Starting phenix.real_space_refine on Fri Oct 23 01:02:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xfh_66822/10_2026/9xfh_66822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xfh_66822/10_2026/9xfh_66822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xfh_66822/10_2026/9xfh_66822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xfh_66822/10_2026/9xfh_66822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xfh_66822/10_2026/9xfh_66822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xfh_66822/10_2026/9xfh_66822.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 39 5.16 5 C 4608 2.51 5 N 1211 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7247 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4433 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 534} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2783 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.94, per 1000 atoms: 0.13 Number of scatterers: 7247 At special positions: 0 Unit cell: (77.35, 95.55, 117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 3 15.00 O 1386 8.00 N 1211 7.00 C 4608 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: 0.30 Conformation dependent library (CDL) restraints added in 195.1 milliseconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1710 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 49.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 79 through 89 removed outlier: 4.476A pdb=" N GLN A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.775A pdb=" N HIS A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 removed outlier: 3.606A pdb=" N LEU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 123 removed outlier: 3.965A pdb=" N GLU A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.614A pdb=" N VAL A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 177 removed outlier: 3.867A pdb=" N THR A 168 " --> pdb=" O LYS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.834A pdb=" N ALA A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Proline residue: A 199 - end of helix removed outlier: 4.154A pdb=" N ILE A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 removed outlier: 3.553A pdb=" N LYS A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.762A pdb=" N ILE A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 272 removed outlier: 4.349A pdb=" N ILE A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 289 removed outlier: 3.515A pdb=" N PHE A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 314 through 319 Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.825A pdb=" N ASN A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 392 removed outlier: 4.787A pdb=" N ASN A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 396 removed outlier: 4.146A pdb=" N ARG A 396 " --> pdb=" O ASP A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 396' Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.613A pdb=" N ILE A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N CYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.986A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.627A pdb=" N GLU A 458 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.595A pdb=" N LYS A 463 " --> pdb=" O ASP A 460 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 464' Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.801A pdb=" N GLN A 487 " --> pdb=" O TYR A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 536 Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.658A pdb=" N GLU A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.714A pdb=" N GLN A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.843A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 590 removed outlier: 3.510A pdb=" N ASP A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.520A pdb=" N LYS A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 616 removed outlier: 3.850A pdb=" N LEU A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 636 removed outlier: 4.168A pdb=" N LYS A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'C' and resid 80 through 93 removed outlier: 3.989A pdb=" N LYS C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.805A pdb=" N GLU C 102 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.520A pdb=" N THR C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 146 removed outlier: 3.524A pdb=" N SER C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 removed outlier: 3.531A pdb=" N THR C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 removed outlier: 3.725A pdb=" N ASP C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 235 removed outlier: 3.925A pdb=" N THR C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.908A pdb=" N ALA C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 319 Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.538A pdb=" N GLY C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 Processing helix chain 'C' and resid 360 through 368 Processing helix chain 'C' and resid 371 through 376 Processing sheet with id=AA1, first strand: chain 'A' and resid 443 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA3, first strand: chain 'C' and resid 18 through 21 Processing sheet with id=AA4, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.577A pdb=" N TYR C 55 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 70 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 39 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR C 68 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.504A pdb=" N LEU C 107 " --> pdb=" O ALA C 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AA8, first strand: chain 'C' and resid 171 through 172 removed outlier: 6.416A pdb=" N ILE C 153 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER C 302 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU C 155 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN C 299 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 240 through 243 232 hydrogen bonds defined for protein. 639 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: 0.56 Time building geometry restraints manager: 0.39 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: 2334 1.34 - 1.46: 1453 1.46 - 1.58: 3536 1.58 - 1.69: 5 1.69 - 1.81: 66 Bond restraints: 7394 Sorted by residual: bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.63e+01 bond pdb=" C5 ATP C 401 " pdb=" C6 ATP C 401 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.50e+01 bond pdb=" C8 ATP C 401 " pdb=" N7 ATP C 401 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.24e+01 bond pdb=" C4 ATP C 401 " pdb=" N9 ATP C 401 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.93e+01 bond pdb=" C5 ATP C 401 " pdb=" N7 ATP C 401 " ideal model delta sigma weight residual 1.387 1.344 0.043 1.00e-02 1.00e+04 1.81e+01 ... (remaining 7389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 9872 3.16 - 6.33: 104 6.33 - 9.49: 15 9.49 - 12.65: 1 12.65 - 15.82: 2 Bond angle restraints: 9994 Sorted by residual: angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 121.01 15.82 1.00e+00 1.00e+00 2.50e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 124.61 15.26 1.00e+00 1.00e+00 2.33e+02 angle pdb=" C5 ATP C 401 " pdb=" C4 ATP C 401 " pdb=" N3 ATP C 401 " ideal model delta sigma weight residual 126.80 118.77 8.03 1.00e+00 1.00e+00 6.45e+01 angle pdb=" N3 ATP C 401 " pdb=" C4 ATP C 401 " pdb=" N9 ATP C 401 " ideal model delta sigma weight residual 127.04 134.66 -7.62 1.15e+00 7.59e-01 4.40e+01 angle pdb=" N1 ATP C 401 " pdb=" C2 ATP C 401 " pdb=" N3 ATP C 401 " ideal model delta sigma weight residual 128.69 123.92 4.77 1.00e+00 1.00e+00 2.27e+01 ... (remaining 9989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 4244 16.73 - 33.45: 214 33.45 - 50.18: 40 50.18 - 66.91: 3 66.91 - 83.63: 6 Dihedral angle restraints: 4507 sinusoidal: 1855 harmonic: 2652 Sorted by residual: dihedral pdb=" CA PHE A 289 " pdb=" C PHE A 289 " pdb=" N VAL A 290 " pdb=" CA VAL A 290 " ideal model delta harmonic sigma weight residual -180.00 -155.53 -24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLU C 261 " pdb=" C GLU C 261 " pdb=" N THR C 262 " pdb=" CA THR C 262 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PRO A 93 " pdb=" C PRO A 93 " pdb=" N LYS A 94 " pdb=" CA LYS A 94 " ideal model delta harmonic sigma weight residual 180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 4504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 810 0.055 - 0.111: 265 0.111 - 0.166: 35 0.166 - 0.222: 5 0.222 - 0.277: 1 Chirality restraints: 1116 Sorted by residual: chirality pdb=" CB ILE A 243 " pdb=" CA ILE A 243 " pdb=" CG1 ILE A 243 " pdb=" CG2 ILE A 243 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE C 371 " pdb=" CA ILE C 371 " pdb=" CG1 ILE C 371 " pdb=" CG2 ILE C 371 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE A 526 " pdb=" CA ILE A 526 " pdb=" CG1 ILE A 526 " pdb=" CG2 ILE A 526 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1113 not shown) Planarity restraints: 1275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 358 " -0.023 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP C 358 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 358 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 358 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 358 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 358 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 358 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 358 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 358 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP C 358 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 165 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO C 166 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 166 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 166 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 368 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO C 369 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 369 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 369 " -0.033 5.00e-02 4.00e+02 ... (remaining 1272 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1992 2.80 - 3.33: 6255 3.33 - 3.85: 11730 3.85 - 4.38: 14327 4.38 - 4.90: 23981 Nonbonded interactions: 58285 Sorted by model distance: nonbonded pdb=" OG SER A 250 " pdb=" OE1 GLN C 356 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR A 484 " pdb=" O ASN C 113 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR A 348 " pdb=" OD2 ASP A 618 " model vdw 2.309 3.040 nonbonded pdb=" O LYS C 240 " pdb=" OG1 THR C 251 " model vdw 2.334 3.040 nonbonded pdb=" OG SER A 221 " pdb=" NH1 ARG A 455 " model vdw 2.347 3.120 ... (remaining 58280 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: 1.020 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.200 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:4.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 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 : 0.005 0.081 7394 Z= 0.268 Angle : 0.914 15.816 9994 Z= 0.541 Chirality : 0.053 0.277 1116 Planarity : 0.007 0.064 1275 Dihedral : 11.356 83.632 2797 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.25 % Allowed : 4.79 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.14 (0.21), residues: 904 helix: -4.44 (0.12), residues: 417 sheet: -3.05 (0.50), residues: 71 loop : -2.14 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 292 TYR 0.020 0.002 TYR C 296 PHE 0.025 0.002 PHE A 269 TRP 0.055 0.005 TRP C 358 HIS 0.008 0.002 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.27 ( 7394) covalent geometry : angle 0.91389 / 0.54 ( 9994) hydrogen bonds : bond 0.32891 / 21.47 ( 230) hydrogen bonds : angle 11.11319 / 7.46 ( 639) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8027 (mtmp) cc_final: 0.7680 (mttp) REVERT: A 164 LYS cc_start: 0.7555 (ptpp) cc_final: 0.7279 (ptpp) REVERT: A 333 THR cc_start: 0.7283 (m) cc_final: 0.6838 (p) REVERT: A 342 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7324 (mt-10) REVERT: A 476 MET cc_start: 0.6415 (mmm) cc_final: 0.6199 (mmp) REVERT: A 578 ASP cc_start: 0.5436 (m-30) cc_final: 0.5117 (m-30) REVERT: C 169 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6387 (mm-30) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.3234 time to fit residues: 66.2269 Evaluate side-chains 148 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.0770 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 GLN A 239 GLN A 242 ASN A 347 GLN A 378 ASN A 505 ASN A 628 ASN C 89 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.152815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.138296 restraints weight = 9744.668| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.03 r_work: 0.3902 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7394 Z= 0.152 Angle : 0.629 8.429 9994 Z= 0.327 Chirality : 0.045 0.176 1116 Planarity : 0.006 0.056 1275 Dihedral : 7.203 58.739 1011 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.15 % Allowed : 12.34 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.23), residues: 904 helix: -2.94 (0.19), residues: 427 sheet: -2.39 (0.53), residues: 70 loop : -1.70 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 179 TYR 0.018 0.002 TYR C 135 PHE 0.025 0.002 PHE A 341 TRP 0.050 0.003 TRP C 358 HIS 0.009 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 7394) covalent geometry : angle 0.62916 / 0.33 ( 9994) hydrogen bonds : bond 0.04617 / 2.91 ( 230) hydrogen bonds : angle 5.78371 / 3.83 ( 639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8012 (mtmp) cc_final: 0.7608 (mttp) REVERT: A 120 ILE cc_start: 0.7578 (mp) cc_final: 0.7364 (tt) REVERT: A 204 LYS cc_start: 0.7599 (mtmm) cc_final: 0.7375 (mtmm) REVERT: A 460 ASP cc_start: 0.7247 (p0) cc_final: 0.6970 (p0) REVERT: C 59 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6897 (tm-30) REVERT: C 244 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7155 (tm) outliers start: 25 outliers final: 10 residues processed: 151 average time/residue: 0.5197 time to fit residues: 83.0938 Evaluate side-chains 147 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 244 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [24, 88, 19, 37, 68, 89, 23, 55, 79, 13, 32] chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 GLN A 242 ASN A 529 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.149509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.135510 restraints weight = 9665.683| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.95 r_work: 0.3894 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7394 Z= 0.153 Angle : 0.592 7.535 9994 Z= 0.307 Chirality : 0.046 0.171 1116 Planarity : 0.005 0.051 1275 Dihedral : 6.723 48.359 1011 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.16 % Allowed : 14.23 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.25), residues: 904 helix: -1.98 (0.22), residues: 427 sheet: -2.18 (0.56), residues: 70 loop : -1.44 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 198 TYR 0.017 0.001 TYR C 135 PHE 0.015 0.002 PHE A 341 TRP 0.058 0.003 TRP C 358 HIS 0.007 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7394) covalent geometry : angle 0.59203 / 0.31 ( 9994) hydrogen bonds : bond 0.04079 / 2.59 ( 230) hydrogen bonds : angle 5.22658 / 3.49 ( 639) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8004 (mtmp) cc_final: 0.7616 (mtmp) REVERT: A 120 ILE cc_start: 0.7655 (mp) cc_final: 0.7439 (tt) REVERT: A 204 LYS cc_start: 0.7631 (mtmm) cc_final: 0.7410 (mtmm) REVERT: A 297 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7684 (t-90) REVERT: A 505 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.6989 (p0) REVERT: C 59 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6937 (tm-30) REVERT: C 244 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7177 (tm) outliers start: 33 outliers final: 12 residues processed: 150 average time/residue: 0.5251 time to fit residues: 83.3739 Evaluate side-chains 145 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 244 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [14, 29, 20, 44, 10, 18, 30, 63, 42, 71, 56] chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 350 ASN A 529 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.150097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.135652 restraints weight = 9815.935| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.99 r_work: 0.3894 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7394 Z= 0.164 Angle : 0.610 8.575 9994 Z= 0.313 Chirality : 0.046 0.149 1116 Planarity : 0.005 0.051 1275 Dihedral : 6.502 47.983 1011 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.03 % Allowed : 15.87 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.26), residues: 904 helix: -1.57 (0.24), residues: 422 sheet: -1.87 (0.58), residues: 70 loop : -1.25 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 344 TYR 0.016 0.001 TYR C 135 PHE 0.019 0.002 PHE C 126 TRP 0.069 0.003 TRP C 358 HIS 0.007 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 7394) covalent geometry : angle 0.60979 / 0.31 ( 9994) hydrogen bonds : bond 0.03861 / 2.45 ( 230) hydrogen bonds : angle 5.03667 / 3.38 ( 639) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7974 (mtmp) cc_final: 0.7575 (mtmp) REVERT: A 120 ILE cc_start: 0.7654 (mp) cc_final: 0.7428 (tt) REVERT: A 297 HIS cc_start: 0.7888 (OUTLIER) cc_final: 0.7669 (t-90) REVERT: C 30 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7539 (ttp80) REVERT: C 59 GLU cc_start: 0.7204 (tm-30) cc_final: 0.7000 (tm-30) REVERT: C 229 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.6027 (mmt) REVERT: C 244 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7190 (tm) outliers start: 32 outliers final: 10 residues processed: 143 average time/residue: 0.5372 time to fit residues: 81.3212 Evaluate side-chains 143 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [79, 39, 24, 57, 64, 4, 44, 34, 49, 51, 15] chunk 79 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 24 optimal weight: 0.4980 chunk 57 optimal weight: 0.0770 chunk 64 optimal weight: 0.0670 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 0.0570 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 350 ASN A 529 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.154564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.140172 restraints weight = 9649.169| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.99 r_work: 0.3952 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7394 Z= 0.099 Angle : 0.560 8.731 9994 Z= 0.283 Chirality : 0.043 0.158 1116 Planarity : 0.004 0.048 1275 Dihedral : 5.982 50.087 1011 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.40 % Allowed : 17.38 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.27), residues: 904 helix: -1.02 (0.26), residues: 418 sheet: -1.41 (0.65), residues: 59 loop : -1.07 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 198 TYR 0.014 0.001 TYR A 622 PHE 0.016 0.001 PHE A 341 TRP 0.071 0.003 TRP C 358 HIS 0.003 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 7394) covalent geometry : angle 0.56008 / 0.28 ( 9994) hydrogen bonds : bond 0.03185 / 2.04 ( 230) hydrogen bonds : angle 4.60474 / 3.08 ( 639) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7934 (mtmp) cc_final: 0.7553 (mtmp) REVERT: A 120 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7371 (tt) REVERT: A 204 LYS cc_start: 0.7588 (mtmm) cc_final: 0.7331 (mtmm) REVERT: C 30 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7550 (ttp80) REVERT: C 244 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6973 (tm) REVERT: C 316 GLN cc_start: 0.6400 (OUTLIER) cc_final: 0.5513 (tm-30) outliers start: 27 outliers final: 8 residues processed: 140 average time/residue: 0.5348 time to fit residues: 79.2826 Evaluate side-chains 134 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [35, 79, 47, 73, 21, 89, 6, 44, 87, 80, 45] chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 45 optimal weight: 0.1980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 529 HIS ** C 14 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 = 0.4211 r_free = 0.4211 target = 0.155171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.140822 restraints weight = 9671.397| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.98 r_work: 0.3934 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7394 Z= 0.110 Angle : 0.567 8.398 9994 Z= 0.286 Chirality : 0.044 0.159 1116 Planarity : 0.004 0.049 1275 Dihedral : 5.965 52.291 1011 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.02 % Allowed : 18.64 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.28), residues: 904 helix: -0.89 (0.26), residues: 419 sheet: -1.40 (0.65), residues: 59 loop : -0.90 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 198 TYR 0.012 0.001 TYR A 622 PHE 0.017 0.001 PHE A 341 TRP 0.054 0.003 TRP C 358 HIS 0.004 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7394) covalent geometry : angle 0.56693 / 0.29 ( 9994) hydrogen bonds : bond 0.03321 / 2.15 ( 230) hydrogen bonds : angle 4.66967 / 3.12 ( 639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7994 (mtmp) cc_final: 0.7656 (mtmp) REVERT: A 204 LYS cc_start: 0.7608 (mtmm) cc_final: 0.7351 (mtmm) REVERT: A 462 GLU cc_start: 0.6494 (mp0) cc_final: 0.6248 (mp0) REVERT: A 544 TYR cc_start: 0.8134 (m-10) cc_final: 0.7925 (m-10) REVERT: C 30 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7589 (ttp80) REVERT: C 207 GLU cc_start: 0.7936 (tt0) cc_final: 0.7655 (tt0) REVERT: C 244 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6976 (tm) REVERT: C 316 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.5447 (tm-30) outliers start: 24 outliers final: 11 residues processed: 140 average time/residue: 0.4981 time to fit residues: 74.1223 Evaluate side-chains 137 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [11, 62, 66, 13, 44, 8, 80, 34, 79, 24, 81] chunk 11 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 79 optimal weight: 0.0030 chunk 24 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 350 ASN A 529 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.153395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.138989 restraints weight = 9743.696| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.99 r_work: 0.3913 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7394 Z= 0.127 Angle : 0.583 8.083 9994 Z= 0.295 Chirality : 0.045 0.149 1116 Planarity : 0.004 0.050 1275 Dihedral : 5.990 50.524 1011 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.53 % Allowed : 19.90 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.28), residues: 904 helix: -0.86 (0.25), residues: 419 sheet: -1.39 (0.66), residues: 59 loop : -0.85 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 198 TYR 0.011 0.001 TYR A 622 PHE 0.017 0.001 PHE A 341 TRP 0.080 0.003 TRP C 358 HIS 0.005 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7394) covalent geometry : angle 0.58323 / 0.29 ( 9994) hydrogen bonds : bond 0.03418 / 2.20 ( 230) hydrogen bonds : angle 4.68709 / 3.15 ( 639) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8119 (mtmp) cc_final: 0.7761 (mttp) REVERT: A 204 LYS cc_start: 0.7638 (mtmm) cc_final: 0.7415 (mtmm) REVERT: A 262 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7353 (mp) REVERT: A 462 GLU cc_start: 0.6570 (mp0) cc_final: 0.6258 (mp0) REVERT: C 30 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7634 (ttp80) REVERT: C 125 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6533 (ppp) REVERT: C 244 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6987 (tm) outliers start: 28 outliers final: 16 residues processed: 137 average time/residue: 0.4930 time to fit residues: 71.7760 Evaluate side-chains 141 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 276 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [72, 0, 80, 67, 88, 59, 42, 70, 85, 33, 57] chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 0.0670 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 GLN A 529 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.148798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.134575 restraints weight = 9830.358| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.96 r_work: 0.3869 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7394 Z= 0.186 Angle : 0.644 8.655 9994 Z= 0.329 Chirality : 0.047 0.168 1116 Planarity : 0.005 0.052 1275 Dihedral : 6.262 48.593 1011 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.53 % Allowed : 19.52 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.27), residues: 904 helix: -1.15 (0.24), residues: 426 sheet: -1.57 (0.64), residues: 60 loop : -0.82 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 198 TYR 0.012 0.002 TYR C 135 PHE 0.019 0.002 PHE A 341 TRP 0.073 0.003 TRP C 358 HIS 0.006 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 7394) covalent geometry : angle 0.64418 / 0.33 ( 9994) hydrogen bonds : bond 0.03857 / 2.48 ( 230) hydrogen bonds : angle 4.93414 / 3.33 ( 639) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8160 (mtmp) cc_final: 0.7803 (mttp) REVERT: A 204 LYS cc_start: 0.7648 (mtmm) cc_final: 0.7382 (mtmm) REVERT: A 462 GLU cc_start: 0.6613 (mp0) cc_final: 0.6241 (mp0) REVERT: C 30 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7685 (ttp80) REVERT: C 244 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7040 (tm) outliers start: 28 outliers final: 17 residues processed: 138 average time/residue: 0.4924 time to fit residues: 72.2339 Evaluate side-chains 142 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [9, 57, 20, 78, 34, 67, 11, 10, 3, 45, 16] chunk 9 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 529 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.149661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.135583 restraints weight = 9716.084| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.95 r_work: 0.3889 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7394 Z= 0.146 Angle : 0.634 8.433 9994 Z= 0.322 Chirality : 0.045 0.161 1116 Planarity : 0.005 0.052 1275 Dihedral : 6.174 49.334 1011 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.53 % Allowed : 20.15 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.27), residues: 904 helix: -1.06 (0.24), residues: 439 sheet: -1.52 (0.66), residues: 60 loop : -0.84 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 198 TYR 0.011 0.001 TYR A 622 PHE 0.027 0.002 PHE C 126 TRP 0.071 0.004 TRP C 358 HIS 0.006 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7394) covalent geometry : angle 0.63421 / 0.32 ( 9994) hydrogen bonds : bond 0.03558 / 2.28 ( 230) hydrogen bonds : angle 4.79343 / 3.23 ( 639) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8123 (mtmp) cc_final: 0.7759 (mttp) REVERT: A 204 LYS cc_start: 0.7639 (mtmm) cc_final: 0.7384 (mtmm) REVERT: A 462 GLU cc_start: 0.6594 (mp0) cc_final: 0.6205 (mp0) REVERT: C 30 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7652 (ttp80) REVERT: C 244 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7104 (tm) outliers start: 28 outliers final: 17 residues processed: 134 average time/residue: 0.5158 time to fit residues: 73.3265 Evaluate side-chains 142 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [51, 5, 37, 82, 9, 84, 87, 28, 24, 42, 53] chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 42 optimal weight: 0.0370 chunk 53 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 529 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.152281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.138065 restraints weight = 9650.354| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.96 r_work: 0.3909 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7394 Z= 0.120 Angle : 0.613 8.921 9994 Z= 0.312 Chirality : 0.044 0.152 1116 Planarity : 0.005 0.053 1275 Dihedral : 5.996 50.108 1011 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.27 % Allowed : 21.16 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.28), residues: 904 helix: -0.80 (0.25), residues: 431 sheet: -1.34 (0.68), residues: 60 loop : -0.73 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 198 TYR 0.012 0.001 TYR A 622 PHE 0.035 0.001 PHE C 126 TRP 0.069 0.004 TRP C 358 HIS 0.004 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7394) covalent geometry : angle 0.61308 / 0.31 ( 9994) hydrogen bonds : bond 0.03422 / 2.22 ( 230) hydrogen bonds : angle 4.68862 / 3.15 ( 639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.255 Fit side-chains REVERT: A 91 LYS cc_start: 0.8142 (mtmp) cc_final: 0.7804 (mttp) REVERT: A 204 LYS cc_start: 0.7591 (mtmm) cc_final: 0.7355 (mtmm) REVERT: A 462 GLU cc_start: 0.6576 (mp0) cc_final: 0.6228 (mp0) REVERT: C 30 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7668 (ttp80) REVERT: C 244 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7250 (tm) outliers start: 18 outliers final: 14 residues processed: 135 average time/residue: 0.5002 time to fit residues: 71.7747 Evaluate side-chains 138 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [22, 78, 70, 25, 55, 38, 61, 30, 36, 83, 9] chunk 22 optimal weight: 0.0370 chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 529 HIS A 571 HIS C 227 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.153623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.139243 restraints weight = 9755.929| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.00 r_work: 0.3919 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7394 Z= 0.118 Angle : 0.628 9.633 9994 Z= 0.314 Chirality : 0.044 0.149 1116 Planarity : 0.005 0.057 1275 Dihedral : 5.902 51.148 1011 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.52 % Allowed : 20.91 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.28), residues: 904 helix: -0.53 (0.26), residues: 420 sheet: -1.13 (0.68), residues: 60 loop : -0.72 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 198 TYR 0.012 0.001 TYR A 622 PHE 0.032 0.001 PHE C 126 TRP 0.067 0.004 TRP C 358 HIS 0.008 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7394) covalent geometry : angle 0.62777 / 0.31 ( 9994) hydrogen bonds : bond 0.03362 / 2.19 ( 230) hydrogen bonds : angle 4.63941 / 3.11 ( 639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.75 seconds wall clock time: 58 minutes 14.39 seconds (3494.39 seconds total)