Starting phenix.real_space_refine on Sat Nov 16 14:35:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbe_36143/11_2024/8jbe_36143.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbe_36143/11_2024/8jbe_36143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbe_36143/11_2024/8jbe_36143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbe_36143/11_2024/8jbe_36143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbe_36143/11_2024/8jbe_36143.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbe_36143/11_2024/8jbe_36143.cif" } resolution = 3.25 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= 0.024 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 7240 2.51 5 N 1923 2.21 5 O 2042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11260 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4674 Classifications: {'peptide': 591} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 566} Chain breaks: 3 Chain: "B" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3206 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 375} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3380 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 404} Time building chain proxies: 6.49, per 1000 atoms: 0.58 Number of scatterers: 11260 At special positions: 0 Unit cell: (68.85, 120.7, 188.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2042 8.00 N 1923 7.00 C 7240 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: 2.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2684 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 13 sheets defined 39.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.573A pdb=" N ALA A 45 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.572A pdb=" N ILE A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.727A pdb=" N LEU A 359 " --> pdb=" O CYS A 355 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 374 Processing helix chain 'A' and resid 380 through 392 removed outlier: 3.509A pdb=" N LYS A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 427 removed outlier: 3.611A pdb=" N LYS A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 415 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.652A pdb=" N MET A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.710A pdb=" N ILE A 468 " --> pdb=" O TYR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 498 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.978A pdb=" N HIS A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 544 removed outlier: 3.666A pdb=" N ILE A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.682A pdb=" N ILE A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.561A pdb=" N ASN A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.665A pdb=" N THR A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 610 Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 42 through 61 Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.841A pdb=" N CYS B 69 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 137 removed outlier: 4.028A pdb=" N TYR B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 157 removed outlier: 3.546A pdb=" N LEU B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 230 through 245 Processing helix chain 'B' and resid 332 through 361 removed outlier: 3.747A pdb=" N TYR B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Proline residue: B 345 - end of helix Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.553A pdb=" N ALA B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 477 Processing helix chain 'C' and resid 139 through 155 Processing helix chain 'C' and resid 189 through 208 removed outlier: 3.607A pdb=" N LEU C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 232 through 242 removed outlier: 3.971A pdb=" N PHE C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.549A pdb=" N THR C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 282 Processing helix chain 'C' and resid 311 through 325 Processing helix chain 'C' and resid 373 through 390 removed outlier: 3.723A pdb=" N SER C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 402 removed outlier: 3.792A pdb=" N ALA C 395 " --> pdb=" O HIS C 391 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 414 Processing helix chain 'C' and resid 443 through 461 Processing helix chain 'C' and resid 498 through 516 removed outlier: 3.875A pdb=" N VAL C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 521 removed outlier: 4.018A pdb=" N TYR C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.530A pdb=" N ILE A 17 " --> pdb=" O MET A 349 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 349 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 341 " --> pdb=" O TRP A 350 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 334 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 124 removed outlier: 6.410A pdb=" N GLU A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 137 through 142 removed outlier: 7.361A pdb=" N VAL A 138 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 158 through 162 removed outlier: 4.122A pdb=" N TRP A 160 " --> pdb=" O CYS A 173 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 191 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 210 through 215 removed outlier: 8.259A pdb=" N MET A 233 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ARG A 254 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 235 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL A 252 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL A 237 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 250 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 296 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 261 through 266 Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.319A pdb=" N ILE B 17 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR B 36 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B 15 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 12 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN B 95 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 14 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 80 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 78 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR B 77 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS C 164 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N THR C 161 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 179 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 130 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 186 through 187 removed outlier: 6.127A pdb=" N ILE B 186 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR B 393 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN B 390 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN B 385 " --> pdb=" O GLN B 390 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 445 " --> pdb=" O GLU B 429 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 429 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU B 430 " --> pdb=" O GLU C 472 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU C 472 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN B 432 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE C 470 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS B 434 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS C 468 " --> pdb=" O ALA C 483 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 470 " --> pdb=" O ALA C 481 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU C 488 " --> pdb=" O TYR C 423 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR C 423 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR C 490 " --> pdb=" O PHE C 421 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE C 421 " --> pdb=" O TYR C 490 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE C 492 " --> pdb=" O ARG C 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 225 removed outlier: 8.214A pdb=" N ILE B 212 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASN B 325 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 214 " --> pdb=" O PHE B 323 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 261 through 262 removed outlier: 6.512A pdb=" N ILE C 261 " --> pdb=" O LEU C 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 333 through 337 removed outlier: 3.784A pdb=" N PHE C 290 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL C 289 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG C 304 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA C 291 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU C 302 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU C 293 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N ALA C 526 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU C 302 " --> pdb=" O ALA C 526 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1455 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: 3.86 Time building geometry restraints manager: 3.02 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: 3626 1.34 - 1.46: 1588 1.46 - 1.57: 6190 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 11484 Sorted by residual: bond pdb=" CA GLU A 137 " pdb=" C GLU A 137 " ideal model delta sigma weight residual 1.530 1.502 0.028 9.10e-03 1.21e+04 9.39e+00 bond pdb=" CA GLU A 137 " pdb=" CB GLU A 137 " ideal model delta sigma weight residual 1.542 1.521 0.022 8.90e-03 1.26e+04 5.89e+00 bond pdb=" CA ASN A 133 " pdb=" C ASN A 133 " ideal model delta sigma weight residual 1.524 1.502 0.022 1.24e-02 6.50e+03 3.14e+00 bond pdb=" C ASN A 133 " pdb=" O ASN A 133 " ideal model delta sigma weight residual 1.236 1.220 0.017 1.15e-02 7.56e+03 2.11e+00 bond pdb=" CA THR A 134 " pdb=" C THR A 134 " ideal model delta sigma weight residual 1.523 1.505 0.018 1.34e-02 5.57e+03 1.76e+00 ... (remaining 11479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 15257 1.82 - 3.63: 243 3.63 - 5.45: 26 5.45 - 7.26: 6 7.26 - 9.08: 2 Bond angle restraints: 15534 Sorted by residual: angle pdb=" C VAL A 138 " pdb=" N TYR A 139 " pdb=" CA TYR A 139 " ideal model delta sigma weight residual 123.03 115.04 7.99 1.79e+00 3.12e-01 1.99e+01 angle pdb=" C GLU A 137 " pdb=" CA GLU A 137 " pdb=" CB GLU A 137 " ideal model delta sigma weight residual 114.87 109.18 5.69 1.51e+00 4.39e-01 1.42e+01 angle pdb=" CA GLU B 9 " pdb=" CB GLU B 9 " pdb=" CG GLU B 9 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.20e+01 angle pdb=" N LYS A 152 " pdb=" CA LYS A 152 " pdb=" C LYS A 152 " ideal model delta sigma weight residual 108.19 111.89 -3.70 1.29e+00 6.01e-01 8.23e+00 angle pdb=" N GLN B 158 " pdb=" CA GLN B 158 " pdb=" C GLN B 158 " ideal model delta sigma weight residual 113.21 110.06 3.15 1.15e+00 7.56e-01 7.49e+00 ... (remaining 15529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6267 17.54 - 35.09: 539 35.09 - 52.63: 117 52.63 - 70.18: 14 70.18 - 87.72: 13 Dihedral angle restraints: 6950 sinusoidal: 2829 harmonic: 4121 Sorted by residual: dihedral pdb=" CA GLN B 158 " pdb=" C GLN B 158 " pdb=" N LYS B 159 " pdb=" CA LYS B 159 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA HIS A 526 " pdb=" C HIS A 526 " pdb=" N SER A 527 " pdb=" CA SER A 527 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA MET A 65 " pdb=" C MET A 65 " pdb=" N SER A 66 " pdb=" CA SER A 66 " ideal model delta harmonic sigma weight residual 180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 6947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1198 0.037 - 0.074: 420 0.074 - 0.111: 131 0.111 - 0.149: 34 0.149 - 0.186: 3 Chirality restraints: 1786 Sorted by residual: chirality pdb=" CA GLU B 9 " pdb=" N GLU B 9 " pdb=" C GLU B 9 " pdb=" CB GLU B 9 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CG LEU B 72 " pdb=" CB LEU B 72 " pdb=" CD1 LEU B 72 " pdb=" CD2 LEU B 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA ILE B 17 " pdb=" N ILE B 17 " pdb=" C ILE B 17 " pdb=" CB ILE B 17 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 1783 not shown) Planarity restraints: 1965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 127 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO C 128 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 128 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 128 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 181 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.70e+00 pdb=" N PRO A 182 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 414 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C TYR A 414 " -0.027 2.00e-02 2.50e+03 pdb=" O TYR A 414 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 415 " 0.009 2.00e-02 2.50e+03 ... (remaining 1962 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1153 2.75 - 3.29: 10560 3.29 - 3.82: 17238 3.82 - 4.36: 19532 4.36 - 4.90: 35942 Nonbonded interactions: 84425 Sorted by model distance: nonbonded pdb=" O LEU A 524 " pdb=" OG SER A 527 " model vdw 2.209 3.040 nonbonded pdb=" O PHE C 264 " pdb=" NH2 ARG C 271 " model vdw 2.225 3.120 nonbonded pdb=" OE2 GLU C 488 " pdb=" OH TYR C 490 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR B 36 " pdb=" OD2 ASP B 49 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 9 " pdb=" O SER A 280 " model vdw 2.252 3.040 ... (remaining 84420 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: 7.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 2.970 Set scattering table: 0.000 Process input model: 24.400 Find NCS groups from input model: 0.150 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11484 Z= 0.222 Angle : 0.577 9.079 15534 Z= 0.316 Chirality : 0.043 0.186 1786 Planarity : 0.004 0.041 1965 Dihedral : 14.009 87.723 4266 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.69 % Favored : 93.88 % Rotamer: Outliers : 0.40 % Allowed : 0.40 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.14 (0.24), residues: 1372 helix: 1.47 (0.24), residues: 525 sheet: -0.39 (0.32), residues: 303 loop : -1.48 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 350 HIS 0.005 0.001 HIS B 391 PHE 0.019 0.001 PHE A 63 TYR 0.017 0.001 TYR C 453 ARG 0.003 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8442 (mp) cc_final: 0.8222 (mp) REVERT: A 240 LEU cc_start: 0.8181 (mt) cc_final: 0.7963 (tt) REVERT: B 277 ARG cc_start: 0.6210 (mmt-90) cc_final: 0.3430 (mmm160) outliers start: 5 outliers final: 2 residues processed: 128 average time/residue: 0.2472 time to fit residues: 45.6036 Evaluate side-chains 98 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 154 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 0.0370 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN C 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11484 Z= 0.263 Angle : 0.576 8.235 15534 Z= 0.306 Chirality : 0.045 0.177 1786 Planarity : 0.004 0.050 1965 Dihedral : 4.746 49.366 1512 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.39 % Favored : 94.31 % Rotamer: Outliers : 0.71 % Allowed : 6.04 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.24), residues: 1372 helix: 1.54 (0.24), residues: 529 sheet: -0.28 (0.31), residues: 318 loop : -1.41 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 350 HIS 0.004 0.001 HIS A 8 PHE 0.014 0.002 PHE C 264 TYR 0.013 0.002 TYR B 16 ARG 0.004 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: A 240 LEU cc_start: 0.8223 (mt) cc_final: 0.7985 (tt) REVERT: A 350 TRP cc_start: 0.8588 (m-90) cc_final: 0.8338 (m-90) REVERT: B 277 ARG cc_start: 0.6201 (mmt-90) cc_final: 0.3408 (mmm160) REVERT: C 311 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.7350 (m90) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.2648 time to fit residues: 38.7334 Evaluate side-chains 95 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 311 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11484 Z= 0.198 Angle : 0.526 7.572 15534 Z= 0.280 Chirality : 0.043 0.160 1786 Planarity : 0.004 0.042 1965 Dihedral : 4.574 45.444 1512 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.25 % Favored : 94.46 % Rotamer: Outliers : 0.79 % Allowed : 8.58 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1372 helix: 1.69 (0.24), residues: 529 sheet: -0.11 (0.32), residues: 313 loop : -1.33 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 350 HIS 0.005 0.001 HIS A 8 PHE 0.012 0.001 PHE C 264 TYR 0.016 0.001 TYR A 609 ARG 0.005 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: A 350 TRP cc_start: 0.8614 (m-90) cc_final: 0.8198 (m-90) REVERT: A 417 TRP cc_start: 0.5745 (p-90) cc_final: 0.5458 (p-90) REVERT: B 153 ARG cc_start: 0.5835 (tpp-160) cc_final: 0.5630 (tpp-160) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.2625 time to fit residues: 37.8980 Evaluate side-chains 91 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 311 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN C 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11484 Z= 0.271 Angle : 0.562 7.973 15534 Z= 0.295 Chirality : 0.045 0.270 1786 Planarity : 0.004 0.042 1965 Dihedral : 4.572 43.127 1512 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.76 % Favored : 93.95 % Rotamer: Outliers : 1.19 % Allowed : 10.72 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1372 helix: 1.59 (0.24), residues: 528 sheet: -0.05 (0.32), residues: 314 loop : -1.30 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 350 HIS 0.004 0.001 HIS B 73 PHE 0.014 0.002 PHE C 170 TYR 0.017 0.002 TYR A 609 ARG 0.005 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 350 TRP cc_start: 0.8671 (m-90) cc_final: 0.8175 (m-90) REVERT: A 417 TRP cc_start: 0.6118 (p-90) cc_final: 0.5850 (p-90) outliers start: 15 outliers final: 9 residues processed: 100 average time/residue: 0.2598 time to fit residues: 37.5894 Evaluate side-chains 92 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 311 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.0010 chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 118 HIS A 214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11484 Z= 0.311 Angle : 0.579 7.972 15534 Z= 0.305 Chirality : 0.045 0.254 1786 Planarity : 0.004 0.039 1965 Dihedral : 4.626 41.712 1512 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.27 % Favored : 93.51 % Rotamer: Outliers : 1.59 % Allowed : 12.15 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1372 helix: 1.49 (0.24), residues: 528 sheet: -0.08 (0.32), residues: 313 loop : -1.31 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 350 HIS 0.004 0.001 HIS C 164 PHE 0.015 0.002 PHE C 170 TYR 0.019 0.002 TYR A 609 ARG 0.003 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8910 (mm) cc_final: 0.8613 (tp) REVERT: A 350 TRP cc_start: 0.8679 (m-90) cc_final: 0.8103 (m-90) REVERT: C 401 GLN cc_start: 0.7457 (mm-40) cc_final: 0.6881 (mp10) outliers start: 20 outliers final: 11 residues processed: 102 average time/residue: 0.2689 time to fit residues: 39.7290 Evaluate side-chains 97 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 289 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11484 Z= 0.175 Angle : 0.504 8.271 15534 Z= 0.268 Chirality : 0.043 0.249 1786 Planarity : 0.003 0.039 1965 Dihedral : 4.274 41.585 1510 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 1.51 % Allowed : 12.79 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.33 (0.24), residues: 1372 helix: 1.72 (0.24), residues: 530 sheet: -0.02 (0.31), residues: 319 loop : -1.20 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 350 HIS 0.003 0.001 HIS B 30 PHE 0.016 0.001 PHE C 328 TYR 0.021 0.001 TYR A 609 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8913 (mm) cc_final: 0.8657 (tp) REVERT: A 77 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6727 (t80) REVERT: A 95 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.5745 (t80) REVERT: A 350 TRP cc_start: 0.8691 (m-90) cc_final: 0.8084 (m-90) REVERT: C 401 GLN cc_start: 0.7395 (mm-40) cc_final: 0.6824 (mp10) outliers start: 19 outliers final: 10 residues processed: 101 average time/residue: 0.2262 time to fit residues: 34.1434 Evaluate side-chains 95 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 454 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11484 Z= 0.312 Angle : 0.577 8.087 15534 Z= 0.304 Chirality : 0.045 0.227 1786 Planarity : 0.004 0.038 1965 Dihedral : 4.404 40.150 1510 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.05 % Favored : 93.80 % Rotamer: Outliers : 1.51 % Allowed : 13.66 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.13 (0.24), residues: 1372 helix: 1.48 (0.24), residues: 533 sheet: -0.07 (0.31), residues: 321 loop : -1.26 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 350 HIS 0.004 0.001 HIS C 164 PHE 0.020 0.002 PHE C 328 TYR 0.023 0.002 TYR A 609 ARG 0.003 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8863 (mm) cc_final: 0.8587 (tp) REVERT: A 77 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6836 (t80) REVERT: A 95 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.5720 (t80) REVERT: A 350 TRP cc_start: 0.8680 (m-90) cc_final: 0.8019 (m-90) REVERT: C 401 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7000 (mp10) outliers start: 19 outliers final: 12 residues processed: 99 average time/residue: 0.2326 time to fit residues: 34.3426 Evaluate side-chains 97 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 479 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11484 Z= 0.191 Angle : 0.522 8.138 15534 Z= 0.277 Chirality : 0.043 0.199 1786 Planarity : 0.003 0.037 1965 Dihedral : 4.264 39.221 1510 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.10 % Favored : 94.75 % Rotamer: Outliers : 1.67 % Allowed : 13.74 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.34 (0.24), residues: 1372 helix: 1.72 (0.24), residues: 530 sheet: 0.04 (0.31), residues: 321 loop : -1.21 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 350 HIS 0.003 0.001 HIS B 30 PHE 0.014 0.001 PHE C 328 TYR 0.023 0.001 TYR A 609 ARG 0.003 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8834 (mm) cc_final: 0.8567 (tp) REVERT: A 77 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6834 (t80) REVERT: A 95 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.5789 (t80) REVERT: A 350 TRP cc_start: 0.8652 (m-90) cc_final: 0.8010 (m-90) REVERT: C 401 GLN cc_start: 0.7471 (mm-40) cc_final: 0.6935 (mp10) REVERT: C 473 MET cc_start: 0.8006 (ttm) cc_final: 0.7648 (ttp) outliers start: 21 outliers final: 15 residues processed: 101 average time/residue: 0.2358 time to fit residues: 35.4148 Evaluate side-chains 96 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 479 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11484 Z= 0.184 Angle : 0.534 9.341 15534 Z= 0.280 Chirality : 0.043 0.190 1786 Planarity : 0.003 0.037 1965 Dihedral : 4.203 38.801 1510 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.61 % Favored : 94.17 % Rotamer: Outliers : 1.67 % Allowed : 13.66 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.43 (0.24), residues: 1372 helix: 1.79 (0.24), residues: 530 sheet: 0.08 (0.31), residues: 322 loop : -1.17 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 350 HIS 0.004 0.001 HIS B 30 PHE 0.013 0.001 PHE C 328 TYR 0.025 0.001 TYR A 609 ARG 0.003 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8808 (mm) cc_final: 0.8533 (tp) REVERT: A 77 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6814 (t80) REVERT: A 95 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.5805 (t80) REVERT: A 257 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7054 (mp) REVERT: A 350 TRP cc_start: 0.8640 (m-90) cc_final: 0.8006 (m-90) REVERT: C 473 MET cc_start: 0.8053 (ttm) cc_final: 0.7692 (ttp) outliers start: 21 outliers final: 13 residues processed: 98 average time/residue: 0.2336 time to fit residues: 34.4032 Evaluate side-chains 94 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11484 Z= 0.179 Angle : 0.537 9.818 15534 Z= 0.281 Chirality : 0.043 0.204 1786 Planarity : 0.003 0.037 1965 Dihedral : 4.155 39.196 1510 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.39 % Favored : 94.39 % Rotamer: Outliers : 1.51 % Allowed : 13.98 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.48 (0.24), residues: 1372 helix: 1.84 (0.24), residues: 530 sheet: 0.13 (0.31), residues: 322 loop : -1.16 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 350 HIS 0.004 0.001 HIS B 30 PHE 0.012 0.001 PHE C 328 TYR 0.025 0.001 TYR A 609 ARG 0.003 0.000 ARG B 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8762 (mm) cc_final: 0.8489 (tp) REVERT: A 77 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6804 (t80) REVERT: A 95 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.5809 (t80) REVERT: A 257 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7125 (mp) REVERT: A 350 TRP cc_start: 0.8640 (m-90) cc_final: 0.8014 (m-90) REVERT: B 161 LEU cc_start: 0.8464 (tp) cc_final: 0.7912 (pp) REVERT: C 323 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7023 (tm-30) REVERT: C 401 GLN cc_start: 0.7341 (mm-40) cc_final: 0.6779 (mp10) REVERT: C 473 MET cc_start: 0.8011 (ttm) cc_final: 0.7669 (ttp) outliers start: 19 outliers final: 16 residues processed: 95 average time/residue: 0.2571 time to fit residues: 36.7000 Evaluate side-chains 98 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS C 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.144143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.110516 restraints weight = 16876.011| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.48 r_work: 0.3267 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11484 Z= 0.246 Angle : 0.554 9.932 15534 Z= 0.289 Chirality : 0.044 0.191 1786 Planarity : 0.004 0.038 1965 Dihedral : 4.212 39.355 1510 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.17 % Rotamer: Outliers : 1.59 % Allowed : 13.90 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.24), residues: 1372 helix: 1.72 (0.24), residues: 530 sheet: 0.06 (0.31), residues: 328 loop : -1.12 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 350 HIS 0.008 0.001 HIS A 8 PHE 0.013 0.001 PHE C 264 TYR 0.022 0.002 TYR B 342 ARG 0.003 0.000 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.58 seconds wall clock time: 42 minutes 48.81 seconds (2568.81 seconds total)