Starting phenix.real_space_refine on Thu Jul 2 21:50:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pmc_13528/07_2026/7pmc_13528.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmc_13528/07_2026/7pmc_13528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pmc_13528/07_2026/7pmc_13528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmc_13528/07_2026/7pmc_13528.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pmc_13528/07_2026/7pmc_13528.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pmc_13528/07_2026/7pmc_13528.cif" model { file = "/net/cci-nas-00/data/ceres_data/7pmc_13528/07_2026/7pmc_13528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmc_13528/07_2026/7pmc_13528.cif" } resolution = 3.7 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 63 5.16 5 C 6457 2.51 5 N 1722 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 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: 10139 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: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 6069 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 5 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 1.86, per 1000 atoms: 0.18 Number of scatterers: 10139 At special positions: 0 Unit cell: (111.3, 140.98, 144.16, 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 63 16.00 P 4 15.00 Mg 2 11.99 O 1891 8.00 N 1722 7.00 C 6457 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: 0.70 Conformation dependent library (CDL) restraints added in 224.7 milliseconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 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: 2372 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 16 sheets defined 55.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.309A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.779A 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 66 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.007A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.509A pdb=" N SER A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.930A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.793A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.587A 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: 3.586A pdb=" N VAL A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 removed outlier: 4.062A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 4.381A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.680A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 315 removed outlier: 3.664A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.789A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.735A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.598A pdb=" N ASN A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 479 Processing helix chain 'A' and resid 483 through 487 removed outlier: 4.006A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 506 through 515 removed outlier: 3.515A pdb=" N CYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.733A 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 Processing helix chain 'A' and resid 573 through 582 removed outlier: 4.130A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.955A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 595 No H-bonds generated for 'chain 'A' and resid 594 through 595' Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 635 through 653 removed outlier: 3.639A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 712 through 715 Processing helix chain 'A' and resid 716 through 720 Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.941A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 792 removed outlier: 3.630A pdb=" N TYR A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.573A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 128 removed outlier: 4.082A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 4.139A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.911A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.705A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.588A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.504A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 4.294A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.787A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.820A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 349 removed outlier: 4.250A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 375 removed outlier: 3.675A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE C 375 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 12 through 15 removed outlier: 3.832A pdb=" N LEU A 48 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA5, first strand: chain 'A' and resid 234 through 242 removed outlier: 3.774A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA8, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AB1, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.671A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.179A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 107 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.721A pdb=" N MET C 176 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.547A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 241 512 hydrogen bonds defined for protein. 1413 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: 1.18 Time building geometry restraints manager: 0.97 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: 1740 1.32 - 1.44: 2695 1.44 - 1.57: 5811 1.57 - 1.69: 6 1.69 - 1.81: 102 Bond restraints: 10354 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 3.72e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.202 0.061 2.00e-02 2.50e+03 9.42e+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 8.61e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.464 0.061 2.10e-02 2.27e+03 8.57e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.398 -0.051 2.00e-02 2.50e+03 6.58e+00 ... (remaining 10349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 13372 2.37 - 4.74: 541 4.74 - 7.12: 62 7.12 - 9.49: 8 9.49 - 11.86: 4 Bond angle restraints: 13987 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 121.70 109.84 11.86 1.80e+00 3.09e-01 4.34e+01 angle pdb=" C VAL A 720 " pdb=" N LEU A 721 " pdb=" CA LEU A 721 " ideal model delta sigma weight residual 121.85 130.82 -8.97 1.77e+00 3.19e-01 2.57e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.80 -4.80 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 110.10 102.06 8.04 1.90e+00 2.77e-01 1.79e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.25 4.15 1.00e+00 1.00e+00 1.72e+01 ... (remaining 13982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.59: 6095 33.59 - 67.18: 109 67.18 - 100.76: 28 100.76 - 134.35: 6 134.35 - 167.94: 1 Dihedral angle restraints: 6239 sinusoidal: 2561 harmonic: 3678 Sorted by residual: dihedral pdb=" O1B ADP A1902 " pdb=" O3A ADP A1902 " pdb=" PB ADP A1902 " pdb=" PA ADP A1902 " ideal model delta sinusoidal sigma weight residual -60.00 107.94 -167.94 1 2.00e+01 2.50e-03 4.75e+01 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 71.54 -131.54 1 2.00e+01 2.50e-03 3.99e+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 300.00 169.31 130.69 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 6236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.021: 1527 1.021 - 2.041: 0 2.041 - 3.062: 0 3.062 - 4.083: 0 4.083 - 5.103: 2 Chirality restraints: 1529 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 6.51e+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 PHE C 255 " pdb=" N PHE C 255 " pdb=" C PHE C 255 " pdb=" CB PHE C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1526 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.139 9.50e-02 1.11e+02 8.14e-02 3.68e+01 pdb=" NE ARG A 248 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " -0.100 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.028 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 4.48e-02 2.01e+01 pdb=" C THR C 89 " 0.078 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 C 312 " -0.106 9.50e-02 1.11e+02 5.91e-02 1.69e+01 pdb=" NE ARG C 312 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG C 312 " -0.067 2.00e-02 2.50e+03 pdb=" NH1 ARG C 312 " 0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG C 312 " 0.019 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 12 2.37 - 3.00: 5761 3.00 - 3.63: 15190 3.63 - 4.27: 22666 4.27 - 4.90: 38044 Nonbonded interactions: 81673 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.952 2.170 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 1.965 2.170 nonbonded pdb=" OH TYR C 218 " pdb=" OE2 GLU C 226 " model vdw 2.164 3.040 nonbonded pdb=" O LYS B 26 " pdb=" NH2 ARG B 64 " model vdw 2.190 3.120 ... (remaining 81668 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: 2.220 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: 0.010 Process input model: 7.870 Find NCS groups from input model: 0.020 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.008 0.122 10356 Z= 0.381 Angle : 1.069 11.861 13993 Z= 0.624 Chirality : 0.191 5.103 1529 Planarity : 0.008 0.106 1783 Dihedral : 16.084 167.941 3861 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.81 % 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: -1.41 (0.21), residues: 1229 helix: -1.52 (0.16), residues: 583 sheet: 0.23 (0.40), residues: 145 loop : -0.26 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.010 ARG A 248 TYR 0.045 0.007 TYR B 89 PHE 0.043 0.004 PHE A 673 TRP 0.029 0.004 TRP A 484 HIS 0.013 0.003 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.38 (10354) covalent geometry : angle 1.06510 / 0.62 (13987) hydrogen bonds : bond 0.16861 / 10.89 ( 510) hydrogen bonds : angle 8.10511 / 5.58 ( 1413) link_TRANS : bond 0.00934 / 0.49 ( 2) link_TRANS : angle 4.27402 / 2.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8846 (tp) cc_final: 0.8405 (pp) REVERT: B 116 LEU cc_start: 0.8707 (mt) cc_final: 0.8505 (mp) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.1012 time to fit residues: 24.7697 Evaluate side-chains 91 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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: 125 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN A 81 HIS A 156 ASN A 191 ASN A 264 GLN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS A 464 GLN A 468 HIS C 121 GLN C 137 GLN C 162 ASN C 225 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.075541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056330 restraints weight = 43704.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.058113 restraints weight = 22301.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.059319 restraints weight = 14290.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.060113 restraints weight = 10415.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.060515 restraints weight = 8350.286| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10356 Z= 0.149 Angle : 0.672 7.463 13993 Z= 0.354 Chirality : 0.044 0.205 1529 Planarity : 0.005 0.065 1783 Dihedral : 10.007 131.661 1392 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.11 % Allowed : 6.94 % Favored : 91.94 % 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: 0.60 (0.23), residues: 1229 helix: 0.57 (0.20), residues: 606 sheet: 0.29 (0.39), residues: 171 loop : 0.48 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 343 TYR 0.016 0.002 TYR B 89 PHE 0.025 0.002 PHE A 360 TRP 0.029 0.003 TRP A 781 HIS 0.011 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (10354) covalent geometry : angle 0.67190 / 0.35 (13987) hydrogen bonds : bond 0.03768 / 2.46 ( 510) hydrogen bonds : angle 5.47237 / 3.69 ( 1413) link_TRANS : bond 0.00464 / 0.22 ( 2) link_TRANS : angle 1.08281 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8924 (tp) cc_final: 0.8529 (pp) REVERT: A 164 GLU cc_start: 0.7205 (tt0) cc_final: 0.6898 (mt-10) REVERT: A 177 MET cc_start: 0.8227 (ppp) cc_final: 0.8004 (ppp) REVERT: A 788 MET cc_start: -0.1909 (mtt) cc_final: -0.2136 (ptp) REVERT: C 305 MET cc_start: 0.8809 (mmt) cc_final: 0.8515 (tpt) outliers start: 12 outliers final: 7 residues processed: 136 average time/residue: 0.0807 time to fit residues: 15.7436 Evaluate side-chains 92 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN A 743 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.074997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.055824 restraints weight = 44168.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057642 restraints weight = 22519.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.058829 restraints weight = 14305.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059604 restraints weight = 10403.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.060067 restraints weight = 8367.789| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10356 Z= 0.131 Angle : 0.601 6.934 13993 Z= 0.311 Chirality : 0.042 0.186 1529 Planarity : 0.004 0.059 1783 Dihedral : 8.390 125.327 1391 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.67 % Allowed : 8.70 % Favored : 89.63 % 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: 1.02 (0.24), residues: 1229 helix: 1.14 (0.21), residues: 607 sheet: 0.33 (0.43), residues: 153 loop : 0.38 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 343 TYR 0.012 0.001 TYR C 91 PHE 0.026 0.002 PHE A 360 TRP 0.020 0.002 TRP A 484 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10354) covalent geometry : angle 0.60143 / 0.31 (13987) hydrogen bonds : bond 0.03406 / 2.22 ( 510) hydrogen bonds : angle 5.06201 / 3.44 ( 1413) link_TRANS : bond 0.00214 / 0.11 ( 2) link_TRANS : angle 0.49499 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.6491 (pmm) cc_final: 0.5842 (mmt) REVERT: A 164 GLU cc_start: 0.7119 (tt0) cc_final: 0.6818 (tt0) REVERT: A 177 MET cc_start: 0.8131 (ppp) cc_final: 0.7901 (ppp) REVERT: C 132 MET cc_start: 0.7888 (tmm) cc_final: 0.7671 (tmm) REVERT: C 225 ASN cc_start: 0.8755 (m-40) cc_final: 0.8539 (m110) REVERT: C 227 MET cc_start: 0.8054 (tpp) cc_final: 0.7620 (tmm) REVERT: C 305 MET cc_start: 0.8788 (mmt) cc_final: 0.8511 (tpt) outliers start: 18 outliers final: 11 residues processed: 116 average time/residue: 0.0818 time to fit residues: 13.9737 Evaluate side-chains 92 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 107 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 98 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN A 464 GLN ** A 638 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 = 0.3668 r_free = 0.3668 target = 0.074755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.055507 restraints weight = 44426.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057321 restraints weight = 22849.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.058461 restraints weight = 14597.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.059228 restraints weight = 10706.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.059729 restraints weight = 8607.090| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10356 Z= 0.125 Angle : 0.585 8.964 13993 Z= 0.297 Chirality : 0.041 0.180 1529 Planarity : 0.004 0.057 1783 Dihedral : 7.173 117.371 1391 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.30 % Allowed : 10.28 % Favored : 88.43 % 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: 1.29 (0.24), residues: 1229 helix: 1.41 (0.21), residues: 607 sheet: 0.42 (0.42), residues: 161 loop : 0.44 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 248 TYR 0.011 0.001 TYR A 259 PHE 0.027 0.001 PHE C 352 TRP 0.012 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10354) covalent geometry : angle 0.58556 / 0.30 (13987) hydrogen bonds : bond 0.03234 / 2.11 ( 510) hydrogen bonds : angle 4.87815 / 3.31 ( 1413) link_TRANS : bond 0.00168 / 0.09 ( 2) link_TRANS : angle 0.36693 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.8135 (ppp) cc_final: 0.7861 (ppp) REVERT: A 477 TYR cc_start: 0.8834 (m-80) cc_final: 0.8279 (t80) REVERT: C 227 MET cc_start: 0.8057 (tpp) cc_final: 0.7650 (tmm) REVERT: C 305 MET cc_start: 0.8896 (mmt) cc_final: 0.8684 (tpt) outliers start: 14 outliers final: 11 residues processed: 106 average time/residue: 0.0761 time to fit residues: 11.8648 Evaluate side-chains 96 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 21 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 0.0040 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 91 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 31 GLN A 111 ASN A 191 ASN ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.074512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.055358 restraints weight = 44511.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057164 restraints weight = 22865.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.058340 restraints weight = 14624.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.059086 restraints weight = 10617.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.059618 restraints weight = 8592.060| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10356 Z= 0.123 Angle : 0.578 8.820 13993 Z= 0.290 Chirality : 0.041 0.180 1529 Planarity : 0.004 0.056 1783 Dihedral : 6.865 112.119 1391 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.76 % Allowed : 10.37 % Favored : 87.87 % 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: 1.33 (0.24), residues: 1229 helix: 1.52 (0.21), residues: 605 sheet: 0.25 (0.43), residues: 154 loop : 0.43 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 343 TYR 0.015 0.001 TYR A 127 PHE 0.023 0.001 PHE A 360 TRP 0.018 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10354) covalent geometry : angle 0.57796 / 0.29 (13987) hydrogen bonds : bond 0.03172 / 2.06 ( 510) hydrogen bonds : angle 4.74355 / 3.21 ( 1413) link_TRANS : bond 0.00168 / 0.09 ( 2) link_TRANS : angle 0.30123 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8858 (mt) cc_final: 0.8480 (pp) REVERT: A 164 GLU cc_start: 0.7231 (tt0) cc_final: 0.6892 (mt-10) REVERT: C 132 MET cc_start: 0.8007 (tmm) cc_final: 0.7728 (tmm) REVERT: C 227 MET cc_start: 0.7951 (tpp) cc_final: 0.7632 (tmm) outliers start: 19 outliers final: 14 residues processed: 110 average time/residue: 0.0827 time to fit residues: 13.2029 Evaluate side-chains 97 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 32 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.074019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.054948 restraints weight = 44849.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.056745 restraints weight = 22997.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.057866 restraints weight = 14640.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058620 restraints weight = 10745.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.059143 restraints weight = 8655.740| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10356 Z= 0.135 Angle : 0.605 9.383 13993 Z= 0.300 Chirality : 0.041 0.182 1529 Planarity : 0.004 0.056 1783 Dihedral : 6.811 111.142 1391 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.04 % Allowed : 10.83 % Favored : 87.13 % 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: 1.41 (0.24), residues: 1229 helix: 1.60 (0.21), residues: 604 sheet: 0.36 (0.42), residues: 162 loop : 0.42 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 343 TYR 0.011 0.001 TYR A 259 PHE 0.022 0.001 PHE A 360 TRP 0.025 0.002 TRP A 484 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (10354) covalent geometry : angle 0.60465 / 0.30 (13987) hydrogen bonds : bond 0.03228 / 2.10 ( 510) hydrogen bonds : angle 4.72829 / 3.20 ( 1413) link_TRANS : bond 0.00188 / 0.10 ( 2) link_TRANS : angle 0.31785 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8917 (mt) cc_final: 0.8522 (pp) REVERT: A 477 TYR cc_start: 0.8934 (m-80) cc_final: 0.8630 (t80) REVERT: C 132 MET cc_start: 0.7920 (tmm) cc_final: 0.7595 (tmm) outliers start: 22 outliers final: 20 residues processed: 105 average time/residue: 0.0786 time to fit residues: 12.0305 Evaluate side-chains 102 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 354 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 0.0970 chunk 93 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 ASN A 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.074371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.055569 restraints weight = 43973.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.057365 restraints weight = 22495.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.058512 restraints weight = 14278.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.059270 restraints weight = 10393.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.059802 restraints weight = 8356.222| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10356 Z= 0.117 Angle : 0.586 9.472 13993 Z= 0.291 Chirality : 0.041 0.182 1529 Planarity : 0.004 0.053 1783 Dihedral : 6.668 110.135 1391 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.22 % Allowed : 11.30 % Favored : 86.48 % 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: 1.37 (0.24), residues: 1229 helix: 1.59 (0.21), residues: 606 sheet: 0.33 (0.44), residues: 154 loop : 0.36 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 343 TYR 0.010 0.001 TYR A 259 PHE 0.026 0.001 PHE C 352 TRP 0.017 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10354) covalent geometry : angle 0.58631 / 0.29 (13987) hydrogen bonds : bond 0.03100 / 2.00 ( 510) hydrogen bonds : angle 4.65479 / 3.13 ( 1413) link_TRANS : bond 0.00156 / 0.08 ( 2) link_TRANS : angle 0.27444 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 477 TYR cc_start: 0.8936 (m-80) cc_final: 0.8523 (t80) REVERT: A 633 LYS cc_start: 0.8551 (pttt) cc_final: 0.8091 (pptt) REVERT: C 132 MET cc_start: 0.7929 (tmm) cc_final: 0.7552 (tmm) outliers start: 24 outliers final: 20 residues processed: 107 average time/residue: 0.0779 time to fit residues: 12.2608 Evaluate side-chains 104 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 109 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.073591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054531 restraints weight = 44755.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056294 restraints weight = 23160.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.057418 restraints weight = 14837.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058187 restraints weight = 10902.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.058677 restraints weight = 8766.217| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10356 Z= 0.147 Angle : 0.626 8.916 13993 Z= 0.311 Chirality : 0.041 0.186 1529 Planarity : 0.004 0.056 1783 Dihedral : 6.726 110.507 1391 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.94 % Allowed : 12.41 % Favored : 85.65 % 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: 1.36 (0.24), residues: 1229 helix: 1.62 (0.21), residues: 601 sheet: 0.35 (0.43), residues: 162 loop : 0.30 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.012 0.001 TYR A 259 PHE 0.026 0.001 PHE C 352 TRP 0.014 0.001 TRP A 484 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (10354) covalent geometry : angle 0.62608 / 0.31 (13987) hydrogen bonds : bond 0.03274 / 2.14 ( 510) hydrogen bonds : angle 4.70129 / 3.18 ( 1413) link_TRANS : bond 0.00215 / 0.11 ( 2) link_TRANS : angle 0.34505 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 477 TYR cc_start: 0.8901 (m-80) cc_final: 0.8613 (t80) REVERT: A 633 LYS cc_start: 0.8578 (pttt) cc_final: 0.8101 (pptt) REVERT: C 14 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7439 (p) REVERT: C 132 MET cc_start: 0.8019 (tmm) cc_final: 0.7605 (tmm) outliers start: 21 outliers final: 16 residues processed: 98 average time/residue: 0.0834 time to fit residues: 12.1723 Evaluate side-chains 100 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.073055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.054208 restraints weight = 44591.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.055974 restraints weight = 22984.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.057114 restraints weight = 14729.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.057864 restraints weight = 10764.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.058370 restraints weight = 8656.130| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10356 Z= 0.152 Angle : 0.636 9.974 13993 Z= 0.315 Chirality : 0.041 0.187 1529 Planarity : 0.004 0.053 1783 Dihedral : 6.762 110.134 1391 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.85 % Allowed : 12.69 % Favored : 85.46 % 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: 1.34 (0.24), residues: 1229 helix: 1.69 (0.21), residues: 598 sheet: 0.12 (0.44), residues: 155 loop : 0.27 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.012 0.001 TYR A 259 PHE 0.023 0.002 PHE C 352 TRP 0.011 0.001 TRP A 484 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (10354) covalent geometry : angle 0.63582 / 0.31 (13987) hydrogen bonds : bond 0.03304 / 2.15 ( 510) hydrogen bonds : angle 4.73346 / 3.20 ( 1413) link_TRANS : bond 0.00223 / 0.12 ( 2) link_TRANS : angle 0.33572 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 467 MET cc_start: 0.8470 (mtm) cc_final: 0.8112 (mpp) REVERT: A 477 TYR cc_start: 0.8876 (m-80) cc_final: 0.8592 (t80) REVERT: A 633 LYS cc_start: 0.8581 (pttt) cc_final: 0.8112 (pptt) REVERT: C 14 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7276 (p) REVERT: C 132 MET cc_start: 0.8073 (tmm) cc_final: 0.7684 (tmm) outliers start: 20 outliers final: 15 residues processed: 96 average time/residue: 0.0774 time to fit residues: 11.0608 Evaluate side-chains 98 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 124 optimal weight: 0.0000 chunk 120 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.075179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056238 restraints weight = 43940.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058051 restraints weight = 22715.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.059224 restraints weight = 14535.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059986 restraints weight = 10646.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.060531 restraints weight = 8570.180| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10356 Z= 0.105 Angle : 0.615 9.802 13993 Z= 0.301 Chirality : 0.040 0.181 1529 Planarity : 0.004 0.052 1783 Dihedral : 6.467 112.897 1391 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.20 % Allowed : 13.52 % Favored : 85.28 % 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: 1.48 (0.25), residues: 1229 helix: 1.78 (0.21), residues: 604 sheet: 0.33 (0.45), residues: 153 loop : 0.29 (0.29), residues: 472 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 0.023 0.001 PHE B 93 TRP 0.011 0.001 TRP A 484 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (10354) covalent geometry : angle 0.61493 / 0.30 (13987) hydrogen bonds : bond 0.02949 / 1.92 ( 510) hydrogen bonds : angle 4.51414 / 3.03 ( 1413) link_TRANS : bond 0.00081 / 0.04 ( 2) link_TRANS : angle 0.21040 / 0.14 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 464 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8424 (tp-100) REVERT: A 467 MET cc_start: 0.8433 (mtm) cc_final: 0.8099 (mpp) REVERT: A 477 TYR cc_start: 0.8779 (m-80) cc_final: 0.8541 (t80) REVERT: A 500 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: A 633 LYS cc_start: 0.8584 (pttt) cc_final: 0.8211 (pttp) REVERT: C 14 SER cc_start: 0.7782 (OUTLIER) cc_final: 0.6968 (p) REVERT: C 132 MET cc_start: 0.8019 (tmm) cc_final: 0.7593 (tmm) outliers start: 13 outliers final: 11 residues processed: 102 average time/residue: 0.0771 time to fit residues: 11.5888 Evaluate side-chains 99 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.0060 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.074518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.055710 restraints weight = 44146.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057531 restraints weight = 22842.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058504 restraints weight = 14568.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.059373 restraints weight = 11028.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.059905 restraints weight = 8729.421| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10356 Z= 0.110 Angle : 0.617 9.655 13993 Z= 0.301 Chirality : 0.040 0.181 1529 Planarity : 0.004 0.052 1783 Dihedral : 6.394 119.834 1391 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.39 % Allowed : 13.61 % Favored : 85.00 % 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: 1.56 (0.25), residues: 1229 helix: 1.84 (0.22), residues: 604 sheet: 0.51 (0.43), residues: 162 loop : 0.27 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.010 0.001 TYR A 259 PHE 0.023 0.001 PHE B 93 TRP 0.010 0.001 TRP A 484 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10354) covalent geometry : angle 0.61720 / 0.30 (13987) hydrogen bonds : bond 0.02968 / 1.93 ( 510) hydrogen bonds : angle 4.48911 / 3.02 ( 1413) link_TRANS : bond 0.00107 / 0.06 ( 2) link_TRANS : angle 0.21835 / 0.14 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1606.12 seconds wall clock time: 28 minutes 30.65 seconds (1710.65 seconds total)