Starting phenix.real_space_refine on Wed Sep 25 00:24:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/09_2024/7zde_14643_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/09_2024/7zde_14643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/09_2024/7zde_14643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/09_2024/7zde_14643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/09_2024/7zde_14643_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zde_14643/09_2024/7zde_14643_neut.cif" } resolution = 3.17 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= 0.005 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 5771 2.51 5 N 1586 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9014 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 4418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4418 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 553} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 4564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4564 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 559} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.77, per 1000 atoms: 0.64 Number of scatterers: 9014 At special positions: 0 Unit cell: (125.55, 75.33, 112.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 3 15.00 Mg 1 11.99 O 1625 8.00 N 1586 7.00 C 5771 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=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 66.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'C' and resid 1 through 3 No H-bonds generated for 'chain 'C' and resid 1 through 3' Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 10 through 13 removed outlier: 3.694A pdb=" N ARG C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 14 through 50 removed outlier: 3.502A pdb=" N ALA C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 54 Processing helix chain 'C' and resid 59 through 104 removed outlier: 3.528A pdb=" N ARG C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 131 Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 137 through 156 removed outlier: 3.619A pdb=" N VAL C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 176 Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 186 through 209 removed outlier: 3.823A pdb=" N GLY C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 removed outlier: 3.540A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 268 removed outlier: 3.907A pdb=" N THR C 224 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 291 removed outlier: 3.588A pdb=" N LEU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 293 No H-bonds generated for 'chain 'C' and resid 292 through 293' Processing helix chain 'C' and resid 294 through 295 No H-bonds generated for 'chain 'C' and resid 294 through 295' Processing helix chain 'C' and resid 296 through 303 Processing helix chain 'C' and resid 303 through 319 Processing helix chain 'C' and resid 381 through 386 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.937A pdb=" N GLU C 460 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'C' and resid 506 through 521 removed outlier: 3.710A pdb=" N SER C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 519 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 removed outlier: 3.610A pdb=" N ARG C 538 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 562 removed outlier: 3.703A pdb=" N ARG C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 571 Processing helix chain 'D' and resid 3 through 14 removed outlier: 3.684A pdb=" N GLU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 19 removed outlier: 3.604A pdb=" N VAL D 18 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 19 " --> pdb=" O GLN D 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 15 through 19' Processing helix chain 'D' and resid 21 through 54 removed outlier: 3.539A pdb=" N ARG D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 109 removed outlier: 3.602A pdb=" N ILE D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 97 " --> pdb=" O HIS D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 4.028A pdb=" N TRP D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.509A pdb=" N ALA D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 133 through 139 removed outlier: 3.919A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 159 removed outlier: 3.919A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 162 through 185 removed outlier: 3.575A pdb=" N ALA D 166 " --> pdb=" O ASN D 162 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix Proline residue: D 177 - end of helix Processing helix chain 'D' and resid 194 through 201 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 224 through 274 removed outlier: 3.531A pdb=" N PHE D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 311 removed outlier: 3.631A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.947A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.555A pdb=" N GLY D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 329 removed outlier: 3.643A pdb=" N ALA D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 397 removed outlier: 3.638A pdb=" N LEU D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 451 through 462 removed outlier: 3.527A pdb=" N ALA D 462 " --> pdb=" O ALA D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 500 removed outlier: 3.697A pdb=" N ARG D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL D 494 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 532 removed outlier: 3.528A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 572 removed outlier: 3.528A pdb=" N LEU D 570 " --> pdb=" O ARG D 566 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 587 removed outlier: 3.795A pdb=" N GLU D 587 " --> pdb=" O HIS D 583 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 339 through 342 Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419 removed outlier: 6.476A pdb=" N VAL C 496 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL C 529 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 498 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 369 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N THR C 530 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE C 371 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 551 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C 546 " --> pdb=" O GLN C 549 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 370 through 372 Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 366 removed outlier: 6.507A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 379 through 381 removed outlier: 6.157A pdb=" N LEU D 507 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL D 540 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU D 509 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 426 " --> pdb=" O LEU D 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 555 through 557 removed outlier: 7.070A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1476 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: 2.59 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2973 1.34 - 1.45: 1172 1.45 - 1.57: 4986 1.57 - 1.69: 6 1.69 - 1.80: 54 Bond restraints: 9191 Sorted by residual: bond pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 1.795 1.625 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" O3A ANP D 602 " pdb=" PB ANP D 602 " ideal model delta sigma weight residual 1.700 1.594 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" N SER C 476 " pdb=" CA SER C 476 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.25e-02 6.40e+03 7.64e+00 bond pdb=" O5' ANP D 602 " pdb=" PA ANP D 602 " ideal model delta sigma weight residual 1.655 1.600 0.055 2.00e-02 2.50e+03 7.53e+00 bond pdb=" N ARG C 374 " pdb=" CA ARG C 374 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.26e+00 ... (remaining 9186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 12151 1.98 - 3.96: 279 3.96 - 5.93: 49 5.93 - 7.91: 8 7.91 - 9.89: 5 Bond angle restraints: 12492 Sorted by residual: angle pdb=" N GLU C 479 " pdb=" CA GLU C 479 " pdb=" C GLU C 479 " ideal model delta sigma weight residual 112.68 104.06 8.62 1.33e+00 5.65e-01 4.20e+01 angle pdb=" N PRO D 448 " pdb=" CA PRO D 448 " pdb=" CB PRO D 448 " ideal model delta sigma weight residual 103.33 109.86 -6.53 1.10e+00 8.26e-01 3.52e+01 angle pdb=" C ASN C 400 " pdb=" N ASP C 401 " pdb=" CA ASP C 401 " ideal model delta sigma weight residual 121.54 128.48 -6.94 1.91e+00 2.74e-01 1.32e+01 angle pdb=" N ARG D 192 " pdb=" CA ARG D 192 " pdb=" C ARG D 192 " ideal model delta sigma weight residual 112.93 108.18 4.75 1.33e+00 5.65e-01 1.28e+01 angle pdb=" CA LYS C 379 " pdb=" C LYS C 379 " pdb=" O LYS C 379 " ideal model delta sigma weight residual 121.84 117.93 3.91 1.16e+00 7.43e-01 1.13e+01 ... (remaining 12487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.63: 5034 19.63 - 39.26: 394 39.26 - 58.90: 43 58.90 - 78.53: 15 78.53 - 98.16: 12 Dihedral angle restraints: 5498 sinusoidal: 2174 harmonic: 3324 Sorted by residual: dihedral pdb=" CA ARG D 422 " pdb=" C ARG D 422 " pdb=" N LYS D 423 " pdb=" CA LYS D 423 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" O2' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O3' ANP D 602 " ideal model delta sinusoidal sigma weight residual 47.90 -50.26 98.16 1 3.00e+01 1.11e-03 1.22e+01 dihedral pdb=" C1' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O3' ANP D 602 " ideal model delta sinusoidal sigma weight residual 164.59 70.84 93.75 1 3.00e+01 1.11e-03 1.14e+01 ... (remaining 5495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1332 0.077 - 0.155: 111 0.155 - 0.232: 10 0.232 - 0.309: 0 0.309 - 0.386: 1 Chirality restraints: 1454 Sorted by residual: chirality pdb=" C3' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C4' ANP D 602 " pdb=" O3' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.74 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA PRO D 448 " pdb=" N PRO D 448 " pdb=" C PRO D 448 " pdb=" CB PRO D 448 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C4' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" C5' ANP D 602 " pdb=" O4' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.45 -2.65 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1451 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 427 " 0.018 2.00e-02 2.50e+03 2.43e-02 1.47e+01 pdb=" CG TRP D 427 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP D 427 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP D 427 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 427 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP D 427 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 427 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 427 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 427 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 427 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 419 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO C 420 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 178 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO C 179 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " 0.028 5.00e-02 4.00e+02 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 96 2.63 - 3.20: 8284 3.20 - 3.77: 13693 3.77 - 4.33: 19889 4.33 - 4.90: 32580 Nonbonded interactions: 74542 Sorted by model distance: nonbonded pdb=" NE2 GLN D 377 " pdb=" OD2 ASP D 551 " model vdw 2.067 3.120 nonbonded pdb=" OG SER D 417 " pdb=" OG SER D 420 " model vdw 2.122 3.040 nonbonded pdb=" NE1 TRP D 463 " pdb=" OE2 GLU D 526 " model vdw 2.172 3.120 nonbonded pdb=" NE2 GLN C 345 " pdb=" O THR C 347 " model vdw 2.222 3.120 nonbonded pdb=" OG SER D 390 " pdb="MG MG D 601 " model vdw 2.227 2.170 ... (remaining 74537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.220 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.008 0.170 9191 Z= 0.501 Angle : 0.777 9.891 12492 Z= 0.431 Chirality : 0.047 0.386 1454 Planarity : 0.004 0.056 1593 Dihedral : 14.795 98.162 3354 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -3.00 (0.23), residues: 1153 helix: -2.34 (0.17), residues: 685 sheet: -0.75 (0.75), residues: 61 loop : -1.12 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP D 427 HIS 0.005 0.001 HIS C 531 PHE 0.016 0.002 PHE D 66 TYR 0.014 0.002 TYR D 88 ARG 0.008 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: C 12 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8396 (mptt) REVERT: C 545 MET cc_start: 0.7939 (tpt) cc_final: 0.7511 (tpt) REVERT: D 15 GLN cc_start: 0.8232 (tm-30) cc_final: 0.8021 (tp-100) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3403 time to fit residues: 51.6479 Evaluate side-chains 102 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 GLN C 421 GLN C 549 GLN D 115 GLN D 377 GLN D 543 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9191 Z= 0.226 Angle : 0.623 10.335 12492 Z= 0.312 Chirality : 0.041 0.187 1454 Planarity : 0.005 0.054 1593 Dihedral : 7.185 56.739 1293 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.32 % Allowed : 7.30 % Favored : 92.38 % 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: -1.41 (0.24), residues: 1153 helix: -0.72 (0.19), residues: 698 sheet: -0.89 (0.72), residues: 61 loop : -1.02 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 427 HIS 0.003 0.001 HIS C 132 PHE 0.008 0.001 PHE D 327 TYR 0.018 0.001 TYR D 88 ARG 0.005 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.010 Fit side-chains REVERT: C 12 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8369 (mmtt) REVERT: C 545 MET cc_start: 0.7947 (tpt) cc_final: 0.7614 (tpt) outliers start: 3 outliers final: 1 residues processed: 122 average time/residue: 0.2983 time to fit residues: 47.9033 Evaluate side-chains 103 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 549 GLN D 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9191 Z= 0.221 Angle : 0.566 9.628 12492 Z= 0.280 Chirality : 0.040 0.146 1454 Planarity : 0.004 0.049 1593 Dihedral : 5.615 50.369 1293 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.75 % Allowed : 10.84 % Favored : 88.41 % 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: -0.29 (0.25), residues: 1153 helix: 0.42 (0.20), residues: 689 sheet: -1.17 (0.68), residues: 61 loop : -0.96 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 81 HIS 0.003 0.001 HIS C 368 PHE 0.010 0.001 PHE C 181 TYR 0.020 0.001 TYR D 88 ARG 0.006 0.000 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: C 12 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8328 (mmtt) REVERT: C 451 ARG cc_start: 0.8874 (ttm110) cc_final: 0.8369 (mtm-85) REVERT: C 452 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7520 (ttp80) REVERT: C 545 MET cc_start: 0.8058 (tpt) cc_final: 0.7824 (tpt) REVERT: C 549 GLN cc_start: 0.7762 (mp-120) cc_final: 0.7215 (mp10) outliers start: 7 outliers final: 5 residues processed: 118 average time/residue: 0.2645 time to fit residues: 41.2248 Evaluate side-chains 110 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 GLN C 345 GLN D 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9191 Z= 0.242 Angle : 0.555 9.505 12492 Z= 0.274 Chirality : 0.040 0.143 1454 Planarity : 0.004 0.049 1593 Dihedral : 5.096 57.137 1293 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.82 % Allowed : 11.80 % Favored : 86.37 % 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: 0.15 (0.25), residues: 1153 helix: 0.87 (0.20), residues: 690 sheet: -1.28 (0.65), residues: 61 loop : -0.92 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 PHE 0.011 0.001 PHE C 181 TYR 0.021 0.001 TYR D 88 ARG 0.004 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.978 Fit side-chains REVERT: C 12 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8303 (mmtt) REVERT: C 431 ARG cc_start: 0.7638 (mtp-110) cc_final: 0.7226 (mtp85) REVERT: C 451 ARG cc_start: 0.8893 (ttm110) cc_final: 0.8384 (mtm-85) REVERT: C 519 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: C 549 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7218 (mp10) outliers start: 17 outliers final: 9 residues processed: 123 average time/residue: 0.2445 time to fit residues: 40.4219 Evaluate side-chains 116 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 536 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN D 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9191 Z= 0.226 Angle : 0.541 9.496 12492 Z= 0.268 Chirality : 0.040 0.144 1454 Planarity : 0.004 0.047 1593 Dihedral : 4.878 51.931 1293 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.50 % Allowed : 13.30 % Favored : 85.19 % 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: 0.41 (0.25), residues: 1153 helix: 1.12 (0.20), residues: 693 sheet: -1.41 (0.69), residues: 56 loop : -0.89 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 PHE 0.010 0.001 PHE C 181 TYR 0.021 0.001 TYR D 88 ARG 0.004 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: C 12 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8306 (mmtt) REVERT: C 431 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.7240 (mtp85) REVERT: C 451 ARG cc_start: 0.8901 (ttm110) cc_final: 0.8388 (mtm-85) REVERT: C 452 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7498 (ttp80) REVERT: C 519 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7360 (pm20) REVERT: C 549 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: D 350 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8085 (mt) REVERT: D 511 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7473 (mt-10) outliers start: 14 outliers final: 8 residues processed: 119 average time/residue: 0.2470 time to fit residues: 39.4365 Evaluate side-chains 118 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 536 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 HIS D 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9191 Z= 0.288 Angle : 0.558 9.321 12492 Z= 0.277 Chirality : 0.041 0.144 1454 Planarity : 0.004 0.048 1593 Dihedral : 4.840 54.144 1293 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.36 % Allowed : 13.52 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.25), residues: 1153 helix: 1.08 (0.20), residues: 694 sheet: -1.49 (0.67), residues: 56 loop : -0.89 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.011 0.001 PHE C 181 TYR 0.021 0.001 TYR D 88 ARG 0.006 0.000 ARG D 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.033 Fit side-chains REVERT: C 12 LYS cc_start: 0.8717 (ttmt) cc_final: 0.8317 (mmtt) REVERT: C 451 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8399 (mtm-85) REVERT: C 519 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: C 549 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: D 350 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8215 (mt) REVERT: D 427 TRP cc_start: 0.6674 (p-90) cc_final: 0.6327 (p-90) outliers start: 22 outliers final: 11 residues processed: 121 average time/residue: 0.2563 time to fit residues: 41.8060 Evaluate side-chains 120 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 536 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 93 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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: 0.8452 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9191 Z= 0.192 Angle : 0.537 10.114 12492 Z= 0.262 Chirality : 0.039 0.143 1454 Planarity : 0.004 0.044 1593 Dihedral : 4.669 53.274 1293 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.04 % Allowed : 14.70 % Favored : 83.26 % 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: 0.69 (0.25), residues: 1153 helix: 1.43 (0.20), residues: 691 sheet: -2.00 (0.68), residues: 47 loop : -0.86 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 81 HIS 0.003 0.001 HIS D 204 PHE 0.009 0.001 PHE C 181 TYR 0.020 0.001 TYR D 88 ARG 0.005 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: C 12 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8298 (mmtt) REVERT: C 451 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8390 (mtm-85) REVERT: C 452 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7590 (ttp80) REVERT: C 519 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: C 549 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7355 (mp10) REVERT: D 350 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8238 (mt) REVERT: D 427 TRP cc_start: 0.6612 (p-90) cc_final: 0.6313 (p-90) outliers start: 19 outliers final: 10 residues processed: 126 average time/residue: 0.2577 time to fit residues: 43.6137 Evaluate side-chains 120 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 536 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8452 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9191 Z= 0.207 Angle : 0.539 10.229 12492 Z= 0.263 Chirality : 0.039 0.143 1454 Planarity : 0.004 0.047 1593 Dihedral : 4.595 52.953 1293 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.82 % Allowed : 15.24 % Favored : 82.94 % 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: 0.79 (0.25), residues: 1153 helix: 1.53 (0.20), residues: 690 sheet: -2.02 (0.68), residues: 47 loop : -0.84 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 81 HIS 0.003 0.001 HIS D 204 PHE 0.009 0.001 PHE C 181 TYR 0.020 0.001 TYR D 88 ARG 0.005 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.008 Fit side-chains REVERT: C 12 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8289 (mmtt) REVERT: C 431 ARG cc_start: 0.7707 (mtp85) cc_final: 0.7117 (mtp85) REVERT: C 443 ASP cc_start: 0.8023 (t0) cc_final: 0.7365 (t0) REVERT: C 451 ARG cc_start: 0.8849 (ttm110) cc_final: 0.8399 (mtm-85) REVERT: C 519 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7398 (pm20) REVERT: C 549 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: D 350 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8228 (mt) REVERT: D 427 TRP cc_start: 0.6583 (p-90) cc_final: 0.6283 (p-90) outliers start: 17 outliers final: 12 residues processed: 120 average time/residue: 0.2538 time to fit residues: 40.5497 Evaluate side-chains 123 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 536 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0870 chunk 106 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 97 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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: 0.8440 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9191 Z= 0.189 Angle : 0.537 11.228 12492 Z= 0.261 Chirality : 0.039 0.180 1454 Planarity : 0.004 0.044 1593 Dihedral : 4.503 52.448 1293 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.04 % Allowed : 14.91 % Favored : 83.05 % 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: 0.96 (0.25), residues: 1153 helix: 1.66 (0.20), residues: 692 sheet: -1.74 (0.65), residues: 57 loop : -0.78 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.003 0.001 HIS D 204 PHE 0.008 0.001 PHE C 181 TYR 0.019 0.001 TYR D 88 ARG 0.007 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.976 Fit side-chains REVERT: C 12 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8279 (mmtt) REVERT: C 431 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7252 (mtp85) REVERT: C 443 ASP cc_start: 0.7972 (t0) cc_final: 0.7542 (t0) REVERT: C 451 ARG cc_start: 0.8846 (ttm110) cc_final: 0.8366 (mtm-85) REVERT: C 519 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: C 549 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: D 14 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7604 (tptt) REVERT: D 350 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8241 (mt) REVERT: D 423 LYS cc_start: 0.9101 (mptt) cc_final: 0.8765 (mptt) REVERT: D 427 TRP cc_start: 0.6543 (p-90) cc_final: 0.6267 (p-90) outliers start: 19 outliers final: 15 residues processed: 122 average time/residue: 0.2464 time to fit residues: 40.4483 Evaluate side-chains 127 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 536 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 0.0370 chunk 97 optimal weight: 2.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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: 0.8444 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9191 Z= 0.201 Angle : 0.543 11.147 12492 Z= 0.263 Chirality : 0.039 0.174 1454 Planarity : 0.004 0.046 1593 Dihedral : 4.489 52.758 1293 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.93 % Allowed : 15.02 % Favored : 83.05 % 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: 0.97 (0.25), residues: 1153 helix: 1.67 (0.20), residues: 692 sheet: -1.76 (0.64), residues: 57 loop : -0.77 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 81 HIS 0.003 0.001 HIS D 204 PHE 0.008 0.001 PHE C 181 TYR 0.020 0.001 TYR D 88 ARG 0.007 0.000 ARG C 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: C 12 LYS cc_start: 0.8644 (ttmt) cc_final: 0.8276 (mmtt) REVERT: C 431 ARG cc_start: 0.7723 (mtp85) cc_final: 0.7163 (mtp85) REVERT: C 443 ASP cc_start: 0.8015 (t0) cc_final: 0.7236 (t0) REVERT: C 451 ARG cc_start: 0.8829 (ttm110) cc_final: 0.8384 (mtm-85) REVERT: C 519 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7404 (pm20) REVERT: C 549 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: D 14 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7615 (tptt) REVERT: D 350 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8259 (mt) REVERT: D 427 TRP cc_start: 0.6585 (p-90) cc_final: 0.6302 (p-90) outliers start: 18 outliers final: 14 residues processed: 123 average time/residue: 0.2476 time to fit residues: 40.8765 Evaluate side-chains 126 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 536 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.100503 restraints weight = 10312.214| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.68 r_work: 0.2807 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9191 Z= 0.192 Angle : 0.538 11.183 12492 Z= 0.261 Chirality : 0.039 0.163 1454 Planarity : 0.003 0.044 1593 Dihedral : 4.446 52.700 1293 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.82 % Allowed : 15.24 % Favored : 82.94 % 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: 1.05 (0.25), residues: 1153 helix: 1.74 (0.20), residues: 692 sheet: -1.63 (0.66), residues: 57 loop : -0.77 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.003 0.001 HIS D 204 PHE 0.008 0.001 PHE C 291 TYR 0.020 0.001 TYR D 88 ARG 0.004 0.000 ARG C 452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.03 seconds wall clock time: 38 minutes 5.55 seconds (2285.55 seconds total)