residue: 0.2219 time to fit residues: 42.4058 Evaluate side-chains 133 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 100 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 502 ASN B 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11238 Z= 0.171 Angle : 0.534 9.770 15273 Z= 0.268 Chirality : 0.042 0.273 1740 Planarity : 0.004 0.037 1904 Dihedral : 8.427 108.835 1767 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.51 % Allowed : 16.82 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1342 helix: 1.58 (0.22), residues: 585 sheet: 0.22 (0.51), residues: 117 loop : -1.73 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 110 HIS 0.006 0.001 HIS D 60 PHE 0.014 0.001 PHE C 329 TYR 0.017 0.001 TYR B 66 ARG 0.003 0.000 ARG C 434 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 1.663 Fit side-chains REVERT: A 125 VAL cc_start: 0.8313 (p) cc_final: 0.8100 (p) REVERT: A 178 TYR cc_start: 0.6183 (t80) cc_final: 0.5846 (t80) REVERT: B 25 LEU cc_start: 0.7050 (mt) cc_final: 0.6805 (tp) REVERT: B 280 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8622 (tt) REVERT: B 424 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6904 (t80) REVERT: C 79 ASP cc_start: 0.7792 (t0) cc_final: 0.7571 (t0) REVERT: C 146 GLU cc_start: 0.8503 (tp30) cc_final: 0.8255 (mt-10) REVERT: C 292 ARG cc_start: 0.7723 (mtp85) cc_final: 0.7192 (mtp85) outliers start: 30 outliers final: 24 residues processed: 128 average time/residue: 0.2202 time to fit residues: 41.4487 Evaluate side-chains 125 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11238 Z= 0.202 Angle : 0.536 9.519 15273 Z= 0.269 Chirality : 0.042 0.265 1740 Planarity : 0.004 0.037 1904 Dihedral : 8.266 110.436 1767 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.68 % Allowed : 16.90 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1342 helix: 1.67 (0.22), residues: 585 sheet: 0.28 (0.51), residues: 119 loop : -1.68 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 110 HIS 0.003 0.001 HIS C 203 PHE 0.014 0.001 PHE C 329 TYR 0.017 0.001 TYR B 66 ARG 0.002 0.000 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 1.307 Fit side-chains REVERT: A 125 VAL cc_start: 0.8362 (p) cc_final: 0.8151 (p) REVERT: A 178 TYR cc_start: 0.6210 (t80) cc_final: 0.5851 (t80) REVERT: B 25 LEU cc_start: 0.7084 (mt) cc_final: 0.6830 (tp) REVERT: B 231 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8358 (t) REVERT: B 280 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8595 (tt) REVERT: B 424 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.6961 (t80) REVERT: C 79 ASP cc_start: 0.7767 (t0) cc_final: 0.7536 (t0) REVERT: C 146 GLU cc_start: 0.8491 (tp30) cc_final: 0.8270 (mt-10) REVERT: C 292 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7165 (mtp85) REVERT: D 5 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7078 (mmtp) outliers start: 32 outliers final: 26 residues processed: 126 average time/residue: 0.2175 time to fit residues: 40.7450 Evaluate side-chains 128 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11238 Z= 0.165 Angle : 0.508 8.917 15273 Z= 0.254 Chirality : 0.041 0.269 1740 Planarity : 0.004 0.039 1904 Dihedral : 8.108 109.768 1767 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.51 % Allowed : 17.15 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.23), residues: 1342 helix: 1.70 (0.22), residues: 595 sheet: 0.41 (0.50), residues: 129 loop : -1.59 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.002 0.001 HIS C 203 PHE 0.014 0.001 PHE C 329 TYR 0.015 0.001 TYR B 66 ARG 0.002 0.000 ARG C 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8259 (p) cc_final: 0.8051 (p) REVERT: A 178 TYR cc_start: 0.6062 (t80) cc_final: 0.5699 (t80) REVERT: B 25 LEU cc_start: 0.7075 (mt) cc_final: 0.6823 (tp) REVERT: B 231 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8317 (t) REVERT: B 280 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8599 (tt) REVERT: B 424 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6811 (t80) REVERT: C 79 ASP cc_start: 0.7710 (t0) cc_final: 0.7500 (t0) REVERT: C 292 ARG cc_start: 0.7661 (mtp85) cc_final: 0.7166 (mtp85) REVERT: C 473 MET cc_start: 0.8492 (mmm) cc_final: 0.8023 (mmt) outliers start: 30 outliers final: 24 residues processed: 127 average time/residue: 0.2450 time to fit residues: 45.4416 Evaluate side-chains 125 residues out of total 1195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 108 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.123003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100019 restraints weight = 17777.309| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.74 r_work: 0.3228 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11238 Z= 0.134 Angle : 0.496 9.043 15273 Z= 0.247 Chirality : 0.040 0.264 1740 Planarity : 0.004 0.039 1904 Dihedral : 7.925 109.081 1767 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.34 % Allowed : 17.49 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.23), residues: 1342 helix: 1.80 (0.22), residues: 597 sheet: 0.30 (0.50), residues: 133 loop : -1.51 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 110 HIS 0.002 0.000 HIS C 514 PHE 0.016 0.001 PHE D 54 TYR 0.014 0.001 TYR B 66 ARG 0.002 0.000 ARG C 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2372.50 seconds wall clock time: 43 minutes 35.60 seconds (2615.60 seconds total)