Starting phenix.real_space_refine on Wed May 14 02:52:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbe_36143/05_2025/8jbe_36143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbe_36143/05_2025/8jbe_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/cci-nas-00/data/ceres_data/8jbe_36143/05_2025/8jbe_36143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbe_36143/05_2025/8jbe_36143.map" model { file = "/net/cci-nas-00/data/ceres_data/8jbe_36143/05_2025/8jbe_36143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbe_36143/05_2025/8jbe_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-5687/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: 7.06, per 1000 atoms: 0.63 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: 2.48 Conformation dependent library (CDL) restraints added in 1.4 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: 1.29 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: 3.34 Time building geometry restraints manager: 2.95 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: 3.900 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 26.750 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.050 ------------------------------------------------------------------------------- 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= 0.159 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 Details of bonding type rmsd hydrogen bonds : bond 0.19022 ( 510) hydrogen bonds : angle 6.43450 ( 1455) covalent geometry : bond 0.00341 (11484) covalent geometry : angle 0.57704 (15534) *********************** 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 : 1.254 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: 0.2299 time to fit residues: 42.5255 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 : 1.312 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.144722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.110907 restraints weight = 16797.800| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.34 r_work: 0.3277 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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= 0.168 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 Details of bonding type rmsd hydrogen bonds : bond 0.05285 ( 510) hydrogen bonds : angle 4.82102 ( 1455) covalent geometry : bond 0.00407 (11484) covalent geometry : angle 0.57578 (15534) *********************** 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 : 1.308 Fit side-chains revert: symmetry clash REVERT: A 240 LEU cc_start: 0.8113 (mt) cc_final: 0.7898 (tt) REVERT: A 350 TRP cc_start: 0.8498 (m-90) cc_final: 0.8222 (m-90) REVERT: B 277 ARG cc_start: 0.6388 (mmt-90) cc_final: 0.3438 (mmm160) REVERT: C 311 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7445 (m90) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.2447 time to fit residues: 35.9036 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 : 1.190 ------------------------------------------------------------------------------- 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 78 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 0.0070 overall best weight: 1.3404 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.144333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109889 restraints weight = 17001.658| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.72 r_work: 0.3273 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11484 Z= 0.159 Angle : 0.555 7.618 15534 Z= 0.294 Chirality : 0.044 0.165 1786 Planarity : 0.004 0.041 1965 Dihedral : 4.659 45.806 1512 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.76 % Favored : 93.95 % Rotamer: Outliers : 0.79 % Allowed : 8.98 % Favored : 90.23 % 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: 1.57 (0.24), residues: 529 sheet: -0.14 (0.32), residues: 314 loop : -1.36 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 350 HIS 0.006 0.001 HIS A 8 PHE 0.014 0.001 PHE C 170 TYR 0.017 0.002 TYR B 439 ARG 0.005 0.000 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 510) hydrogen bonds : angle 4.54297 ( 1455) covalent geometry : bond 0.00387 (11484) covalent geometry : angle 0.55456 (15534) *********************** 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 103 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 350 TRP cc_start: 0.8536 (m-90) cc_final: 0.8094 (m-90) REVERT: A 417 TRP cc_start: 0.6279 (p-90) cc_final: 0.5901 (p-90) REVERT: B 153 ARG cc_start: 0.6330 (tpp-160) cc_final: 0.6113 (tpp-160) outliers start: 10 outliers final: 6 residues processed: 100 average time/residue: 0.2459 time to fit residues: 35.6435 Evaluate side-chains 93 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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: 2.9990 chunk 108 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 chunk 105 optimal weight: 5.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN B 30 HIS C 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.141847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107526 restraints weight = 16841.026| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.55 r_work: 0.3225 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11484 Z= 0.219 Angle : 0.614 8.323 15534 Z= 0.322 Chirality : 0.046 0.267 1786 Planarity : 0.004 0.041 1965 Dihedral : 4.774 44.249 1512 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.34 % Favored : 93.37 % Rotamer: Outliers : 1.27 % Allowed : 11.83 % Favored : 86.89 % 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: -0.02 (0.24), residues: 1372 helix: 1.38 (0.24), residues: 528 sheet: -0.13 (0.32), residues: 314 loop : -1.35 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 350 HIS 0.005 0.001 HIS B 73 PHE 0.017 0.002 PHE C 170 TYR 0.019 0.002 TYR A 609 ARG 0.005 0.000 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.05674 ( 510) hydrogen bonds : angle 4.55254 ( 1455) covalent geometry : bond 0.00543 (11484) covalent geometry : angle 0.61443 (15534) *********************** 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 111 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 350 TRP cc_start: 0.8582 (m-90) cc_final: 0.7966 (m-90) REVERT: B 9 GLU cc_start: 0.7128 (pm20) cc_final: 0.6923 (pm20) REVERT: C 401 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7247 (mp10) outliers start: 16 outliers final: 9 residues processed: 106 average time/residue: 0.2510 time to fit residues: 38.1998 Evaluate side-chains 96 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 214 GLN 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 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 44 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 117 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 109 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 118 HIS A 214 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.144474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.110652 restraints weight = 16868.757| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.44 r_work: 0.3276 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1694 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= 0.119 Angle : 0.524 8.189 15534 Z= 0.278 Chirality : 0.043 0.255 1786 Planarity : 0.004 0.040 1965 Dihedral : 4.409 42.201 1510 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.32 % Favored : 94.46 % Rotamer: Outliers : 1.43 % Allowed : 12.79 % Favored : 85.78 % 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: 0.25 (0.24), residues: 1372 helix: 1.68 (0.24), residues: 525 sheet: -0.03 (0.32), residues: 313 loop : -1.25 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 350 HIS 0.005 0.001 HIS C 311 PHE 0.020 0.001 PHE C 328 TYR 0.019 0.001 TYR A 609 ARG 0.003 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 510) hydrogen bonds : angle 4.31352 ( 1455) covalent geometry : bond 0.00277 (11484) covalent geometry : angle 0.52436 (15534) *********************** 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 109 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8989 (mm) cc_final: 0.8695 (tp) REVERT: A 95 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.5537 (t80) REVERT: A 350 TRP cc_start: 0.8618 (m-90) cc_final: 0.7996 (m-90) REVERT: B 10 ILE cc_start: 0.8609 (mp) cc_final: 0.8400 (mt) REVERT: C 152 PHE cc_start: 0.7842 (t80) cc_final: 0.7518 (t80) REVERT: C 311 HIS cc_start: 0.7608 (OUTLIER) cc_final: 0.7181 (m90) REVERT: C 401 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7224 (mp10) outliers start: 18 outliers final: 9 residues processed: 106 average time/residue: 0.2210 time to fit residues: 34.3763 Evaluate side-chains 100 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 137 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 137 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN B 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.140255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107230 restraints weight = 16816.667| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.37 r_work: 0.3223 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11484 Z= 0.236 Angle : 0.622 8.228 15534 Z= 0.326 Chirality : 0.047 0.304 1786 Planarity : 0.004 0.040 1965 Dihedral : 4.629 43.449 1510 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.56 % Favored : 93.22 % Rotamer: Outliers : 2.07 % Allowed : 13.34 % 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: -0.04 (0.24), residues: 1372 helix: 1.36 (0.24), residues: 528 sheet: -0.08 (0.32), residues: 314 loop : -1.39 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 350 HIS 0.005 0.001 HIS C 164 PHE 0.018 0.002 PHE A 601 TYR 0.021 0.002 TYR A 609 ARG 0.004 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.05794 ( 510) hydrogen bonds : angle 4.50904 ( 1455) covalent geometry : bond 0.00586 (11484) covalent geometry : angle 0.62172 (15534) *********************** 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 116 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8957 (mm) cc_final: 0.8641 (tp) REVERT: A 77 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6531 (t80) REVERT: A 95 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.5621 (t80) REVERT: A 350 TRP cc_start: 0.8595 (m-90) cc_final: 0.7942 (m-90) REVERT: C 344 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8066 (ttp) REVERT: C 401 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7390 (mp10) outliers start: 26 outliers final: 13 residues processed: 109 average time/residue: 0.2145 time to fit residues: 34.8622 Evaluate side-chains 102 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 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 B residue 60 THR Chi-restraints excluded: chain B residue 481 VAL 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 344 MET Chi-restraints excluded: chain C residue 479 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 137 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.144635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.110502 restraints weight = 17081.539| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.58 r_work: 0.3271 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11484 Z= 0.112 Angle : 0.516 8.071 15534 Z= 0.275 Chirality : 0.043 0.223 1786 Planarity : 0.003 0.037 1965 Dihedral : 4.362 43.741 1510 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.88 % Favored : 94.97 % Rotamer: Outliers : 1.91 % Allowed : 14.06 % Favored : 84.03 % 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: 0.23 (0.24), residues: 1372 helix: 1.67 (0.24), residues: 530 sheet: -0.11 (0.31), residues: 321 loop : -1.25 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 417 HIS 0.003 0.001 HIS B 391 PHE 0.024 0.001 PHE C 328 TYR 0.023 0.001 TYR A 609 ARG 0.004 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 510) hydrogen bonds : angle 4.20527 ( 1455) covalent geometry : bond 0.00257 (11484) covalent geometry : angle 0.51575 (15534) *********************** 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 112 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8945 (mm) cc_final: 0.8646 (tp) REVERT: A 77 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6466 (t80) REVERT: A 95 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.5628 (t80) REVERT: A 350 TRP cc_start: 0.8589 (m-90) cc_final: 0.7914 (m-90) REVERT: C 152 PHE cc_start: 0.7816 (t80) cc_final: 0.7329 (t80) REVERT: C 344 MET cc_start: 0.8191 (ttp) cc_final: 0.7911 (ttp) REVERT: C 398 GLU cc_start: 0.8705 (tp30) cc_final: 0.8450 (tp30) REVERT: C 401 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7287 (mp10) outliers start: 24 outliers final: 14 residues processed: 107 average time/residue: 0.2176 time to fit residues: 34.4993 Evaluate side-chains 100 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 444 ILE Chi-restraints excluded: chain B residue 60 THR 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 289 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 502 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 133 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 112 optimal weight: 0.0270 chunk 6 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.144000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.110289 restraints weight = 16978.854| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.43 r_work: 0.3268 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11484 Z= 0.138 Angle : 0.549 10.622 15534 Z= 0.286 Chirality : 0.043 0.213 1786 Planarity : 0.004 0.039 1965 Dihedral : 4.343 44.163 1510 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.98 % Favored : 93.88 % Rotamer: Outliers : 2.07 % Allowed : 13.90 % Favored : 84.03 % 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: 0.25 (0.24), residues: 1372 helix: 1.70 (0.24), residues: 530 sheet: -0.08 (0.31), residues: 322 loop : -1.27 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 417 HIS 0.003 0.001 HIS A 8 PHE 0.016 0.001 PHE C 328 TYR 0.025 0.001 TYR A 609 ARG 0.004 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 510) hydrogen bonds : angle 4.19213 ( 1455) covalent geometry : bond 0.00330 (11484) covalent geometry : angle 0.54905 (15534) *********************** 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 111 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8913 (mm) cc_final: 0.8624 (tp) REVERT: A 77 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6536 (t80) REVERT: A 95 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.5679 (t80) REVERT: A 257 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7174 (mp) REVERT: A 350 TRP cc_start: 0.8570 (m-90) cc_final: 0.7883 (m-90) REVERT: C 152 PHE cc_start: 0.7801 (t80) cc_final: 0.7428 (t80) REVERT: C 344 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7923 (ttp) REVERT: C 398 GLU cc_start: 0.8675 (tp30) cc_final: 0.8438 (tp30) REVERT: C 473 MET cc_start: 0.8604 (ttm) cc_final: 0.8271 (ttp) outliers start: 26 outliers final: 14 residues processed: 104 average time/residue: 0.2052 time to fit residues: 32.4109 Evaluate side-chains 101 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 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 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 344 MET Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 502 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 121 optimal weight: 0.0670 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.144386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.110354 restraints weight = 16928.334| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.54 r_work: 0.3272 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11484 Z= 0.131 Angle : 0.542 9.945 15534 Z= 0.283 Chirality : 0.043 0.206 1786 Planarity : 0.003 0.038 1965 Dihedral : 4.300 44.312 1510 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 1.51 % Allowed : 14.61 % Favored : 83.88 % 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: 0.31 (0.24), residues: 1372 helix: 1.74 (0.24), residues: 530 sheet: -0.03 (0.31), residues: 322 loop : -1.24 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 417 HIS 0.003 0.001 HIS A 8 PHE 0.014 0.001 PHE C 328 TYR 0.026 0.001 TYR A 609 ARG 0.003 0.000 ARG A 461 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 510) hydrogen bonds : angle 4.15041 ( 1455) covalent geometry : bond 0.00314 (11484) covalent geometry : angle 0.54243 (15534) *********************** 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: 19 poor density : 84 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8877 (mm) cc_final: 0.8593 (tp) REVERT: A 18 ARG cc_start: 0.7993 (tpp80) cc_final: 0.7483 (mmm-85) REVERT: A 77 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6550 (t80) REVERT: A 95 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.5651 (t80) REVERT: A 257 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7215 (mp) REVERT: A 350 TRP cc_start: 0.8561 (m-90) cc_final: 0.7872 (m-90) REVERT: B 161 LEU cc_start: 0.8752 (tp) cc_final: 0.8145 (pp) REVERT: B 229 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8551 (mp) REVERT: C 152 PHE cc_start: 0.7812 (t80) cc_final: 0.7463 (t80) REVERT: C 344 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7886 (ttp) REVERT: C 398 GLU cc_start: 0.8659 (tp30) cc_final: 0.8436 (tp30) REVERT: C 401 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7188 (mp10) REVERT: C 473 MET cc_start: 0.8577 (ttm) cc_final: 0.8263 (ttp) outliers start: 19 outliers final: 13 residues processed: 99 average time/residue: 0.2354 time to fit residues: 35.0030 Evaluate side-chains 101 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 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 186 ILE Chi-restraints excluded: chain B residue 229 LEU 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 311 HIS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 502 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 99 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 overall best weight: 0.9778 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.144617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.111069 restraints weight = 16883.740| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.44 r_work: 0.3276 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2104 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= 0.129 Angle : 0.534 9.696 15534 Z= 0.278 Chirality : 0.043 0.192 1786 Planarity : 0.003 0.038 1965 Dihedral : 4.250 43.342 1510 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.83 % Favored : 94.02 % Rotamer: Outliers : 1.51 % Allowed : 14.54 % Favored : 83.96 % 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: 0.37 (0.24), residues: 1372 helix: 1.77 (0.24), residues: 530 sheet: 0.03 (0.31), residues: 320 loop : -1.21 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 417 HIS 0.003 0.001 HIS B 73 PHE 0.013 0.001 PHE C 328 TYR 0.026 0.001 TYR A 609 ARG 0.003 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 510) hydrogen bonds : angle 4.12383 ( 1455) covalent geometry : bond 0.00309 (11484) covalent geometry : angle 0.53352 (15534) ********************** 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 104 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8835 (mm) cc_final: 0.8546 (tp) REVERT: A 77 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6480 (t80) REVERT: A 95 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.5636 (t80) REVERT: A 257 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7116 (mp) REVERT: A 350 TRP cc_start: 0.8494 (m-90) cc_final: 0.7824 (m-90) REVERT: B 161 LEU cc_start: 0.8741 (tp) cc_final: 0.8108 (pp) REVERT: B 229 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8658 (mp) REVERT: C 152 PHE cc_start: 0.7779 (t80) cc_final: 0.7503 (t80) REVERT: C 344 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7905 (ttp) REVERT: C 398 GLU cc_start: 0.8676 (tp30) cc_final: 0.8456 (tp30) REVERT: C 401 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7109 (mp10) REVERT: C 473 MET cc_start: 0.8621 (ttm) cc_final: 0.8293 (ttp) outliers start: 19 outliers final: 13 residues processed: 100 average time/residue: 0.2288 time to fit residues: 33.9108 Evaluate side-chains 100 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 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 186 ILE Chi-restraints excluded: chain B residue 229 LEU 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 344 MET Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 502 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 86 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 136 optimal weight: 0.0670 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.145589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.111961 restraints weight = 16851.868| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.53 r_work: 0.3295 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2178 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= 0.114 Angle : 0.515 9.279 15534 Z= 0.269 Chirality : 0.043 0.185 1786 Planarity : 0.003 0.037 1965 Dihedral : 4.180 43.270 1510 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 1.51 % Allowed : 14.61 % Favored : 83.88 % 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: 1.85 (0.24), residues: 531 sheet: 0.10 (0.32), residues: 319 loop : -1.14 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 417 HIS 0.002 0.001 HIS C 133 PHE 0.013 0.001 PHE A 310 TYR 0.019 0.001 TYR A 609 ARG 0.005 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 510) hydrogen bonds : angle 4.07118 ( 1455) covalent geometry : bond 0.00269 (11484) covalent geometry : angle 0.51548 (15534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5504.79 seconds wall clock time: 96 minutes 6.18 seconds (5766.18 seconds total)