Starting phenix.real_space_refine on Thu Feb 13 12:17:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdv_14671/02_2025/7zdv_14671_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdv_14671/02_2025/7zdv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zdv_14671/02_2025/7zdv_14671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdv_14671/02_2025/7zdv_14671.map" model { file = "/net/cci-nas-00/data/ceres_data/7zdv_14671/02_2025/7zdv_14671_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdv_14671/02_2025/7zdv_14671_neut.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 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: 5.73, per 1000 atoms: 0.65 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: 2.21 Conformation dependent library (CDL) restraints added in 963.3 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: 0.98 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: 2.86 Time building geometry restraints manager: 2.57 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.550 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- 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= 0.364 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.002 TRP D 427 HIS 0.007 0.001 HIS C 94 PHE 0.009 0.001 PHE D 371 TYR 0.014 0.001 TYR D 88 ARG 0.006 0.000 ARG C 522 *********************** 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 : 0.954 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: 0.3157 time to fit residues: 44.8634 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 : 0.996 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.0070 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 0.0670 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.149196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.103909 restraints weight = 9999.447| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.71 r_work: 0.2897 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1411 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= 0.179 Angle : 0.613 7.812 12299 Z= 0.306 Chirality : 0.040 0.164 1435 Planarity : 0.005 0.040 1565 Dihedral : 8.149 93.646 1276 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.33 % Allowed : 4.68 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.24), residues: 1133 helix: -0.35 (0.19), residues: 690 sheet: -0.84 (0.76), residues: 48 loop : -0.75 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 81 HIS 0.003 0.001 HIS D 542 PHE 0.014 0.001 PHE D 32 TYR 0.021 0.001 TYR D 88 ARG 0.008 0.000 ARG D 139 *********************** 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 122 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 1.025 Fit side-chains REVERT: C 160 PHE cc_start: 0.7796 (m-80) cc_final: 0.7282 (m-80) REVERT: C 364 ASN cc_start: 0.8461 (m-40) cc_final: 0.7947 (m110) REVERT: C 422 ARG cc_start: 0.8429 (tpt90) cc_final: 0.7143 (tmt170) REVERT: C 519 GLU cc_start: 0.7780 (tp30) cc_final: 0.7436 (tt0) REVERT: D 115 GLN cc_start: 0.8304 (mm110) cc_final: 0.7489 (pp30) REVERT: D 234 ASP cc_start: 0.8441 (t0) cc_final: 0.8178 (t0) REVERT: D 522 GLN cc_start: 0.7293 (mp10) cc_final: 0.6908 (mp10) REVERT: D 560 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7227 (ttp-110) outliers start: 3 outliers final: 3 residues processed: 121 average time/residue: 0.2731 time to fit residues: 43.4961 Evaluate side-chains 102 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 390 TRP 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 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.0270 chunk 30 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 248 GLN C 541 GLN D 334 HIS D 424 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.150318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104164 restraints weight = 10061.429| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.77 r_work: 0.2895 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9050 Z= 0.176 Angle : 0.537 6.804 12299 Z= 0.266 Chirality : 0.040 0.157 1435 Planarity : 0.004 0.036 1565 Dihedral : 6.599 72.097 1276 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.87 % Allowed : 8.28 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1133 helix: 0.74 (0.20), residues: 690 sheet: -0.79 (0.69), residues: 56 loop : -0.61 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 81 HIS 0.004 0.001 HIS C 94 PHE 0.011 0.001 PHE D 32 TYR 0.020 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 *********************** 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 116 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.969 Fit side-chains REVERT: C 114 TYR cc_start: 0.7214 (m-80) cc_final: 0.6936 (m-80) REVERT: C 160 PHE cc_start: 0.7787 (m-80) cc_final: 0.7297 (m-80) REVERT: C 422 ARG cc_start: 0.8381 (tpt90) cc_final: 0.7163 (tmt170) REVERT: C 470 GLU cc_start: 0.7536 (tp30) cc_final: 0.6851 (tt0) REVERT: C 519 GLU cc_start: 0.7844 (tp30) cc_final: 0.7352 (tt0) REVERT: C 568 GLN cc_start: 0.7765 (mp10) cc_final: 0.7472 (mp10) REVERT: D 115 GLN cc_start: 0.8300 (mm110) cc_final: 0.7554 (pp30) REVERT: D 180 MET cc_start: 0.8362 (mtm) cc_final: 0.8109 (mtt) REVERT: D 414 ARG cc_start: 0.8046 (ptm160) cc_final: 0.7829 (ptm160) REVERT: D 522 GLN cc_start: 0.7287 (mp10) cc_final: 0.6876 (mp10) REVERT: D 560 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7181 (ttp-110) outliers start: 8 outliers final: 5 residues processed: 111 average time/residue: 0.3382 time to fit residues: 48.7907 Evaluate side-chains 106 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.149427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.102739 restraints weight = 10008.447| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.83 r_work: 0.2853 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9050 Z= 0.215 Angle : 0.543 6.943 12299 Z= 0.267 Chirality : 0.041 0.151 1435 Planarity : 0.004 0.036 1565 Dihedral : 6.183 66.349 1276 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.09 % Allowed : 9.69 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1133 helix: 1.01 (0.20), residues: 690 sheet: -0.69 (0.75), residues: 50 loop : -0.56 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.005 0.001 HIS C 94 PHE 0.011 0.001 PHE C 181 TYR 0.021 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 *********************** 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 : 1.055 Fit side-chains REVERT: C 114 TYR cc_start: 0.7199 (m-80) cc_final: 0.6933 (m-80) REVERT: C 160 PHE cc_start: 0.7804 (m-80) cc_final: 0.7326 (m-80) REVERT: C 422 ARG cc_start: 0.8394 (tpt90) cc_final: 0.7176 (tmt170) REVERT: C 452 ARG cc_start: 0.8509 (mtp180) cc_final: 0.8177 (mtm110) REVERT: C 470 GLU cc_start: 0.7591 (tp30) cc_final: 0.6845 (tt0) REVERT: C 519 GLU cc_start: 0.7819 (tp30) cc_final: 0.7311 (tt0) REVERT: C 568 GLN cc_start: 0.7786 (mp10) cc_final: 0.7436 (mp10) REVERT: D 115 GLN cc_start: 0.8350 (mm110) cc_final: 0.7618 (pp30) REVERT: D 180 MET cc_start: 0.8394 (mtm) cc_final: 0.8124 (mtt) REVERT: D 234 ASP cc_start: 0.8533 (t0) cc_final: 0.8241 (t0) REVERT: D 403 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: D 414 ARG cc_start: 0.8075 (ptm160) cc_final: 0.7837 (ptm160) REVERT: D 522 GLN cc_start: 0.7390 (mp10) cc_final: 0.6968 (mp10) REVERT: D 560 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7227 (ttp-110) outliers start: 10 outliers final: 7 residues processed: 113 average time/residue: 0.2890 time to fit residues: 42.1328 Evaluate side-chains 108 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 403 GLN 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 52 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 111 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.150665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104775 restraints weight = 9964.712| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.74 r_work: 0.2920 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2001 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= 0.169 Angle : 0.519 6.871 12299 Z= 0.256 Chirality : 0.039 0.150 1435 Planarity : 0.004 0.036 1565 Dihedral : 5.883 60.683 1276 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.53 % Allowed : 10.02 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1133 helix: 1.28 (0.20), residues: 690 sheet: -0.51 (0.76), residues: 50 loop : -0.53 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.004 0.001 HIS C 94 PHE 0.010 0.001 PHE D 256 TYR 0.020 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 *********************** 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 124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.998 Fit side-chains REVERT: C 114 TYR cc_start: 0.7176 (m-80) cc_final: 0.6915 (m-80) REVERT: C 160 PHE cc_start: 0.7763 (m-80) cc_final: 0.7303 (m-80) REVERT: C 422 ARG cc_start: 0.8384 (tpt90) cc_final: 0.7208 (tmt170) REVERT: C 470 GLU cc_start: 0.7585 (tp30) cc_final: 0.6851 (tt0) REVERT: C 519 GLU cc_start: 0.7798 (tp30) cc_final: 0.7270 (tt0) REVERT: C 530 THR cc_start: 0.8439 (p) cc_final: 0.7991 (t) REVERT: D 115 GLN cc_start: 0.8345 (mm110) cc_final: 0.7665 (pp30) REVERT: D 180 MET cc_start: 0.8374 (mtm) cc_final: 0.8121 (mtt) REVERT: D 234 ASP cc_start: 0.8490 (t0) cc_final: 0.8200 (t0) REVERT: D 522 GLN cc_start: 0.7398 (mp10) cc_final: 0.6988 (mp10) REVERT: D 560 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7199 (ttp-110) outliers start: 14 outliers final: 9 residues processed: 117 average time/residue: 0.3061 time to fit residues: 46.4809 Evaluate side-chains 113 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.142593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.094295 restraints weight = 10095.713| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.88 r_work: 0.2793 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 0.035 9050 Z= 0.194 Angle : 0.527 6.925 12299 Z= 0.259 Chirality : 0.040 0.149 1435 Planarity : 0.004 0.037 1565 Dihedral : 5.722 57.086 1276 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.31 % Allowed : 11.33 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1133 helix: 1.37 (0.20), residues: 690 sheet: -0.40 (0.77), residues: 50 loop : -0.52 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.004 0.001 HIS C 94 PHE 0.011 0.001 PHE C 181 TYR 0.021 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 *********************** 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: 12 poor density : 109 time to evaluate : 0.964 Fit side-chains REVERT: C 114 TYR cc_start: 0.7121 (m-80) cc_final: 0.6851 (m-80) REVERT: C 160 PHE cc_start: 0.7768 (m-80) cc_final: 0.7311 (m-80) REVERT: C 422 ARG cc_start: 0.8430 (tpt90) cc_final: 0.7198 (tmt170) REVERT: C 470 GLU cc_start: 0.7525 (tp30) cc_final: 0.6770 (tt0) REVERT: C 519 GLU cc_start: 0.7850 (tp30) cc_final: 0.7272 (tt0) REVERT: C 530 THR cc_start: 0.8383 (p) cc_final: 0.7909 (t) REVERT: C 568 GLN cc_start: 0.7729 (mp10) cc_final: 0.7506 (mp10) REVERT: D 115 GLN cc_start: 0.8360 (mm110) cc_final: 0.7635 (pp30) REVERT: D 180 MET cc_start: 0.8368 (mtm) cc_final: 0.8101 (mtt) REVERT: D 234 ASP cc_start: 0.8508 (t0) cc_final: 0.8200 (t0) REVERT: D 522 GLN cc_start: 0.7384 (mp10) cc_final: 0.6952 (mp10) REVERT: D 525 MET cc_start: 0.8132 (mmt) cc_final: 0.7719 (mmt) REVERT: D 560 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7120 (ttp-110) outliers start: 12 outliers final: 10 residues processed: 114 average time/residue: 0.2961 time to fit residues: 43.4570 Evaluate side-chains 116 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 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 103 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 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 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 = 0.3716 r_free = 0.3716 target = 0.151243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108272 restraints weight = 10060.374| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.73 r_work: 0.2902 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2199 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= 0.164 Angle : 0.508 6.894 12299 Z= 0.250 Chirality : 0.039 0.149 1435 Planarity : 0.004 0.038 1565 Dihedral : 5.417 50.713 1276 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.42 % Allowed : 11.44 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1133 helix: 1.59 (0.20), residues: 690 sheet: -0.32 (0.77), residues: 50 loop : -0.47 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 81 HIS 0.003 0.001 HIS C 94 PHE 0.010 0.001 PHE D 256 TYR 0.020 0.001 TYR D 88 ARG 0.010 0.000 ARG D 139 *********************** 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 128 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.940 Fit side-chains REVERT: C 114 TYR cc_start: 0.7144 (m-80) cc_final: 0.6896 (m-80) REVERT: C 160 PHE cc_start: 0.7744 (m-80) cc_final: 0.7303 (m-80) REVERT: C 214 THR cc_start: 0.9063 (m) cc_final: 0.8855 (p) REVERT: C 422 ARG cc_start: 0.8344 (tpt90) cc_final: 0.7153 (tmt170) REVERT: C 470 GLU cc_start: 0.7555 (tp30) cc_final: 0.6821 (tt0) REVERT: C 519 GLU cc_start: 0.7828 (tp30) cc_final: 0.7293 (tt0) REVERT: C 530 THR cc_start: 0.8390 (p) cc_final: 0.7943 (t) REVERT: C 568 GLN cc_start: 0.7761 (mp10) cc_final: 0.7542 (mp10) REVERT: D 115 GLN cc_start: 0.8272 (mm110) cc_final: 0.7648 (pp30) REVERT: D 180 MET cc_start: 0.8358 (mtm) cc_final: 0.8085 (mtt) REVERT: D 234 ASP cc_start: 0.8481 (t0) cc_final: 0.8191 (t0) REVERT: D 522 GLN cc_start: 0.7402 (mp10) cc_final: 0.6976 (mp10) REVERT: D 560 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7195 (ttp-110) outliers start: 13 outliers final: 10 residues processed: 121 average time/residue: 0.2846 time to fit residues: 44.8436 Evaluate side-chains 117 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 D residue 52 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 108 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 248 GLN C 541 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.101676 restraints weight = 10232.976| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.76 r_work: 0.2870 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9050 Z= 0.249 Angle : 0.555 7.493 12299 Z= 0.271 Chirality : 0.041 0.147 1435 Planarity : 0.004 0.037 1565 Dihedral : 5.446 50.081 1276 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.85 % Allowed : 11.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1133 helix: 1.49 (0.20), residues: 690 sheet: -0.38 (0.76), residues: 50 loop : -0.51 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 81 HIS 0.006 0.001 HIS C 94 PHE 0.013 0.001 PHE C 181 TYR 0.021 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 *********************** 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 124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.057 Fit side-chains REVERT: C 114 TYR cc_start: 0.7230 (m-80) cc_final: 0.7011 (m-80) REVERT: C 160 PHE cc_start: 0.7783 (m-80) cc_final: 0.7327 (m-80) REVERT: C 422 ARG cc_start: 0.8429 (tpt90) cc_final: 0.7221 (tmt170) REVERT: C 452 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8089 (mtm110) REVERT: C 470 GLU cc_start: 0.7597 (tp30) cc_final: 0.6855 (tt0) REVERT: C 519 GLU cc_start: 0.7951 (tp30) cc_final: 0.7423 (tt0) REVERT: C 530 THR cc_start: 0.8457 (p) cc_final: 0.7973 (t) REVERT: D 115 GLN cc_start: 0.8350 (mm110) cc_final: 0.7671 (pp30) REVERT: D 180 MET cc_start: 0.8400 (mtm) cc_final: 0.8105 (mtt) REVERT: D 234 ASP cc_start: 0.8492 (t0) cc_final: 0.8198 (t0) REVERT: D 522 GLN cc_start: 0.7404 (mp10) cc_final: 0.6974 (mp10) REVERT: D 560 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7157 (ttp-110) outliers start: 17 outliers final: 10 residues processed: 117 average time/residue: 0.3136 time to fit residues: 47.7128 Evaluate side-chains 117 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 52 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 21 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 83 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 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 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 = 0.3708 r_free = 0.3708 target = 0.150445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.103812 restraints weight = 10028.869| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.77 r_work: 0.2875 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2194 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= 0.184 Angle : 0.521 7.771 12299 Z= 0.255 Chirality : 0.040 0.148 1435 Planarity : 0.004 0.037 1565 Dihedral : 5.332 48.010 1276 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.42 % Allowed : 11.98 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1133 helix: 1.62 (0.20), residues: 690 sheet: -0.33 (0.77), residues: 50 loop : -0.49 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 81 HIS 0.004 0.001 HIS C 94 PHE 0.010 0.001 PHE C 181 TYR 0.020 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 *********************** 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 120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.908 Fit side-chains REVERT: C 114 TYR cc_start: 0.7198 (m-80) cc_final: 0.6973 (m-80) REVERT: C 160 PHE cc_start: 0.7761 (m-80) cc_final: 0.7303 (m-80) REVERT: C 422 ARG cc_start: 0.8420 (tpt90) cc_final: 0.7214 (tmt170) REVERT: C 470 GLU cc_start: 0.7593 (tp30) cc_final: 0.6844 (tt0) REVERT: C 519 GLU cc_start: 0.7889 (tp30) cc_final: 0.7356 (tt0) REVERT: C 530 THR cc_start: 0.8399 (p) cc_final: 0.7939 (t) REVERT: D 115 GLN cc_start: 0.8318 (mm110) cc_final: 0.7665 (pp30) REVERT: D 180 MET cc_start: 0.8365 (mtm) cc_final: 0.8069 (mtt) REVERT: D 234 ASP cc_start: 0.8479 (t0) cc_final: 0.8188 (t0) REVERT: D 522 GLN cc_start: 0.7374 (mp10) cc_final: 0.6949 (mp10) REVERT: D 525 MET cc_start: 0.8127 (mmt) cc_final: 0.7710 (mmt) REVERT: D 560 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7198 (ttp-110) outliers start: 13 outliers final: 13 residues processed: 114 average time/residue: 0.3076 time to fit residues: 45.1648 Evaluate side-chains 119 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 452 ARG Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 533 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 46 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.0000 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 0.0030 chunk 3 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.151052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.104726 restraints weight = 10028.447| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.74 r_work: 0.2956 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9050 Z= 0.146 Angle : 0.503 8.242 12299 Z= 0.247 Chirality : 0.039 0.149 1435 Planarity : 0.004 0.038 1565 Dihedral : 5.153 47.235 1276 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.31 % Allowed : 12.09 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1133 helix: 1.83 (0.20), residues: 690 sheet: -0.39 (0.77), residues: 51 loop : -0.41 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 81 HIS 0.003 0.001 HIS C 94 PHE 0.010 0.001 PHE D 256 TYR 0.019 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 ********************** 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 123 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.126 Fit side-chains REVERT: C 114 TYR cc_start: 0.7152 (m-80) cc_final: 0.6931 (m-80) REVERT: C 160 PHE cc_start: 0.7743 (m-80) cc_final: 0.7343 (m-80) REVERT: C 422 ARG cc_start: 0.8361 (tpt90) cc_final: 0.7187 (tmt170) REVERT: C 470 GLU cc_start: 0.7561 (tp30) cc_final: 0.6827 (tt0) REVERT: C 519 GLU cc_start: 0.7897 (tp30) cc_final: 0.7382 (tt0) REVERT: C 530 THR cc_start: 0.8285 (p) cc_final: 0.7851 (t) REVERT: D 115 GLN cc_start: 0.8295 (mm110) cc_final: 0.7677 (pp30) REVERT: D 180 MET cc_start: 0.8366 (mtm) cc_final: 0.8103 (mtt) REVERT: D 234 ASP cc_start: 0.8452 (t0) cc_final: 0.8178 (t0) REVERT: D 522 GLN cc_start: 0.7385 (mp10) cc_final: 0.6959 (mp10) REVERT: D 525 MET cc_start: 0.8105 (mmt) cc_final: 0.7781 (mmt) REVERT: D 560 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7220 (ttp-110) outliers start: 12 outliers final: 11 residues processed: 117 average time/residue: 0.3053 time to fit residues: 46.5310 Evaluate side-chains 117 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 544 VAL Chi-restraints excluded: chain D residue 52 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 18 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.152062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.105871 restraints weight = 10033.422| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.75 r_work: 0.2925 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9050 Z= 0.151 Angle : 0.504 8.256 12299 Z= 0.247 Chirality : 0.039 0.157 1435 Planarity : 0.004 0.039 1565 Dihedral : 5.062 46.645 1276 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.53 % Allowed : 12.20 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1133 helix: 1.91 (0.20), residues: 690 sheet: -0.19 (0.77), residues: 50 loop : -0.40 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.003 0.001 HIS C 94 PHE 0.009 0.001 PHE D 256 TYR 0.020 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4939.09 seconds wall clock time: 88 minutes 3.83 seconds (5283.83 seconds total)