Starting phenix.real_space_refine on Thu Jul 2 21:29:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pma_13526/07_2026/7pma_13526.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pma_13526/07_2026/7pma_13526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pma_13526/07_2026/7pma_13526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pma_13526/07_2026/7pma_13526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pma_13526/07_2026/7pma_13526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pma_13526/07_2026/7pma_13526.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pma_13526/07_2026/7pma_13526.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pma_13526/07_2026/7pma_13526.cif" } resolution = 3.6 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= 0.001 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 4 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 6412 2.51 5 N 1710 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10066 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5987 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 6 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.80, per 1000 atoms: 0.18 Number of scatterers: 10066 At special positions: 0 Unit cell: (102.82, 142.04, 149.46, 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 62 16.00 P 4 15.00 Mg 2 11.99 O 1876 8.00 N 1710 7.00 C 6412 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 360.5 milliseconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 14 sheets defined 55.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.054A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.696A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.693A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.740A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.505A pdb=" N VAL A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.051A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 4.371A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.624A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 4.367A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.887A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.699A pdb=" N LYS A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 423 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 479 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.837A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.504A pdb=" N ILE A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.561A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.505A pdb=" N LYS A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.550A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.839A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 removed outlier: 3.724A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 685 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 removed outlier: 4.053A pdb=" N SER A 709 " --> pdb=" O GLN A 705 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.769A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.921A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.827A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.960A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.589A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.145A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.830A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.574A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.344A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.791A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 349 removed outlier: 4.397A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.536A pdb=" N GLN C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 354' Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.725A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.532A pdb=" N VAL B 65 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 17 removed outlier: 3.972A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP A 17 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLN A 39 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.534A pdb=" N SER A 162 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.640A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.674A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 521 hydrogen bonds defined for protein. 1479 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: 1.60 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1671 1.32 - 1.44: 2728 1.44 - 1.56: 5775 1.56 - 1.69: 6 1.69 - 1.81: 100 Bond restraints: 10280 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.201 0.062 2.00e-02 2.50e+03 9.59e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.64e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.40e-02 5.10e+03 8.47e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.47e+00 ... (remaining 10275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13529 2.38 - 4.75: 295 4.75 - 7.13: 50 7.13 - 9.50: 7 9.50 - 11.88: 6 Bond angle restraints: 13887 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 109.82 11.88 1.80e+00 3.09e-01 4.36e+01 angle pdb=" C LYS A 668 " pdb=" N PHE A 669 " pdb=" CA PHE A 669 " ideal model delta sigma weight residual 122.48 130.29 -7.81 1.77e+00 3.19e-01 1.95e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.79 -4.79 1.10e+00 8.26e-01 1.90e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.08 8.02 1.90e+00 2.77e-01 1.78e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.28 4.12 1.00e+00 1.00e+00 1.70e+01 ... (remaining 13882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 6022 31.82 - 63.65: 120 63.65 - 95.47: 40 95.47 - 127.29: 3 127.29 - 159.12: 2 Dihedral angle restraints: 6187 sinusoidal: 2539 harmonic: 3648 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 99.12 -159.12 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.39 -135.39 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 175.57 124.43 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 6184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 1515 1.020 - 2.040: 0 2.040 - 3.060: 0 3.060 - 4.081: 0 4.081 - 5.101: 2 Chirality restraints: 1517 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.40 4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" CA TYR A 10 " pdb=" N TYR A 10 " pdb=" C TYR A 10 " pdb=" CB TYR A 10 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1514 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.111 9.50e-02 1.11e+02 6.47e-02 2.29e+01 pdb=" NE ARG A 248 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " -0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 89 " -0.022 2.00e-02 2.50e+03 4.41e-02 1.94e+01 pdb=" C THR C 89 " 0.076 2.00e-02 2.50e+03 pdb=" O THR C 89 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE C 90 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 231 " 0.233 9.50e-02 1.11e+02 1.08e-01 1.45e+01 pdb=" NE ARG A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 231 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A 231 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 231 " 0.025 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 12 2.37 - 3.00: 5465 3.00 - 3.63: 15172 3.63 - 4.27: 22395 4.27 - 4.90: 37952 Nonbonded interactions: 80996 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 2.060 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.073 2.170 nonbonded pdb="MG MG A1901 " pdb=" O3B ADP A1902 " model vdw 2.155 2.170 nonbonded pdb=" O PHE A 698 " pdb=" NH1 ARG A 701 " model vdw 2.184 3.120 ... (remaining 80991 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 group one per residue 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: 2.380 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.004 0.122 10282 Z= 0.216 Angle : 0.887 11.880 13893 Z= 0.516 Chirality : 0.189 5.101 1517 Planarity : 0.008 0.108 1770 Dihedral : 15.793 159.118 3829 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.08 % 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: -1.07 (0.21), residues: 1218 helix: -1.28 (0.17), residues: 572 sheet: 0.60 (0.37), residues: 165 loop : -0.16 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.080 0.012 ARG A 248 TYR 0.035 0.006 TYR A 113 PHE 0.029 0.002 PHE A 673 TRP 0.059 0.003 TRP A 484 HIS 0.006 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.22 (10280) covalent geometry : angle 0.88298 / 0.51 (13887) hydrogen bonds : bond 0.16761 / 11.45 ( 519) hydrogen bonds : angle 7.40991 / 5.21 ( 1479) link_TRANS : bond 0.00886 / 0.46 ( 2) link_TRANS : angle 4.26422 / 2.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ILE cc_start: 0.8764 (pt) cc_final: 0.8528 (pt) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.0937 time to fit residues: 20.7344 Evaluate side-chains 90 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.0370 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN A 264 GLN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS A 395 HIS A 410 ASN ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 533 ASN A 642 ASN A 652 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.067166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.047673 restraints weight = 45569.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049346 restraints weight = 22240.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.050435 restraints weight = 13762.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.051210 restraints weight = 9819.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.051663 restraints weight = 7697.323| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10282 Z= 0.149 Angle : 0.705 11.063 13893 Z= 0.360 Chirality : 0.044 0.191 1517 Planarity : 0.004 0.044 1770 Dihedral : 9.548 168.442 1382 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 0.65 % Allowed : 6.16 % Favored : 93.18 % Cbeta Deviations : 0.08 % 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: 1.12 (0.23), residues: 1218 helix: 1.02 (0.20), residues: 592 sheet: 0.89 (0.38), residues: 166 loop : 0.53 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 95 TYR 0.016 0.001 TYR A 711 PHE 0.029 0.002 PHE A 360 TRP 0.015 0.002 TRP C 356 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (10280) covalent geometry : angle 0.70510 / 0.36 (13887) hydrogen bonds : bond 0.04431 / 2.85 ( 519) hydrogen bonds : angle 5.27095 / 3.67 ( 1479) link_TRANS : bond 0.00115 / 0.06 ( 2) link_TRANS : angle 1.03590 / 0.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.7366 (tp40) cc_final: 0.7101 (tp-100) REVERT: A 305 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8124 (ptp) REVERT: C 217 CYS cc_start: 0.8638 (m) cc_final: 0.7854 (m) outliers start: 7 outliers final: 3 residues processed: 112 average time/residue: 0.0924 time to fit residues: 15.1263 Evaluate side-chains 87 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.066114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.046905 restraints weight = 45970.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048542 restraints weight = 22353.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.049639 restraints weight = 13708.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.050352 restraints weight = 9781.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.050833 restraints weight = 7714.881| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10282 Z= 0.157 Angle : 0.646 10.857 13893 Z= 0.327 Chirality : 0.043 0.222 1517 Planarity : 0.004 0.041 1770 Dihedral : 8.836 178.440 1381 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.31 % Allowed : 7.10 % Favored : 91.60 % Cbeta Deviations : 0.08 % 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: 1.58 (0.24), residues: 1218 helix: 1.45 (0.21), residues: 604 sheet: 1.02 (0.39), residues: 165 loop : 0.70 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.009 0.001 TYR A 711 PHE 0.017 0.002 PHE B 96 TRP 0.013 0.002 TRP C 356 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (10280) covalent geometry : angle 0.64588 / 0.33 (13887) hydrogen bonds : bond 0.04072 / 2.61 ( 519) hydrogen bonds : angle 5.02331 / 3.49 ( 1479) link_TRANS : bond 0.00166 / 0.09 ( 2) link_TRANS : angle 0.33348 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 HIS cc_start: 0.8734 (OUTLIER) cc_final: 0.8485 (m90) REVERT: C 78 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8327 (p0) REVERT: C 217 CYS cc_start: 0.8733 (m) cc_final: 0.7984 (m) REVERT: C 225 ASN cc_start: 0.8954 (m-40) cc_final: 0.8206 (t0) outliers start: 14 outliers final: 6 residues processed: 91 average time/residue: 0.0739 time to fit residues: 10.0418 Evaluate side-chains 77 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.0980 chunk 96 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 70 optimal weight: 0.0870 chunk 9 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.067015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.047678 restraints weight = 45889.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049353 restraints weight = 22167.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.050520 restraints weight = 13609.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.051197 restraints weight = 9565.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051702 restraints weight = 7591.689| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10282 Z= 0.117 Angle : 0.617 10.096 13893 Z= 0.309 Chirality : 0.042 0.205 1517 Planarity : 0.004 0.038 1770 Dihedral : 8.337 169.688 1381 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.21 % Allowed : 7.66 % Favored : 91.13 % Cbeta Deviations : 0.08 % 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: 1.72 (0.24), residues: 1218 helix: 1.66 (0.22), residues: 598 sheet: 1.00 (0.39), residues: 167 loop : 0.66 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 343 TYR 0.010 0.001 TYR A 658 PHE 0.028 0.001 PHE A 360 TRP 0.009 0.001 TRP C 356 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10280) covalent geometry : angle 0.61693 / 0.31 (13887) hydrogen bonds : bond 0.03654 / 2.31 ( 519) hydrogen bonds : angle 4.88815 / 3.38 ( 1479) link_TRANS : bond 0.00109 / 0.06 ( 2) link_TRANS : angle 0.12880 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.8720 (mp0) cc_final: 0.8412 (mp0) REVERT: A 418 HIS cc_start: 0.8994 (OUTLIER) cc_final: 0.8742 (m170) REVERT: A 520 ASP cc_start: 0.8325 (m-30) cc_final: 0.7972 (m-30) REVERT: C 86 TRP cc_start: 0.9213 (m-10) cc_final: 0.9011 (m-10) REVERT: C 189 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9251 (tp) REVERT: C 217 CYS cc_start: 0.8711 (m) cc_final: 0.7912 (m) REVERT: C 225 ASN cc_start: 0.8870 (m-40) cc_final: 0.8116 (t0) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.0971 time to fit residues: 13.8947 Evaluate side-chains 83 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.066317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047040 restraints weight = 45972.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.048710 restraints weight = 22196.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.049795 restraints weight = 13645.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050545 restraints weight = 9750.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050984 restraints weight = 7683.755| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10282 Z= 0.138 Angle : 0.612 11.019 13893 Z= 0.301 Chirality : 0.042 0.231 1517 Planarity : 0.004 0.037 1770 Dihedral : 7.699 149.765 1381 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.31 % Allowed : 8.03 % Favored : 90.66 % Cbeta Deviations : 0.08 % 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: 1.76 (0.24), residues: 1218 helix: 1.71 (0.22), residues: 602 sheet: 0.97 (0.39), residues: 167 loop : 0.66 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 257 TYR 0.010 0.001 TYR A 658 PHE 0.031 0.001 PHE A 360 TRP 0.009 0.001 TRP C 356 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10280) covalent geometry : angle 0.61180 / 0.30 (13887) hydrogen bonds : bond 0.03612 / 2.29 ( 519) hydrogen bonds : angle 4.81258 / 3.33 ( 1479) link_TRANS : bond 0.00191 / 0.10 ( 2) link_TRANS : angle 0.20204 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.8672 (mp0) cc_final: 0.8342 (mp0) REVERT: A 135 MET cc_start: 0.8785 (mmm) cc_final: 0.8145 (mmm) REVERT: A 418 HIS cc_start: 0.8790 (OUTLIER) cc_final: 0.8500 (m90) REVERT: A 477 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8474 (t80) REVERT: A 702 TRP cc_start: 0.8163 (t-100) cc_final: 0.7689 (t-100) REVERT: C 217 CYS cc_start: 0.8821 (m) cc_final: 0.8124 (m) REVERT: C 225 ASN cc_start: 0.8906 (m-40) cc_final: 0.8153 (t0) outliers start: 14 outliers final: 9 residues processed: 88 average time/residue: 0.0935 time to fit residues: 12.3892 Evaluate side-chains 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 681 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.047106 restraints weight = 46077.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.048765 restraints weight = 22408.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049918 restraints weight = 13808.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050568 restraints weight = 9779.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.051078 restraints weight = 7815.629| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10282 Z= 0.126 Angle : 0.609 10.049 13893 Z= 0.297 Chirality : 0.041 0.208 1517 Planarity : 0.004 0.036 1770 Dihedral : 7.188 129.858 1381 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.59 % Allowed : 8.50 % Favored : 89.92 % Cbeta Deviations : 0.08 % 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: 1.82 (0.24), residues: 1218 helix: 1.77 (0.22), residues: 601 sheet: 1.01 (0.39), residues: 163 loop : 0.68 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 257 TYR 0.010 0.001 TYR A 284 PHE 0.029 0.001 PHE A 360 TRP 0.009 0.001 TRP C 356 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10280) covalent geometry : angle 0.60934 / 0.30 (13887) hydrogen bonds : bond 0.03418 / 2.18 ( 519) hydrogen bonds : angle 4.77287 / 3.29 ( 1479) link_TRANS : bond 0.00162 / 0.08 ( 2) link_TRANS : angle 0.16884 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7620 (tt0) REVERT: B 68 GLU cc_start: 0.8637 (mp0) cc_final: 0.8300 (mp0) REVERT: A 418 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8517 (m170) REVERT: A 442 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7744 (pp20) REVERT: A 477 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8473 (t80) REVERT: A 702 TRP cc_start: 0.8134 (t-100) cc_final: 0.7663 (t-100) REVERT: A 788 MET cc_start: -0.1125 (mmm) cc_final: -0.1365 (mmm) REVERT: C 86 TRP cc_start: 0.9154 (m-10) cc_final: 0.8944 (m-10) REVERT: C 132 MET cc_start: 0.9041 (tmm) cc_final: 0.8755 (tmm) REVERT: C 176 MET cc_start: 0.8266 (mmm) cc_final: 0.8044 (mmt) REVERT: C 217 CYS cc_start: 0.8865 (m) cc_final: 0.8180 (m) REVERT: C 225 ASN cc_start: 0.8863 (m-40) cc_final: 0.8150 (t0) outliers start: 17 outliers final: 11 residues processed: 92 average time/residue: 0.0945 time to fit residues: 12.9940 Evaluate side-chains 84 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS A 775 GLN C 12 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.046522 restraints weight = 46130.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.048144 restraints weight = 22533.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049246 restraints weight = 14047.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049924 restraints weight = 10049.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.050392 restraints weight = 8019.994| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10282 Z= 0.148 Angle : 0.608 11.975 13893 Z= 0.297 Chirality : 0.041 0.197 1517 Planarity : 0.004 0.036 1770 Dihedral : 6.842 113.310 1381 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.49 % Allowed : 9.24 % Favored : 89.26 % Cbeta Deviations : 0.08 % 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: 1.87 (0.24), residues: 1218 helix: 1.85 (0.22), residues: 601 sheet: 1.00 (0.40), residues: 163 loop : 0.65 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 257 TYR 0.009 0.001 TYR A 284 PHE 0.028 0.001 PHE A 360 TRP 0.010 0.001 TRP A 781 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10280) covalent geometry : angle 0.60834 / 0.30 (13887) hydrogen bonds : bond 0.03439 / 2.22 ( 519) hydrogen bonds : angle 4.80637 / 3.32 ( 1479) link_TRANS : bond 0.00213 / 0.11 ( 2) link_TRANS : angle 0.25021 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.7805 (tp-100) cc_final: 0.7464 (tt0) REVERT: B 68 GLU cc_start: 0.8625 (mp0) cc_final: 0.8289 (mp0) REVERT: A 418 HIS cc_start: 0.8664 (OUTLIER) cc_final: 0.8432 (m90) REVERT: A 442 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7833 (pp20) REVERT: A 477 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8492 (t80) REVERT: A 648 MET cc_start: 0.9121 (tpp) cc_final: 0.8836 (tpp) REVERT: A 702 TRP cc_start: 0.8160 (t-100) cc_final: 0.7688 (t-100) REVERT: C 86 TRP cc_start: 0.9154 (m-10) cc_final: 0.8923 (m-10) REVERT: C 217 CYS cc_start: 0.8898 (m) cc_final: 0.8206 (m) REVERT: C 225 ASN cc_start: 0.8872 (m-40) cc_final: 0.8160 (t0) outliers start: 16 outliers final: 10 residues processed: 88 average time/residue: 0.0839 time to fit residues: 10.9661 Evaluate side-chains 86 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.066369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.046858 restraints weight = 45866.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.048517 restraints weight = 22463.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.049603 restraints weight = 13953.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050286 restraints weight = 10007.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050810 restraints weight = 7978.034| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10282 Z= 0.130 Angle : 0.617 11.761 13893 Z= 0.297 Chirality : 0.041 0.195 1517 Planarity : 0.004 0.038 1770 Dihedral : 6.690 107.928 1381 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.68 % Allowed : 9.06 % Favored : 89.26 % Cbeta Deviations : 0.08 % 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: 1.83 (0.24), residues: 1218 helix: 1.84 (0.22), residues: 601 sheet: 0.90 (0.40), residues: 163 loop : 0.63 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 343 TYR 0.011 0.001 TYR A 284 PHE 0.027 0.001 PHE A 360 TRP 0.009 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10280) covalent geometry : angle 0.61721 / 0.30 (13887) hydrogen bonds : bond 0.03369 / 2.16 ( 519) hydrogen bonds : angle 4.74584 / 3.27 ( 1479) link_TRANS : bond 0.00167 / 0.09 ( 2) link_TRANS : angle 0.18113 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7508 (tt0) REVERT: A 477 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8509 (t80) REVERT: A 648 MET cc_start: 0.9084 (tpp) cc_final: 0.8762 (tpp) REVERT: A 702 TRP cc_start: 0.8147 (t-100) cc_final: 0.7668 (t-100) REVERT: C 86 TRP cc_start: 0.9042 (m-10) cc_final: 0.8834 (m-10) REVERT: C 132 MET cc_start: 0.9095 (tmm) cc_final: 0.8655 (tmm) REVERT: C 176 MET cc_start: 0.8175 (mmm) cc_final: 0.7902 (mmt) REVERT: C 217 CYS cc_start: 0.8903 (m) cc_final: 0.8200 (m) REVERT: C 225 ASN cc_start: 0.8860 (m-40) cc_final: 0.8155 (t0) outliers start: 18 outliers final: 10 residues processed: 89 average time/residue: 0.0769 time to fit residues: 10.2664 Evaluate side-chains 79 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS A 418 HIS C 12 ASN C 161 HIS ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.064570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.045144 restraints weight = 45927.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.046720 restraints weight = 22583.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047763 restraints weight = 14103.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048429 restraints weight = 10134.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048921 restraints weight = 8086.632| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10282 Z= 0.216 Angle : 0.670 12.066 13893 Z= 0.328 Chirality : 0.043 0.203 1517 Planarity : 0.004 0.035 1770 Dihedral : 6.906 107.575 1381 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.40 % Allowed : 9.62 % Favored : 88.98 % Cbeta Deviations : 0.08 % 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: 1.66 (0.24), residues: 1218 helix: 1.73 (0.22), residues: 600 sheet: 0.82 (0.41), residues: 153 loop : 0.53 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 343 TYR 0.012 0.001 TYR A 284 PHE 0.025 0.002 PHE A 360 TRP 0.030 0.002 TRP A 781 HIS 0.009 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (10280) covalent geometry : angle 0.67024 / 0.33 (13887) hydrogen bonds : bond 0.03840 / 2.48 ( 519) hydrogen bonds : angle 4.94702 / 3.42 ( 1479) link_TRANS : bond 0.00342 / 0.18 ( 2) link_TRANS : angle 0.38035 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.8606 (mp0) cc_final: 0.8235 (mp0) REVERT: A 477 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.8561 (t80) REVERT: A 702 TRP cc_start: 0.8204 (t-100) cc_final: 0.7752 (t-100) REVERT: C 217 CYS cc_start: 0.8931 (m) cc_final: 0.8286 (m) REVERT: C 225 ASN cc_start: 0.8911 (m-40) cc_final: 0.8194 (t0) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.0918 time to fit residues: 11.3565 Evaluate side-chains 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 102 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 105 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS C 12 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.046446 restraints weight = 45151.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048068 restraints weight = 22282.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049101 restraints weight = 13893.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049837 restraints weight = 10039.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.050287 restraints weight = 8003.548| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10282 Z= 0.126 Angle : 0.647 11.630 13893 Z= 0.310 Chirality : 0.041 0.199 1517 Planarity : 0.004 0.037 1770 Dihedral : 6.626 100.578 1381 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.21 % Allowed : 9.80 % Favored : 88.98 % Cbeta Deviations : 0.08 % 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: 1.77 (0.24), residues: 1218 helix: 1.88 (0.22), residues: 597 sheet: 0.68 (0.40), residues: 163 loop : 0.57 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 343 TYR 0.012 0.001 TYR A 284 PHE 0.026 0.001 PHE A 360 TRP 0.025 0.002 TRP A 781 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10280) covalent geometry : angle 0.64709 / 0.31 (13887) hydrogen bonds : bond 0.03453 / 2.19 ( 519) hydrogen bonds : angle 4.81407 / 3.32 ( 1479) link_TRANS : bond 0.00149 / 0.08 ( 2) link_TRANS : angle 0.12983 / 0.08 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7667 (tt0) REVERT: A 135 MET cc_start: 0.8807 (mmm) cc_final: 0.8239 (mmm) REVERT: A 477 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8526 (t80) REVERT: A 702 TRP cc_start: 0.8191 (t-100) cc_final: 0.7735 (t-100) REVERT: C 86 TRP cc_start: 0.9206 (m-10) cc_final: 0.8949 (m-10) REVERT: C 217 CYS cc_start: 0.8911 (m) cc_final: 0.8192 (m) REVERT: C 225 ASN cc_start: 0.8875 (m-40) cc_final: 0.8175 (t0) outliers start: 13 outliers final: 9 residues processed: 85 average time/residue: 0.0998 time to fit residues: 12.2929 Evaluate side-chains 80 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.066204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.046521 restraints weight = 45521.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.048189 restraints weight = 22305.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.049284 restraints weight = 13842.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050036 restraints weight = 9901.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.050560 restraints weight = 7819.965| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10282 Z= 0.126 Angle : 0.659 11.341 13893 Z= 0.316 Chirality : 0.041 0.194 1517 Planarity : 0.004 0.037 1770 Dihedral : 6.567 99.265 1381 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.03 % Allowed : 10.18 % Favored : 88.80 % Cbeta Deviations : 0.08 % 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: 1.78 (0.24), residues: 1218 helix: 1.90 (0.22), residues: 598 sheet: 0.66 (0.40), residues: 163 loop : 0.55 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 343 TYR 0.012 0.001 TYR A 284 PHE 0.026 0.001 PHE A 360 TRP 0.023 0.002 TRP A 781 HIS 0.008 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10280) covalent geometry : angle 0.65894 / 0.32 (13887) hydrogen bonds : bond 0.03379 / 2.16 ( 519) hydrogen bonds : angle 4.74225 / 3.28 ( 1479) link_TRANS : bond 0.00149 / 0.08 ( 2) link_TRANS : angle 0.14161 / 0.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.91 seconds wall clock time: 34 minutes 9.92 seconds (2049.92 seconds total)