Starting phenix.real_space_refine on Tue Mar 3 22:15:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdv_14671/03_2026/7zdv_14671_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdv_14671/03_2026/7zdv_14671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zdv_14671/03_2026/7zdv_14671_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdv_14671/03_2026/7zdv_14671_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zdv_14671/03_2026/7zdv_14671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdv_14671/03_2026/7zdv_14671.map" } resolution = 3.05 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= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 5685 2.51 5 N 1566 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8877 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4292 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 17, 'TRANS': 537} Chain breaks: 2 Chain: "D" Number of atoms: 4553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4553 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 27, 'TRANS': 558} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.27, per 1000 atoms: 0.26 Number of scatterers: 8877 At special positions: 0 Unit cell: (123.039, 75.33, 112.158, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 3 15.00 Mg 1 11.99 O 1594 8.00 N 1566 7.00 C 5685 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: 0.78 Conformation dependent library (CDL) restraints added in 352.8 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 5 sheets defined 69.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'C' and resid 1 through 3 No H-bonds generated for 'chain 'C' and resid 1 through 3' Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 10 through 13 removed outlier: 3.627A pdb=" N ARG C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 14 through 50 removed outlier: 3.577A pdb=" N ILE C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 4.516A pdb=" N TYR C 55 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 104 removed outlier: 3.589A pdb=" N TYR C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 130 removed outlier: 3.549A pdb=" N ASN C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 137 through 156 Processing helix chain 'C' and resid 159 through 176 removed outlier: 3.674A pdb=" N THR C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 185 through 209 removed outlier: 3.738A pdb=" N THR C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 220 through 269 removed outlier: 3.580A pdb=" N GLN C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY C 269 " --> pdb=" O MET C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 removed outlier: 3.577A pdb=" N LEU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 296 through 319 removed outlier: 3.985A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 387 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 442 through 453 removed outlier: 3.596A pdb=" N LEU C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 460 removed outlier: 4.268A pdb=" N LEU C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU C 460 " --> pdb=" O GLU C 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 455 through 460' Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.617A pdb=" N ASN C 465 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 491 removed outlier: 3.903A pdb=" N ARG C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 521 removed outlier: 3.532A pdb=" N SER C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLN C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 562 removed outlier: 3.660A pdb=" N ARG C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 570 removed outlier: 3.656A pdb=" N GLN C 568 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 569 " --> pdb=" O ARG C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 20 through 54 removed outlier: 3.661A pdb=" N GLY D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 109 removed outlier: 3.694A pdb=" N ILE D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.972A pdb=" N TRP D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 133 through 139 removed outlier: 3.931A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 162 removed outlier: 4.200A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix Proline residue: D 160 - end of helix Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.713A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 191 removed outlier: 3.990A pdb=" N GLY D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 190 " --> pdb=" O GLY D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 201 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 211 through 217 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 224 through 273 removed outlier: 4.104A pdb=" N GLU D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.575A pdb=" N GLY D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 removed outlier: 4.031A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 311 through 329 removed outlier: 3.642A pdb=" N ALA D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 398 removed outlier: 4.098A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 438 through 444 removed outlier: 3.520A pdb=" N VAL D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 462 removed outlier: 3.802A pdb=" N ALA D 462 " --> pdb=" O ALA D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 477 removed outlier: 4.428A pdb=" N ASP D 476 " --> pdb=" O GLN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 484 Processing helix chain 'D' and resid 487 through 502 removed outlier: 3.527A pdb=" N ARG D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 498 " --> pdb=" O VAL D 494 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN D 502 " --> pdb=" O ARG D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 532 removed outlier: 3.792A pdb=" N GLU D 521 " --> pdb=" O ASP D 517 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 572 removed outlier: 3.778A pdb=" N LEU D 570 " --> pdb=" O ARG D 566 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 587 removed outlier: 3.724A pdb=" N ARG D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN D 585 " --> pdb=" O LEU D 581 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU D 587 " --> pdb=" O HIS D 583 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.622A pdb=" N ARG C 342 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 396 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 418 removed outlier: 6.202A pdb=" N VAL C 496 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL C 529 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 498 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE C 369 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N THR C 530 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE C 371 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 370 through 373 Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 366 removed outlier: 6.617A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 425 through 428 removed outlier: 7.636A pdb=" N ARG D 378 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N TRP D 554 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 380 " --> pdb=" O TRP D 554 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N MET D 556 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 382 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1539 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: 1.50 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1847 1.33 - 1.45: 1994 1.45 - 1.57: 5149 1.57 - 1.69: 5 1.69 - 1.81: 55 Bond restraints: 9050 Sorted by residual: bond pdb=" O3A ANP D 602 " pdb=" PB ANP D 602 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.15e+01 bond pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O5' ANP D 602 " pdb=" PA ANP D 602 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" N GLN D 302 " pdb=" CA GLN D 302 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.36e+00 bond pdb=" N GLN D 473 " pdb=" CA GLN D 473 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.29e-02 6.01e+03 7.84e+00 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 12240 3.91 - 7.81: 55 7.81 - 11.72: 3 11.72 - 15.62: 0 15.62 - 19.53: 1 Bond angle restraints: 12299 Sorted by residual: angle pdb=" N PRO D 448 " pdb=" CA PRO D 448 " pdb=" CB PRO D 448 " ideal model delta sigma weight residual 103.51 110.11 -6.60 9.60e-01 1.09e+00 4.73e+01 angle pdb=" PB ANP D 602 " pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 126.95 107.42 19.53 3.00e+00 1.11e-01 4.24e+01 angle pdb=" N ASN C 191 " pdb=" CA ASN C 191 " pdb=" C ASN C 191 " ideal model delta sigma weight residual 113.18 105.90 7.28 1.21e+00 6.83e-01 3.62e+01 angle pdb=" N ALA C 389 " pdb=" CA ALA C 389 " pdb=" C ALA C 389 " ideal model delta sigma weight residual 111.28 105.59 5.69 1.09e+00 8.42e-01 2.73e+01 angle pdb=" N GLN C 202 " pdb=" CA GLN C 202 " pdb=" C GLN C 202 " ideal model delta sigma weight residual 113.23 108.21 5.02 1.24e+00 6.50e-01 1.64e+01 ... (remaining 12294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4865 17.66 - 35.32: 444 35.32 - 52.98: 72 52.98 - 70.64: 16 70.64 - 88.30: 17 Dihedral angle restraints: 5414 sinusoidal: 2142 harmonic: 3272 Sorted by residual: dihedral pdb=" CA PRO C 296 " pdb=" C PRO C 296 " pdb=" N VAL C 297 " pdb=" CA VAL C 297 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASN C 273 " pdb=" C ASN C 273 " pdb=" N ALA C 274 " pdb=" CA ALA C 274 " ideal model delta harmonic sigma weight residual 180.00 163.58 16.42 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" C GLN D 430 " pdb=" N GLN D 430 " pdb=" CA GLN D 430 " pdb=" CB GLN D 430 " ideal model delta harmonic sigma weight residual -122.60 -114.46 -8.14 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 5411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1222 0.061 - 0.121: 192 0.121 - 0.181: 18 0.181 - 0.242: 1 0.242 - 0.302: 2 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA GLN D 430 " pdb=" N GLN D 430 " pdb=" C GLN D 430 " pdb=" CB GLN D 430 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C3' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C4' ANP D 602 " pdb=" O3' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA PRO D 448 " pdb=" N PRO D 448 " pdb=" C PRO D 448 " pdb=" CB PRO D 448 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1432 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 190 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C GLN C 190 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN C 190 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN C 191 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 427 " 0.011 2.00e-02 2.50e+03 1.11e-02 3.07e+00 pdb=" CG TRP D 427 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP D 427 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP D 427 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 427 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 427 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 427 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 427 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 427 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 427 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 201 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C GLN C 201 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN C 201 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN C 202 " 0.010 2.00e-02 2.50e+03 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 64 2.57 - 3.16: 7153 3.16 - 3.74: 13620 3.74 - 4.32: 19763 4.32 - 4.90: 32775 Nonbonded interactions: 73375 Sorted by model distance: nonbonded pdb=" OG SER D 390 " pdb="MG MG D 601 " model vdw 1.993 2.170 nonbonded pdb="MG MG D 601 " pdb=" O3G ANP D 602 " model vdw 2.002 2.170 nonbonded pdb="MG MG D 601 " pdb=" O1B ANP D 602 " model vdw 2.079 2.170 nonbonded pdb=" OE1 GLN D 129 " pdb=" OG SER D 323 " model vdw 2.157 3.040 nonbonded pdb=" NH1 ARG C 431 " pdb=" OD2 ASP C 443 " model vdw 2.196 3.120 ... (remaining 73370 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: 1.720 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.210 Find NCS groups from input model: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.006 0.143 9050 Z= 0.270 Angle : 0.738 19.529 12299 Z= 0.407 Chirality : 0.045 0.302 1435 Planarity : 0.004 0.041 1565 Dihedral : 14.827 88.301 3302 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.11 % Allowed : 0.44 % Favored : 99.46 % 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: -2.81 (0.23), residues: 1133 helix: -2.29 (0.17), residues: 683 sheet: -1.18 (0.76), residues: 49 loop : -0.72 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 522 TYR 0.014 0.001 TYR D 88 PHE 0.009 0.001 PHE D 371 TRP 0.029 0.002 TRP D 427 HIS 0.007 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 9050) covalent geometry : angle 0.73771 (12299) hydrogen bonds : bond 0.27002 ( 526) hydrogen bonds : angle 10.32652 ( 1539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.334 Fit side-chains REVERT: C 160 PHE cc_start: 0.7661 (m-80) cc_final: 0.7191 (m-80) REVERT: C 364 ASN cc_start: 0.8404 (m-40) cc_final: 0.7888 (m110) REVERT: C 390 TRP cc_start: 0.8477 (OUTLIER) cc_final: 0.7729 (p90) REVERT: C 422 ARG cc_start: 0.8085 (tpt90) cc_final: 0.7178 (tmt170) REVERT: C 541 GLN cc_start: 0.7793 (mm110) cc_final: 0.7536 (tp40) REVERT: D 560 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7527 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1474 time to fit residues: 20.7981 Evaluate side-chains 92 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 390 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN C 202 GLN C 208 GLN C 210 GLN C 302 GLN C 320 GLN D 237 GLN D 336 GLN D 370 ASN D 456 GLN D 473 GLN D 542 HIS D 543 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.105780 restraints weight = 10009.358| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.76 r_work: 0.2888 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9050 Z= 0.150 Angle : 0.625 7.756 12299 Z= 0.313 Chirality : 0.041 0.162 1435 Planarity : 0.005 0.039 1565 Dihedral : 8.240 94.609 1276 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.54 % Allowed : 5.01 % Favored : 94.44 % 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: -1.03 (0.24), residues: 1133 helix: -0.45 (0.19), residues: 695 sheet: -0.85 (0.76), residues: 48 loop : -0.81 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 139 TYR 0.021 0.001 TYR D 88 PHE 0.013 0.001 PHE D 32 TRP 0.019 0.001 TRP D 81 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9050) covalent geometry : angle 0.62547 (12299) hydrogen bonds : bond 0.05319 ( 526) hydrogen bonds : angle 4.92308 ( 1539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.326 Fit side-chains REVERT: C 364 ASN cc_start: 0.8472 (m-40) cc_final: 0.7955 (m110) REVERT: C 422 ARG cc_start: 0.8411 (tpt90) cc_final: 0.7145 (tmt170) REVERT: C 519 GLU cc_start: 0.7770 (tp30) cc_final: 0.7427 (tt0) REVERT: D 115 GLN cc_start: 0.8324 (mm110) cc_final: 0.7518 (pp30) REVERT: D 180 MET cc_start: 0.8332 (mtm) cc_final: 0.8091 (mtt) REVERT: D 234 ASP cc_start: 0.8444 (t0) cc_final: 0.8189 (t0) REVERT: D 522 GLN cc_start: 0.7303 (mp10) cc_final: 0.6909 (mp10) REVERT: D 560 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7239 (ttp-110) outliers start: 5 outliers final: 5 residues processed: 122 average time/residue: 0.1264 time to fit residues: 20.1473 Evaluate side-chains 102 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 533 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 32 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN C 541 GLN D 334 HIS D 424 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.150236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104341 restraints weight = 9898.659| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.74 r_work: 0.2898 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9050 Z= 0.124 Angle : 0.539 6.823 12299 Z= 0.267 Chirality : 0.040 0.152 1435 Planarity : 0.004 0.037 1565 Dihedral : 6.683 74.223 1276 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.87 % Allowed : 8.50 % Favored : 90.63 % 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: 0.12 (0.25), residues: 1133 helix: 0.66 (0.20), residues: 691 sheet: -0.87 (0.74), residues: 50 loop : -0.67 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 139 TYR 0.020 0.001 TYR D 88 PHE 0.011 0.001 PHE D 32 TRP 0.019 0.001 TRP D 81 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9050) covalent geometry : angle 0.53902 (12299) hydrogen bonds : bond 0.04421 ( 526) hydrogen bonds : angle 4.29814 ( 1539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.311 Fit side-chains REVERT: C 114 TYR cc_start: 0.7216 (m-80) cc_final: 0.6942 (m-80) REVERT: C 160 PHE cc_start: 0.7822 (m-80) cc_final: 0.7330 (m-80) REVERT: C 422 ARG cc_start: 0.8377 (tpt90) cc_final: 0.7155 (tmt170) REVERT: C 470 GLU cc_start: 0.7519 (tp30) cc_final: 0.6835 (tt0) REVERT: C 519 GLU cc_start: 0.7848 (tp30) cc_final: 0.7338 (tt0) REVERT: C 568 GLN cc_start: 0.7728 (mp10) cc_final: 0.7424 (mp10) REVERT: D 115 GLN cc_start: 0.8306 (mm110) cc_final: 0.7557 (pp30) REVERT: D 522 GLN cc_start: 0.7283 (mp10) cc_final: 0.6865 (mp10) REVERT: D 560 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7181 (ttp-110) outliers start: 8 outliers final: 6 residues processed: 113 average time/residue: 0.1436 time to fit residues: 20.6249 Evaluate side-chains 108 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN C 541 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104023 restraints weight = 10092.819| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.75 r_work: 0.2910 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9050 Z= 0.132 Angle : 0.533 6.898 12299 Z= 0.263 Chirality : 0.040 0.149 1435 Planarity : 0.004 0.036 1565 Dihedral : 6.216 67.966 1276 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.09 % Allowed : 9.37 % Favored : 89.54 % 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: 0.51 (0.25), residues: 1133 helix: 0.99 (0.20), residues: 690 sheet: -0.70 (0.75), residues: 50 loop : -0.57 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 139 TYR 0.020 0.001 TYR D 88 PHE 0.011 0.001 PHE D 256 TRP 0.018 0.001 TRP D 81 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9050) covalent geometry : angle 0.53299 (12299) hydrogen bonds : bond 0.04176 ( 526) hydrogen bonds : angle 4.14825 ( 1539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.385 Fit side-chains REVERT: C 114 TYR cc_start: 0.7203 (m-80) cc_final: 0.6934 (m-80) REVERT: C 160 PHE cc_start: 0.7802 (m-80) cc_final: 0.7318 (m-80) REVERT: C 422 ARG cc_start: 0.8387 (tpt90) cc_final: 0.7190 (tmt170) REVERT: C 470 GLU cc_start: 0.7569 (tp30) cc_final: 0.6849 (tt0) REVERT: C 519 GLU cc_start: 0.7765 (tp30) cc_final: 0.7311 (tt0) REVERT: C 568 GLN cc_start: 0.7776 (mp10) cc_final: 0.7429 (mp10) REVERT: D 115 GLN cc_start: 0.8333 (mm110) cc_final: 0.7604 (pp30) REVERT: D 180 MET cc_start: 0.8380 (mtm) cc_final: 0.8079 (mtt) REVERT: D 234 ASP cc_start: 0.8513 (t0) cc_final: 0.8214 (t0) REVERT: D 522 GLN cc_start: 0.7278 (mp10) cc_final: 0.6871 (mp10) REVERT: D 560 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7207 (ttp-110) outliers start: 10 outliers final: 7 residues processed: 112 average time/residue: 0.1457 time to fit residues: 20.7988 Evaluate side-chains 109 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 77 optimal weight: 0.0070 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN D 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104651 restraints weight = 10046.220| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.75 r_work: 0.2920 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9050 Z= 0.122 Angle : 0.515 6.878 12299 Z= 0.255 Chirality : 0.039 0.151 1435 Planarity : 0.004 0.037 1565 Dihedral : 5.812 60.122 1276 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.31 % Allowed : 10.57 % Favored : 88.13 % 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: 0.82 (0.25), residues: 1133 helix: 1.27 (0.20), residues: 690 sheet: -0.46 (0.76), residues: 50 loop : -0.52 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 139 TYR 0.020 0.001 TYR D 88 PHE 0.010 0.001 PHE C 181 TRP 0.018 0.001 TRP D 81 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9050) covalent geometry : angle 0.51533 (12299) hydrogen bonds : bond 0.04011 ( 526) hydrogen bonds : angle 4.01866 ( 1539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.333 Fit side-chains REVERT: C 114 TYR cc_start: 0.7173 (m-80) cc_final: 0.6913 (m-80) REVERT: C 160 PHE cc_start: 0.7788 (m-80) cc_final: 0.7326 (m-80) REVERT: C 422 ARG cc_start: 0.8384 (tpt90) cc_final: 0.7196 (tmt170) REVERT: C 470 GLU cc_start: 0.7569 (tp30) cc_final: 0.6816 (tt0) REVERT: C 519 GLU cc_start: 0.7828 (tp30) cc_final: 0.7280 (tt0) REVERT: C 530 THR cc_start: 0.8413 (p) cc_final: 0.7985 (t) REVERT: D 115 GLN cc_start: 0.8332 (mm110) cc_final: 0.7650 (pp30) REVERT: D 180 MET cc_start: 0.8348 (mtm) cc_final: 0.8056 (mtt) REVERT: D 234 ASP cc_start: 0.8494 (t0) cc_final: 0.8197 (t0) REVERT: D 522 GLN cc_start: 0.7380 (mp10) cc_final: 0.6975 (mp10) REVERT: D 525 MET cc_start: 0.8398 (mmp) cc_final: 0.8030 (mmt) REVERT: D 560 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7185 (ttp-110) outliers start: 12 outliers final: 8 residues processed: 116 average time/residue: 0.1401 time to fit residues: 20.9281 Evaluate side-chains 113 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.106933 restraints weight = 10048.619| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.73 r_work: 0.2944 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9050 Z= 0.139 Angle : 0.530 7.686 12299 Z= 0.261 Chirality : 0.040 0.149 1435 Planarity : 0.004 0.037 1565 Dihedral : 5.702 57.335 1276 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.42 % Allowed : 11.55 % Favored : 87.04 % 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: 0.91 (0.25), residues: 1133 helix: 1.35 (0.20), residues: 690 sheet: -0.35 (0.77), residues: 50 loop : -0.51 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 139 TYR 0.021 0.001 TYR D 88 PHE 0.011 0.001 PHE C 181 TRP 0.018 0.001 TRP D 81 HIS 0.005 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9050) covalent geometry : angle 0.52968 (12299) hydrogen bonds : bond 0.04096 ( 526) hydrogen bonds : angle 4.02348 ( 1539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.357 Fit side-chains REVERT: C 114 TYR cc_start: 0.7249 (m-80) cc_final: 0.7006 (m-80) REVERT: C 160 PHE cc_start: 0.7822 (m-80) cc_final: 0.7367 (m-80) REVERT: C 422 ARG cc_start: 0.8410 (tpt90) cc_final: 0.7244 (tmt170) REVERT: C 470 GLU cc_start: 0.7590 (tp30) cc_final: 0.6881 (tt0) REVERT: C 519 GLU cc_start: 0.7888 (tp30) cc_final: 0.7342 (tt0) REVERT: C 530 THR cc_start: 0.8501 (p) cc_final: 0.8024 (t) REVERT: C 568 GLN cc_start: 0.7795 (mp10) cc_final: 0.7580 (mp10) REVERT: D 115 GLN cc_start: 0.8351 (mm110) cc_final: 0.7690 (pp30) REVERT: D 180 MET cc_start: 0.8404 (mtm) cc_final: 0.8121 (mtt) REVERT: D 234 ASP cc_start: 0.8506 (t0) cc_final: 0.8233 (t0) REVERT: D 522 GLN cc_start: 0.7422 (mp10) cc_final: 0.6988 (mp10) REVERT: D 560 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7226 (ttp-110) outliers start: 13 outliers final: 11 residues processed: 114 average time/residue: 0.1427 time to fit residues: 20.8806 Evaluate side-chains 116 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 74 optimal weight: 0.0670 chunk 82 optimal weight: 3.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN C 541 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.102717 restraints weight = 10101.891| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.75 r_work: 0.2852 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9050 Z= 0.141 Angle : 0.529 7.174 12299 Z= 0.261 Chirality : 0.040 0.149 1435 Planarity : 0.004 0.037 1565 Dihedral : 5.556 53.962 1276 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.74 % Allowed : 11.55 % Favored : 86.71 % 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: 1.00 (0.25), residues: 1133 helix: 1.43 (0.20), residues: 690 sheet: -0.36 (0.77), residues: 50 loop : -0.50 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 139 TYR 0.021 0.001 TYR D 88 PHE 0.011 0.001 PHE C 181 TRP 0.017 0.001 TRP D 81 HIS 0.005 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9050) covalent geometry : angle 0.52853 (12299) hydrogen bonds : bond 0.04115 ( 526) hydrogen bonds : angle 4.01961 ( 1539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.319 Fit side-chains REVERT: C 114 TYR cc_start: 0.7154 (m-80) cc_final: 0.6914 (m-80) REVERT: C 160 PHE cc_start: 0.7780 (m-80) cc_final: 0.7303 (m-80) REVERT: C 422 ARG cc_start: 0.8409 (tpt90) cc_final: 0.7171 (tmt170) REVERT: C 470 GLU cc_start: 0.7574 (tp30) cc_final: 0.6809 (tt0) REVERT: C 519 GLU cc_start: 0.7853 (tp30) cc_final: 0.7315 (tt0) REVERT: C 530 THR cc_start: 0.8451 (p) cc_final: 0.7981 (t) REVERT: C 568 GLN cc_start: 0.7727 (mp10) cc_final: 0.7495 (mp10) REVERT: D 115 GLN cc_start: 0.8318 (mm110) cc_final: 0.7605 (pp30) REVERT: D 180 MET cc_start: 0.8302 (mtm) cc_final: 0.7997 (mtt) REVERT: D 234 ASP cc_start: 0.8478 (t0) cc_final: 0.8163 (t0) REVERT: D 522 GLN cc_start: 0.7376 (mp10) cc_final: 0.6963 (mp10) REVERT: D 525 MET cc_start: 0.8185 (mmp) cc_final: 0.7777 (mmt) REVERT: D 560 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7147 (ttp-110) outliers start: 16 outliers final: 12 residues processed: 119 average time/residue: 0.1370 time to fit residues: 21.0054 Evaluate side-chains 120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105521 restraints weight = 10069.077| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.74 r_work: 0.2961 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9050 Z= 0.114 Angle : 0.504 7.173 12299 Z= 0.249 Chirality : 0.039 0.148 1435 Planarity : 0.004 0.038 1565 Dihedral : 5.331 48.547 1276 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.53 % Allowed : 11.98 % Favored : 86.49 % 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: 1.22 (0.25), residues: 1133 helix: 1.63 (0.20), residues: 690 sheet: -0.38 (0.77), residues: 50 loop : -0.45 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 139 TYR 0.020 0.001 TYR D 88 PHE 0.011 0.001 PHE D 256 TRP 0.019 0.001 TRP D 81 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9050) covalent geometry : angle 0.50392 (12299) hydrogen bonds : bond 0.03863 ( 526) hydrogen bonds : angle 3.92128 ( 1539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.338 Fit side-chains REVERT: C 114 TYR cc_start: 0.7219 (m-80) cc_final: 0.6988 (m-80) REVERT: C 160 PHE cc_start: 0.7813 (m-80) cc_final: 0.7364 (m-80) REVERT: C 422 ARG cc_start: 0.8351 (tpt90) cc_final: 0.7192 (tmt170) REVERT: C 470 GLU cc_start: 0.7604 (tp30) cc_final: 0.6895 (tt0) REVERT: C 519 GLU cc_start: 0.7891 (tp30) cc_final: 0.7391 (tt0) REVERT: C 530 THR cc_start: 0.8418 (p) cc_final: 0.7966 (t) REVERT: D 115 GLN cc_start: 0.8334 (mm110) cc_final: 0.7698 (pp30) REVERT: D 180 MET cc_start: 0.8379 (mtm) cc_final: 0.8106 (mtt) REVERT: D 234 ASP cc_start: 0.8470 (t0) cc_final: 0.8195 (t0) REVERT: D 522 GLN cc_start: 0.7447 (mp10) cc_final: 0.7015 (mp10) REVERT: D 525 MET cc_start: 0.8322 (mmp) cc_final: 0.7975 (mmt) REVERT: D 560 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7219 (ttp-110) outliers start: 14 outliers final: 12 residues processed: 118 average time/residue: 0.1376 time to fit residues: 20.9795 Evaluate side-chains 120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.103291 restraints weight = 10056.830| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.74 r_work: 0.2873 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9050 Z= 0.163 Angle : 0.550 7.541 12299 Z= 0.270 Chirality : 0.042 0.177 1435 Planarity : 0.004 0.038 1565 Dihedral : 5.382 48.963 1276 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.74 % Allowed : 12.31 % Favored : 85.95 % 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: 1.10 (0.25), residues: 1133 helix: 1.52 (0.20), residues: 690 sheet: -0.42 (0.77), residues: 50 loop : -0.48 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 139 TYR 0.021 0.001 TYR D 88 PHE 0.013 0.001 PHE C 181 TRP 0.016 0.001 TRP D 81 HIS 0.005 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9050) covalent geometry : angle 0.55022 (12299) hydrogen bonds : bond 0.04222 ( 526) hydrogen bonds : angle 4.04238 ( 1539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.330 Fit side-chains REVERT: C 114 TYR cc_start: 0.7273 (m-80) cc_final: 0.7007 (m-80) REVERT: C 160 PHE cc_start: 0.7779 (m-80) cc_final: 0.7310 (m-80) REVERT: C 422 ARG cc_start: 0.8422 (tpt90) cc_final: 0.7215 (tmt170) REVERT: C 470 GLU cc_start: 0.7625 (tp30) cc_final: 0.6925 (tt0) REVERT: C 519 GLU cc_start: 0.7882 (tp30) cc_final: 0.7380 (tt0) REVERT: C 530 THR cc_start: 0.8481 (p) cc_final: 0.7964 (t) REVERT: D 115 GLN cc_start: 0.8372 (mm110) cc_final: 0.7667 (pp30) REVERT: D 180 MET cc_start: 0.8374 (mtm) cc_final: 0.8064 (mtt) REVERT: D 234 ASP cc_start: 0.8499 (t0) cc_final: 0.8198 (t0) REVERT: D 522 GLN cc_start: 0.7348 (mp10) cc_final: 0.6937 (mp10) REVERT: D 560 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7203 (ttp-110) outliers start: 16 outliers final: 13 residues processed: 115 average time/residue: 0.1423 time to fit residues: 20.9445 Evaluate side-chains 117 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 69 optimal weight: 0.0370 chunk 109 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.104526 restraints weight = 10034.378| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.75 r_work: 0.2899 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9050 Z= 0.118 Angle : 0.518 7.442 12299 Z= 0.257 Chirality : 0.040 0.177 1435 Planarity : 0.004 0.038 1565 Dihedral : 5.236 46.511 1276 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.42 % Allowed : 12.85 % Favored : 85.73 % 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: 1.28 (0.25), residues: 1133 helix: 1.69 (0.20), residues: 690 sheet: -0.34 (0.77), residues: 50 loop : -0.44 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 139 TYR 0.020 0.001 TYR D 88 PHE 0.011 0.001 PHE D 256 TRP 0.019 0.001 TRP D 81 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9050) covalent geometry : angle 0.51796 (12299) hydrogen bonds : bond 0.03904 ( 526) hydrogen bonds : angle 3.93992 ( 1539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.382 Fit side-chains REVERT: C 114 TYR cc_start: 0.7170 (m-80) cc_final: 0.6959 (m-80) REVERT: C 160 PHE cc_start: 0.7750 (m-80) cc_final: 0.7288 (m-80) REVERT: C 422 ARG cc_start: 0.8383 (tpt90) cc_final: 0.7153 (tmt170) REVERT: C 470 GLU cc_start: 0.7560 (tp30) cc_final: 0.6817 (tt0) REVERT: C 519 GLU cc_start: 0.7875 (tp30) cc_final: 0.7410 (tt0) REVERT: C 530 THR cc_start: 0.8348 (p) cc_final: 0.7888 (t) REVERT: D 115 GLN cc_start: 0.8336 (mm110) cc_final: 0.7652 (pp30) REVERT: D 180 MET cc_start: 0.8339 (mtm) cc_final: 0.8033 (mtt) REVERT: D 234 ASP cc_start: 0.8456 (t0) cc_final: 0.8166 (t0) REVERT: D 522 GLN cc_start: 0.7383 (mp10) cc_final: 0.6955 (mp10) REVERT: D 525 MET cc_start: 0.8123 (mmt) cc_final: 0.7698 (mmt) REVERT: D 560 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7222 (ttp-110) outliers start: 13 outliers final: 12 residues processed: 114 average time/residue: 0.1358 time to fit residues: 20.0165 Evaluate side-chains 115 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 555 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.105087 restraints weight = 9955.864| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.75 r_work: 0.2906 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9050 Z= 0.116 Angle : 0.505 7.649 12299 Z= 0.249 Chirality : 0.040 0.179 1435 Planarity : 0.004 0.039 1565 Dihedral : 5.128 46.002 1276 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.42 % Allowed : 12.75 % Favored : 85.84 % 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: 1.39 (0.25), residues: 1133 helix: 1.78 (0.20), residues: 690 sheet: -0.26 (0.78), residues: 50 loop : -0.41 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 139 TYR 0.020 0.001 TYR D 88 PHE 0.010 0.001 PHE D 256 TRP 0.018 0.001 TRP D 81 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9050) covalent geometry : angle 0.50505 (12299) hydrogen bonds : bond 0.03846 ( 526) hydrogen bonds : angle 3.89809 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2516.62 seconds wall clock time: 43 minutes 37.90 seconds (2617.90 seconds total)