Starting phenix.real_space_refine on Wed Mar 4 03:26:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmc_13528/03_2026/7pmc_13528.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmc_13528/03_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_13528/03_2026/7pmc_13528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmc_13528/03_2026/7pmc_13528.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmc_13528/03_2026/7pmc_13528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmc_13528/03_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-5986/lib/python3.9/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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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: 2.02, per 1000 atoms: 0.20 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: 0.86 Conformation dependent library (CDL) restraints added in 486.2 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: 0.37 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: 1.81 Time building geometry restraints manager: 1.14 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: 6097 33.59 - 67.18: 117 67.18 - 100.76: 28 100.76 - 134.35: 6 134.35 - 167.94: 1 Dihedral angle restraints: 6249 sinusoidal: 2571 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 6246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 861 0.041 - 0.081: 413 0.081 - 0.122: 171 0.122 - 0.163: 63 0.163 - 0.203: 21 Chirality restraints: 1529 Sorted by residual: 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 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA MET A 364 " pdb=" N MET A 364 " pdb=" C MET A 364 " pdb=" CB MET A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.68e-01 ... (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: 3.230 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.060 0.203 1529 Planarity : 0.008 0.106 1783 Dihedral : 16.215 167.941 3871 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 covalent geometry : bond 0.00844 (10354) covalent geometry : angle 1.06510 (13987) hydrogen bonds : bond 0.16861 ( 510) hydrogen bonds : angle 8.10511 ( 1413) link_TRANS : bond 0.00934 ( 2) link_TRANS : angle 4.27402 ( 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 : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8846 (tp) cc_final: 0.8406 (pp) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.1144 time to fit residues: 27.6772 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 : 0.361 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 455 ASN A 464 GLN A 468 HIS C 121 GLN C 137 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.075308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.056140 restraints weight = 43815.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057922 restraints weight = 22318.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059112 restraints weight = 14297.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.059918 restraints weight = 10406.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.060304 restraints weight = 8330.461| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2751 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= 0.143 Angle : 0.671 7.610 13993 Z= 0.353 Chirality : 0.044 0.257 1529 Planarity : 0.005 0.064 1783 Dihedral : 10.724 132.157 1402 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.02 % Allowed : 7.41 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1229 helix: 0.60 (0.20), residues: 597 sheet: 0.29 (0.38), residues: 171 loop : 0.48 (0.29), residues: 461 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 0.030 0.002 PHE A 360 TRP 0.030 0.003 TRP A 781 HIS 0.011 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00310 (10354) covalent geometry : angle 0.67068 (13987) hydrogen bonds : bond 0.03812 ( 510) hydrogen bonds : angle 5.49624 ( 1413) link_TRANS : bond 0.00376 ( 2) link_TRANS : angle 1.44773 ( 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 138 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8575 (ttm) cc_final: 0.8262 (tpp) REVERT: B 109 LEU cc_start: 0.8946 (tp) cc_final: 0.8564 (pp) REVERT: A 164 GLU cc_start: 0.7159 (tt0) cc_final: 0.6839 (mt-10) REVERT: A 177 MET cc_start: 0.8198 (ppp) cc_final: 0.7971 (ppp) REVERT: C 305 MET cc_start: 0.8770 (mmt) cc_final: 0.8461 (tpt) outliers start: 11 outliers final: 6 residues processed: 134 average time/residue: 0.0907 time to fit residues: 17.6409 Evaluate side-chains 92 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS 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 767 LEU 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: 0.9980 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 130 GLN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN A 464 GLN C 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.073549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054267 restraints weight = 44607.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.056050 restraints weight = 22986.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057183 restraints weight = 14686.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057950 restraints weight = 10780.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.058417 restraints weight = 8687.145| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10356 Z= 0.181 Angle : 0.638 7.019 13993 Z= 0.332 Chirality : 0.043 0.176 1529 Planarity : 0.004 0.059 1783 Dihedral : 9.448 125.635 1402 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.94 % Allowed : 8.98 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1229 helix: 1.01 (0.21), residues: 596 sheet: 0.30 (0.41), residues: 162 loop : 0.35 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 768 TYR 0.014 0.002 TYR A 259 PHE 0.024 0.002 PHE A 360 TRP 0.012 0.002 TRP C 340 HIS 0.008 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00401 (10354) covalent geometry : angle 0.63821 (13987) hydrogen bonds : bond 0.03709 ( 510) hydrogen bonds : angle 5.24901 ( 1413) link_TRANS : bond 0.00308 ( 2) link_TRANS : angle 1.11408 ( 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 118 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.6619 (pmm) cc_final: 0.5948 (mmt) REVERT: A 164 GLU cc_start: 0.7132 (tt0) cc_final: 0.6722 (tt0) REVERT: A 177 MET cc_start: 0.8157 (ppp) cc_final: 0.7935 (ppp) REVERT: A 477 TYR cc_start: 0.8942 (m-80) cc_final: 0.8284 (t80) REVERT: C 132 MET cc_start: 0.7890 (tmm) cc_final: 0.7650 (tmm) REVERT: C 225 ASN cc_start: 0.8747 (m-40) cc_final: 0.8489 (m110) REVERT: C 227 MET cc_start: 0.7967 (tpp) cc_final: 0.7544 (tmm) REVERT: C 299 MET cc_start: 0.8320 (mmp) cc_final: 0.8116 (mmp) REVERT: C 305 MET cc_start: 0.8866 (mmt) cc_final: 0.8628 (tpt) REVERT: C 311 ASP cc_start: 0.8768 (t0) cc_final: 0.8552 (t0) outliers start: 21 outliers final: 17 residues processed: 112 average time/residue: 0.0882 time to fit residues: 14.3534 Evaluate side-chains 93 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 87 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 276 THR Chi-restraints excluded: chain A residue 315 LEU 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 633 LYS Chi-restraints excluded: chain A residue 735 LEU 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: 1.9990 chunk 6 optimal weight: 0.0670 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.074550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.055269 restraints weight = 44707.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.057074 restraints weight = 23115.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058240 restraints weight = 14798.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059019 restraints weight = 10812.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.059486 restraints weight = 8665.185| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10356 Z= 0.121 Angle : 0.585 6.945 13993 Z= 0.298 Chirality : 0.041 0.171 1529 Planarity : 0.004 0.059 1783 Dihedral : 7.869 118.466 1402 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.76 % Allowed : 9.81 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.24), residues: 1229 helix: 1.31 (0.21), residues: 605 sheet: 0.21 (0.43), residues: 155 loop : 0.43 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 768 TYR 0.011 0.001 TYR C 91 PHE 0.024 0.001 PHE C 352 TRP 0.008 0.001 TRP A 523 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00266 (10354) covalent geometry : angle 0.58489 (13987) hydrogen bonds : bond 0.03216 ( 510) hydrogen bonds : angle 4.91346 ( 1413) link_TRANS : bond 0.00247 ( 2) link_TRANS : angle 0.94360 ( 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 119 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8891 (mt) cc_final: 0.8535 (pp) REVERT: A 132 MET cc_start: 0.6738 (pmm) cc_final: 0.5817 (mmt) REVERT: A 164 GLU cc_start: 0.7197 (tt0) cc_final: 0.6968 (tt0) REVERT: A 177 MET cc_start: 0.8146 (ppp) cc_final: 0.7894 (ppp) REVERT: A 477 TYR cc_start: 0.8857 (m-80) cc_final: 0.8479 (t80) REVERT: C 132 MET cc_start: 0.8041 (tmm) cc_final: 0.7840 (tmm) REVERT: C 227 MET cc_start: 0.7976 (tpp) cc_final: 0.7571 (tmm) REVERT: C 299 MET cc_start: 0.8288 (mmp) cc_final: 0.8045 (mmm) outliers start: 19 outliers final: 10 residues processed: 112 average time/residue: 0.0909 time to fit residues: 14.5867 Evaluate side-chains 93 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS 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 767 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 354 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 21 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 191 ASN A 705 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.074012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.054953 restraints weight = 44753.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.056729 restraints weight = 22795.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.057886 restraints weight = 14556.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.058635 restraints weight = 10581.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.059146 restraints weight = 8518.613| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4009 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= 0.127 Angle : 0.585 8.934 13993 Z= 0.294 Chirality : 0.041 0.169 1529 Planarity : 0.004 0.056 1783 Dihedral : 7.503 112.835 1402 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.50 % Allowed : 10.09 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.24), residues: 1229 helix: 1.45 (0.21), residues: 603 sheet: 0.17 (0.43), residues: 155 loop : 0.41 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.014 0.001 TYR A 127 PHE 0.022 0.001 PHE A 360 TRP 0.008 0.001 TRP C 340 HIS 0.006 0.001 HIS A 638 Details of bonding type rmsd covalent geometry : bond 0.00280 (10354) covalent geometry : angle 0.58467 (13987) hydrogen bonds : bond 0.03209 ( 510) hydrogen bonds : angle 4.78181 ( 1413) link_TRANS : bond 0.00255 ( 2) link_TRANS : angle 0.89502 ( 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 118 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8473 (pp) REVERT: A 132 MET cc_start: 0.6707 (pmm) cc_final: 0.5651 (mmt) REVERT: A 477 TYR cc_start: 0.8798 (m-80) cc_final: 0.8484 (t80) REVERT: C 225 ASN cc_start: 0.8639 (m-40) cc_final: 0.8388 (m110) REVERT: C 227 MET cc_start: 0.7985 (tpp) cc_final: 0.7734 (tmm) REVERT: C 241 GLU cc_start: 0.8197 (pp20) cc_final: 0.7955 (tm-30) outliers start: 27 outliers final: 19 residues processed: 111 average time/residue: 0.0891 time to fit residues: 14.4080 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 : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 109 LEU 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 385 GLU Chi-restraints excluded: chain A residue 418 HIS 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 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 328 LYS Chi-restraints excluded: chain C residue 354 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 32 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 0.0070 chunk 90 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.074276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.055392 restraints weight = 44844.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.057187 restraints weight = 22846.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.058359 restraints weight = 14427.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.059103 restraints weight = 10508.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.059637 restraints weight = 8465.145| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10356 Z= 0.115 Angle : 0.584 9.247 13993 Z= 0.289 Chirality : 0.041 0.169 1529 Planarity : 0.004 0.055 1783 Dihedral : 7.246 111.500 1402 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.76 % Allowed : 11.30 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.24), residues: 1229 helix: 1.62 (0.21), residues: 598 sheet: 0.27 (0.43), residues: 154 loop : 0.42 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.010 0.001 TYR C 91 PHE 0.028 0.001 PHE C 352 TRP 0.007 0.001 TRP A 414 HIS 0.005 0.001 HIS A 638 Details of bonding type rmsd covalent geometry : bond 0.00257 (10354) covalent geometry : angle 0.58364 (13987) hydrogen bonds : bond 0.03069 ( 510) hydrogen bonds : angle 4.67583 ( 1413) link_TRANS : bond 0.00249 ( 2) link_TRANS : angle 0.86913 ( 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 114 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8726 (mt) cc_final: 0.8357 (pp) REVERT: A 477 TYR cc_start: 0.8811 (m-80) cc_final: 0.8539 (t80) outliers start: 19 outliers final: 18 residues processed: 110 average time/residue: 0.0950 time to fit residues: 15.0907 Evaluate side-chains 105 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS 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 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 385 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 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 257 CYS 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: 4.9990 chunk 85 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 286 HIS A 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.074145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055098 restraints weight = 44500.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.056833 restraints weight = 22978.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.057998 restraints weight = 14749.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.058738 restraints weight = 10805.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.059294 restraints weight = 8734.785| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10356 Z= 0.124 Angle : 0.591 8.873 13993 Z= 0.291 Chirality : 0.041 0.169 1529 Planarity : 0.004 0.052 1783 Dihedral : 7.115 110.363 1402 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.85 % Allowed : 12.22 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.24), residues: 1229 helix: 1.71 (0.21), residues: 598 sheet: 0.29 (0.44), residues: 154 loop : 0.43 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 768 TYR 0.011 0.001 TYR A 259 PHE 0.024 0.001 PHE C 352 TRP 0.028 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00279 (10354) covalent geometry : angle 0.59055 (13987) hydrogen bonds : bond 0.03088 ( 510) hydrogen bonds : angle 4.62847 ( 1413) link_TRANS : bond 0.00265 ( 2) link_TRANS : angle 0.85011 ( 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 107 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 TYR cc_start: 0.8850 (m-80) cc_final: 0.8561 (t80) REVERT: C 14 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7409 (p) REVERT: C 61 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8668 (mmtm) outliers start: 20 outliers final: 14 residues processed: 102 average time/residue: 0.0925 time to fit residues: 13.6782 Evaluate side-chains 100 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 111 ASN 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 385 GLU 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 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: 0.7980 chunk 43 optimal weight: 0.2980 chunk 117 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 chunk 23 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.074759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.055794 restraints weight = 44222.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057575 restraints weight = 22821.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.058735 restraints weight = 14628.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059541 restraints weight = 10642.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060043 restraints weight = 8521.945| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10356 Z= 0.105 Angle : 0.582 8.294 13993 Z= 0.286 Chirality : 0.040 0.169 1529 Planarity : 0.004 0.052 1783 Dihedral : 6.920 110.680 1402 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.48 % Allowed : 12.69 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.25), residues: 1229 helix: 1.77 (0.21), residues: 602 sheet: 0.42 (0.45), residues: 153 loop : 0.44 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 768 TYR 0.009 0.001 TYR C 91 PHE 0.021 0.001 PHE C 352 TRP 0.033 0.001 TRP A 484 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00232 (10354) covalent geometry : angle 0.58224 (13987) hydrogen bonds : bond 0.03006 ( 510) hydrogen bonds : angle 4.52659 ( 1413) link_TRANS : bond 0.00240 ( 2) link_TRANS : angle 0.84214 ( 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 112 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 TYR cc_start: 0.8779 (m-80) cc_final: 0.8542 (t80) REVERT: A 500 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8364 (pt0) REVERT: A 783 MET cc_start: 0.7212 (mmp) cc_final: 0.6987 (mmp) REVERT: C 14 SER cc_start: 0.8091 (OUTLIER) cc_final: 0.7281 (p) outliers start: 16 outliers final: 13 residues processed: 109 average time/residue: 0.0938 time to fit residues: 14.7515 Evaluate side-chains 100 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR 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 385 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 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: 2.9990 chunk 99 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 121 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.074367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.055331 restraints weight = 44297.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.057114 restraints weight = 23112.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.058291 restraints weight = 14817.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.059043 restraints weight = 10789.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.059625 restraints weight = 8690.795| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10356 Z= 0.119 Angle : 0.612 10.026 13993 Z= 0.298 Chirality : 0.041 0.170 1529 Planarity : 0.004 0.052 1783 Dihedral : 6.855 112.358 1402 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.94 % Allowed : 12.78 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.25), residues: 1229 helix: 1.80 (0.21), residues: 598 sheet: 0.54 (0.43), residues: 162 loop : 0.41 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 768 TYR 0.011 0.001 TYR A 259 PHE 0.022 0.001 PHE C 352 TRP 0.025 0.001 TRP A 484 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00266 (10354) covalent geometry : angle 0.61229 (13987) hydrogen bonds : bond 0.03050 ( 510) hydrogen bonds : angle 4.58334 ( 1413) link_TRANS : bond 0.00257 ( 2) link_TRANS : angle 0.83711 ( 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 107 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 TYR cc_start: 0.8819 (m-80) cc_final: 0.8529 (t80) REVERT: A 500 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: C 14 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7069 (p) REVERT: C 61 LYS cc_start: 0.8710 (mmtm) cc_final: 0.8484 (mmtm) outliers start: 21 outliers final: 16 residues processed: 103 average time/residue: 0.0926 time to fit residues: 13.9459 Evaluate side-chains 102 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 111 ASN 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 385 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 777 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 221 LEU 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: 9.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.0270 chunk 124 optimal weight: 0.0670 chunk 120 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.075146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.056276 restraints weight = 43807.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058073 restraints weight = 22737.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059242 restraints weight = 14562.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.059882 restraints weight = 10617.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.060511 restraints weight = 8709.209| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10356 Z= 0.103 Angle : 0.621 9.792 13993 Z= 0.299 Chirality : 0.040 0.206 1529 Planarity : 0.004 0.049 1783 Dihedral : 6.725 114.441 1402 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.57 % Allowed : 13.43 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.25), residues: 1229 helix: 1.84 (0.21), residues: 600 sheet: 0.44 (0.45), residues: 153 loop : 0.45 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 768 TYR 0.011 0.001 TYR A 113 PHE 0.023 0.001 PHE B 93 TRP 0.020 0.001 TRP A 484 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00226 (10354) covalent geometry : angle 0.62137 (13987) hydrogen bonds : bond 0.02935 ( 510) hydrogen bonds : angle 4.50759 ( 1413) link_TRANS : bond 0.00226 ( 2) link_TRANS : angle 0.84458 ( 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 105 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 CYS cc_start: 0.4602 (OUTLIER) cc_final: 0.2681 (m) REVERT: A 477 TYR cc_start: 0.8736 (m-80) cc_final: 0.8491 (t80) REVERT: A 500 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8401 (pt0) REVERT: A 633 LYS cc_start: 0.8568 (pttt) cc_final: 0.8226 (pttp) outliers start: 17 outliers final: 13 residues processed: 102 average time/residue: 0.0849 time to fit residues: 12.7326 Evaluate side-chains 100 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 385 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 737 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 221 LEU 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: 0.6980 chunk 74 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.1980 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 26 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.074816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.056042 restraints weight = 43998.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.057837 restraints weight = 22833.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.059015 restraints weight = 14575.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.059728 restraints weight = 10619.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.060294 restraints weight = 8576.514| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10356 Z= 0.109 Angle : 0.627 10.515 13993 Z= 0.302 Chirality : 0.041 0.195 1529 Planarity : 0.004 0.050 1783 Dihedral : 6.681 117.361 1402 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.39 % Allowed : 14.17 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.25), residues: 1229 helix: 1.87 (0.21), residues: 601 sheet: 0.56 (0.43), residues: 160 loop : 0.46 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 768 TYR 0.010 0.001 TYR A 127 PHE 0.022 0.001 PHE B 93 TRP 0.018 0.001 TRP A 484 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00245 (10354) covalent geometry : angle 0.62642 (13987) hydrogen bonds : bond 0.02968 ( 510) hydrogen bonds : angle 4.49225 ( 1413) link_TRANS : bond 0.00238 ( 2) link_TRANS : angle 0.83808 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1815.19 seconds wall clock time: 32 minutes 6.79 seconds (1926.79 seconds total)