Starting phenix.real_space_refine on Tue Jan 13 23:35:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tr0_26077/01_2026/7tr0_26077.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tr0_26077/01_2026/7tr0_26077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tr0_26077/01_2026/7tr0_26077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tr0_26077/01_2026/7tr0_26077.map" model { file = "/net/cci-nas-00/data/ceres_data/7tr0_26077/01_2026/7tr0_26077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tr0_26077/01_2026/7tr0_26077.cif" } resolution = 2.7 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= 0.001 sd= 0.005 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 8 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6146 2.51 5 N 1706 2.21 5 O 1909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9833 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3376 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "K" Number of atoms: 2866 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 360, 2843 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 360, 2843 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain breaks: 1 bond proxies already assigned to first conformer: 2855 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.69, per 1000 atoms: 0.27 Number of scatterers: 9833 At special positions: 0 Unit cell: (70.55, 107.9, 110.39, 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 8 15.00 Mg 1 11.99 O 1909 8.00 N 1706 7.00 C 6146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 646.2 milliseconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 9 sheets defined 48.9% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 42 removed outlier: 4.155A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.859A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.642A pdb=" N GLY A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.680A pdb=" N GLU A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.567A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.892A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.880A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.887A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.759A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.216A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.978A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.081A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.090A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.598A pdb=" N ILE B 84 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 85' Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 108 through 126 removed outlier: 4.024A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.700A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.531A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.616A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.716A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.892A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 43 removed outlier: 3.960A pdb=" N LEU K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 124 through 132 removed outlier: 3.586A pdb=" N GLN K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN K 130 " --> pdb=" O LYS K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 166 removed outlier: 3.561A pdb=" N VAL K 161 " --> pdb=" O THR K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 176 removed outlier: 3.714A pdb=" N LEU K 170 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP K 171 " --> pdb=" O GLN K 167 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER K 172 " --> pdb=" O PRO K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 196 Processing helix chain 'K' and resid 203 through 219 Processing helix chain 'K' and resid 274 through 287 Processing helix chain 'K' and resid 339 through 343 Processing helix chain 'K' and resid 347 through 372 removed outlier: 3.938A pdb=" N ASN K 351 " --> pdb=" O GLY K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 378 removed outlier: 3.785A pdb=" N ASN K 377 " --> pdb=" O ARG K 374 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS K 378 " --> pdb=" O ARG K 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 374 through 378' Processing helix chain 'K' and resid 380 through 383 removed outlier: 3.671A pdb=" N ASP K 383 " --> pdb=" O PRO K 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 380 through 383' Processing helix chain 'K' and resid 384 through 390 Processing helix chain 'K' and resid 391 through 394 removed outlier: 4.311A pdb=" N LEU K 394 " --> pdb=" O LYS K 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 391 through 394' Processing helix chain 'K' and resid 409 through 411 No H-bonds generated for 'chain 'K' and resid 409 through 411' Processing helix chain 'K' and resid 412 through 426 removed outlier: 4.071A pdb=" N ALA K 426 " --> pdb=" O TYR K 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 removed outlier: 8.012A pdb=" N LEU A 92 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE A 67 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 removed outlier: 6.668A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.129A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.811A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'K' and resid 150 through 152 removed outlier: 6.353A pdb=" N THR K 180 " --> pdb=" O VAL K 401 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE K 403 " --> pdb=" O THR K 180 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE K 182 " --> pdb=" O ILE K 403 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N CYS K 405 " --> pdb=" O PHE K 182 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR K 184 " --> pdb=" O CYS K 405 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA K 179 " --> pdb=" O SER K 330 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE K 332 " --> pdb=" O ALA K 179 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL K 181 " --> pdb=" O ILE K 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 106 through 110 removed outlier: 3.866A pdb=" N VAL K 109 " --> pdb=" O MET K 113 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET K 113 " --> pdb=" O VAL K 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 254 through 256 Processing sheet with id=AA9, first strand: chain 'K' and resid 291 through 292 removed outlier: 3.790A pdb=" N SER K 300 " --> pdb=" O SER K 292 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1276 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: 1.62 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1752 1.32 - 1.45: 2579 1.45 - 1.57: 5590 1.57 - 1.69: 21 1.69 - 1.81: 98 Bond restraints: 10040 Sorted by residual: bond pdb=" N3B ANP K 501 " pdb=" PG ANP K 501 " ideal model delta sigma weight residual 1.795 1.633 0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C ARG K 240 " pdb=" O ARG K 240 " ideal model delta sigma weight residual 1.235 1.297 -0.062 1.19e-02 7.06e+03 2.72e+01 bond pdb=" O3A ANP K 501 " pdb=" PB ANP K 501 " ideal model delta sigma weight residual 1.700 1.600 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N GLU K 295 " pdb=" CA GLU K 295 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.16e-02 7.43e+03 7.10e+00 bond pdb=" O5' ANP K 501 " pdb=" PA ANP K 501 " ideal model delta sigma weight residual 1.655 1.604 0.051 2.00e-02 2.50e+03 6.46e+00 ... (remaining 10035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 13325 2.34 - 4.69: 256 4.69 - 7.03: 49 7.03 - 9.38: 5 9.38 - 11.72: 2 Bond angle restraints: 13637 Sorted by residual: angle pdb=" N ARG K 129 " pdb=" CA ARG K 129 " pdb=" C ARG K 129 " ideal model delta sigma weight residual 112.23 103.75 8.48 1.26e+00 6.30e-01 4.53e+01 angle pdb=" CB LYS K 430 " pdb=" CG LYS K 430 " pdb=" CD LYS K 430 " ideal model delta sigma weight residual 111.30 123.02 -11.72 2.30e+00 1.89e-01 2.60e+01 angle pdb=" O ARG K 240 " pdb=" C ARG K 240 " pdb=" CA BARG K 240 " ideal model delta sigma weight residual 120.25 126.00 -5.75 1.26e+00 6.30e-01 2.09e+01 angle pdb=" O ARG K 240 " pdb=" C ARG K 240 " pdb=" CA AARG K 240 " ideal model delta sigma weight residual 120.25 125.82 -5.57 1.26e+00 6.30e-01 1.96e+01 angle pdb=" N LEU K 242 " pdb=" CA LEU K 242 " pdb=" C LEU K 242 " ideal model delta sigma weight residual 113.41 108.34 5.07 1.22e+00 6.72e-01 1.73e+01 ... (remaining 13632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.14: 5862 30.14 - 60.28: 239 60.28 - 90.42: 29 90.42 - 120.56: 1 120.56 - 150.70: 13 Dihedral angle restraints: 6144 sinusoidal: 2570 harmonic: 3574 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -140.03 -150.70 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -37.46 142.05 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O3B GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 291.08 169.39 121.69 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 6141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1193 0.052 - 0.104: 231 0.104 - 0.156: 86 0.156 - 0.208: 2 0.208 - 0.260: 2 Chirality restraints: 1514 Sorted by residual: chirality pdb=" C3' ANP K 501 " pdb=" C2' ANP K 501 " pdb=" C4' ANP K 501 " pdb=" O3' ANP K 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ARG K 129 " pdb=" N ARG K 129 " pdb=" C ARG K 129 " pdb=" CB ARG K 129 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR K 165 " pdb=" CA THR K 165 " pdb=" OG1 THR K 165 " pdb=" CG2 THR K 165 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.56e-01 ... (remaining 1511 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN K 128 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C GLN K 128 " -0.049 2.00e-02 2.50e+03 pdb=" O GLN K 128 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG K 129 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR K 422 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C TYR K 422 " 0.031 2.00e-02 2.50e+03 pdb=" O TYR K 422 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA K 423 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " 0.030 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO A 89 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.025 5.00e-02 4.00e+02 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 70 2.58 - 3.16: 8013 3.16 - 3.74: 14907 3.74 - 4.32: 21690 4.32 - 4.90: 37137 Nonbonded interactions: 81817 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 2.005 2.170 nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 2.121 2.170 nonbonded pdb=" O SER B 278 " pdb=" OG SER B 278 " model vdw 2.192 3.040 nonbonded pdb=" O TYR K 235 " pdb=" OG1 THR K 238 " model vdw 2.194 3.040 nonbonded pdb=" OH TYR K 162 " pdb=" OE1 GLU K 211 " model vdw 2.221 3.040 ... (remaining 81812 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.060 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.005 0.162 10040 Z= 0.272 Angle : 0.815 11.724 13637 Z= 0.443 Chirality : 0.049 0.260 1514 Planarity : 0.005 0.054 1770 Dihedral : 18.003 150.698 3844 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.66 % Allowed : 12.27 % Favored : 87.08 % 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: -0.37 (0.24), residues: 1224 helix: 0.83 (0.24), residues: 486 sheet: -0.47 (0.33), residues: 230 loop : -1.14 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 269 TYR 0.021 0.001 TYR K 235 PHE 0.014 0.001 PHE A 149 TRP 0.017 0.002 TRP A 21 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00530 (10040) covalent geometry : angle 0.81460 (13637) hydrogen bonds : bond 0.15725 ( 448) hydrogen bonds : angle 6.16941 ( 1276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 221 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: K 244 ASN cc_start: 0.8480 (t0) cc_final: 0.8142 (t0) REVERT: K 349 ARG cc_start: 0.5922 (mmm-85) cc_final: 0.5450 (mtt180) REVERT: K 424 ASP cc_start: 0.7649 (t70) cc_final: 0.7443 (t0) outliers start: 7 outliers final: 5 residues processed: 228 average time/residue: 0.6090 time to fit residues: 148.3380 Evaluate side-chains 220 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 215 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 372 GLN B 6 HIS B 134 GLN K 130 ASN K 259 ASN K 288 ASN K 310 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.134264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106454 restraints weight = 29604.978| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.91 r_work: 0.3243 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10040 Z= 0.151 Angle : 0.588 9.930 13637 Z= 0.287 Chirality : 0.045 0.235 1514 Planarity : 0.004 0.040 1770 Dihedral : 13.035 148.615 1520 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.50 % Allowed : 12.83 % Favored : 85.67 % 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: 0.25 (0.24), residues: 1224 helix: 1.42 (0.24), residues: 495 sheet: -0.25 (0.33), residues: 230 loop : -0.86 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 269 TYR 0.016 0.001 TYR A 103 PHE 0.011 0.001 PHE B 367 TRP 0.016 0.002 TRP A 21 HIS 0.005 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00358 (10040) covalent geometry : angle 0.58774 (13637) hydrogen bonds : bond 0.04664 ( 448) hydrogen bonds : angle 4.57699 ( 1276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8406 (mtt90) cc_final: 0.8182 (mtm180) REVERT: B 306 ARG cc_start: 0.7763 (mpp80) cc_final: 0.7535 (mpp80) REVERT: K 223 LYS cc_start: 0.7439 (ttmm) cc_final: 0.7238 (ttpt) REVERT: K 288 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8085 (t0) REVERT: K 349 ARG cc_start: 0.6313 (mmm-85) cc_final: 0.5919 (mtt-85) REVERT: K 424 ASP cc_start: 0.8052 (t70) cc_final: 0.7808 (t0) outliers start: 16 outliers final: 10 residues processed: 226 average time/residue: 0.6114 time to fit residues: 147.7158 Evaluate side-chains 226 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 288 ASN Chi-restraints excluded: chain K residue 307 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 28 optimal weight: 0.0000 chunk 32 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 52 ASN B 204 ASN B 307 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106134 restraints weight = 22897.573| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.52 r_work: 0.3251 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10040 Z= 0.200 Angle : 0.588 8.283 13637 Z= 0.290 Chirality : 0.048 0.427 1514 Planarity : 0.004 0.043 1770 Dihedral : 10.046 147.752 1516 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.97 % Allowed : 13.11 % Favored : 84.93 % 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: 0.31 (0.24), residues: 1224 helix: 1.38 (0.24), residues: 497 sheet: 0.04 (0.33), residues: 224 loop : -0.87 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 269 TYR 0.016 0.001 TYR A 103 PHE 0.014 0.002 PHE A 149 TRP 0.017 0.002 TRP A 21 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00497 (10040) covalent geometry : angle 0.58755 (13637) hydrogen bonds : bond 0.04793 ( 448) hydrogen bonds : angle 4.47780 ( 1276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8506 (mtt90) cc_final: 0.8305 (mtm180) REVERT: A 411 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7979 (mm-30) REVERT: K 349 ARG cc_start: 0.6561 (mmm-85) cc_final: 0.6130 (mtt-85) REVERT: K 424 ASP cc_start: 0.8226 (t70) cc_final: 0.7981 (t0) outliers start: 21 outliers final: 14 residues processed: 220 average time/residue: 0.6227 time to fit residues: 146.1242 Evaluate side-chains 227 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 307 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 116 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 43 GLN B 52 ASN B 307 HIS K 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.106612 restraints weight = 32302.554| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.07 r_work: 0.3231 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10040 Z= 0.127 Angle : 0.523 9.219 13637 Z= 0.258 Chirality : 0.044 0.296 1514 Planarity : 0.004 0.041 1770 Dihedral : 9.493 142.507 1516 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.15 % Allowed : 14.14 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.24), residues: 1224 helix: 1.47 (0.24), residues: 505 sheet: 0.20 (0.33), residues: 225 loop : -0.86 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 269 TYR 0.012 0.001 TYR A 103 PHE 0.012 0.001 PHE A 149 TRP 0.016 0.001 TRP A 21 HIS 0.003 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00299 (10040) covalent geometry : angle 0.52313 (13637) hydrogen bonds : bond 0.04019 ( 448) hydrogen bonds : angle 4.27778 ( 1276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.399 Fit side-chains REVERT: K 349 ARG cc_start: 0.6574 (mmm-85) cc_final: 0.6134 (mtt-85) outliers start: 23 outliers final: 9 residues processed: 228 average time/residue: 0.5892 time to fit residues: 143.9451 Evaluate side-chains 211 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 312 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.0170 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 258 ASN B 43 GLN B 307 HIS B 375 GLN K 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.135907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108755 restraints weight = 27456.241| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.80 r_work: 0.3276 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10040 Z= 0.104 Angle : 0.517 15.377 13637 Z= 0.251 Chirality : 0.043 0.251 1514 Planarity : 0.004 0.039 1770 Dihedral : 9.046 138.877 1511 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.59 % Allowed : 15.36 % Favored : 83.05 % 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: 0.61 (0.24), residues: 1224 helix: 1.60 (0.24), residues: 509 sheet: 0.35 (0.33), residues: 225 loop : -0.83 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 221 TYR 0.010 0.001 TYR A 103 PHE 0.011 0.001 PHE A 149 TRP 0.014 0.001 TRP A 21 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00231 (10040) covalent geometry : angle 0.51664 (13637) hydrogen bonds : bond 0.03609 ( 448) hydrogen bonds : angle 4.12398 ( 1276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.373 Fit side-chains REVERT: B 410 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: K 349 ARG cc_start: 0.6560 (mmm-85) cc_final: 0.6099 (mtt-85) outliers start: 17 outliers final: 11 residues processed: 217 average time/residue: 0.5822 time to fit residues: 135.7364 Evaluate side-chains 207 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain K residue 288 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 52 ASN B 264 HIS B 307 HIS K 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107808 restraints weight = 19805.635| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.33 r_work: 0.3281 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10040 Z= 0.158 Angle : 0.547 15.307 13637 Z= 0.269 Chirality : 0.045 0.250 1514 Planarity : 0.004 0.040 1770 Dihedral : 9.172 139.870 1511 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.34 % Allowed : 15.17 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.24), residues: 1224 helix: 1.67 (0.24), residues: 497 sheet: 0.25 (0.33), residues: 230 loop : -0.79 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 221 TYR 0.011 0.001 TYR B 310 PHE 0.014 0.001 PHE A 149 TRP 0.013 0.002 TRP A 21 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00386 (10040) covalent geometry : angle 0.54749 (13637) hydrogen bonds : bond 0.04177 ( 448) hydrogen bonds : angle 4.20832 ( 1276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.361 Fit side-chains REVERT: A 254 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7572 (mt-10) REVERT: B 280 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: B 410 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: K 349 ARG cc_start: 0.6687 (mmm-85) cc_final: 0.6210 (mtt-85) outliers start: 25 outliers final: 17 residues processed: 219 average time/residue: 0.5605 time to fit residues: 132.3144 Evaluate side-chains 228 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain K residue 288 ASN Chi-restraints excluded: chain K residue 312 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 6 HIS B 43 GLN B 52 ASN B 307 HIS ** K 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.107389 restraints weight = 24656.058| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.62 r_work: 0.3260 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10040 Z= 0.145 Angle : 0.547 14.583 13637 Z= 0.268 Chirality : 0.045 0.241 1514 Planarity : 0.004 0.040 1770 Dihedral : 9.132 139.380 1511 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.43 % Allowed : 15.36 % Favored : 82.21 % 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: 0.57 (0.24), residues: 1224 helix: 1.59 (0.24), residues: 504 sheet: 0.24 (0.33), residues: 230 loop : -0.81 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 221 TYR 0.010 0.001 TYR A 103 PHE 0.013 0.001 PHE A 149 TRP 0.014 0.001 TRP A 21 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00350 (10040) covalent geometry : angle 0.54702 (13637) hydrogen bonds : bond 0.04075 ( 448) hydrogen bonds : angle 4.20789 ( 1276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.367 Fit side-chains REVERT: B 280 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: K 349 ARG cc_start: 0.6736 (mmm-85) cc_final: 0.6276 (mtt-85) outliers start: 26 outliers final: 19 residues processed: 223 average time/residue: 0.5322 time to fit residues: 128.1899 Evaluate side-chains 228 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 312 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 78 optimal weight: 0.0010 chunk 77 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.0040 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN B 43 GLN B 307 HIS ** K 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.135189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108497 restraints weight = 22335.357| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.53 r_work: 0.3284 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10040 Z= 0.118 Angle : 0.542 14.393 13637 Z= 0.265 Chirality : 0.044 0.230 1514 Planarity : 0.004 0.040 1770 Dihedral : 8.973 138.060 1511 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.15 % Allowed : 16.29 % Favored : 81.55 % 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: 0.66 (0.24), residues: 1224 helix: 1.61 (0.24), residues: 508 sheet: 0.46 (0.33), residues: 225 loop : -0.80 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 221 TYR 0.009 0.001 TYR A 103 PHE 0.013 0.001 PHE A 149 TRP 0.014 0.001 TRP A 21 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00272 (10040) covalent geometry : angle 0.54246 (13637) hydrogen bonds : bond 0.03758 ( 448) hydrogen bonds : angle 4.15418 ( 1276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.418 Fit side-chains REVERT: A 123 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6994 (ttm170) REVERT: B 125 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7737 (mp0) REVERT: B 280 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: K 269 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7341 (tpp80) REVERT: K 349 ARG cc_start: 0.6713 (mmm-85) cc_final: 0.6245 (mtt-85) outliers start: 23 outliers final: 19 residues processed: 214 average time/residue: 0.5674 time to fit residues: 130.7794 Evaluate side-chains 221 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 312 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 256 GLN B 52 ASN B 134 GLN B 307 HIS K 288 ASN K 310 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.132449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105162 restraints weight = 26996.305| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.77 r_work: 0.3222 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10040 Z= 0.221 Angle : 0.607 15.498 13637 Z= 0.299 Chirality : 0.047 0.238 1514 Planarity : 0.004 0.042 1770 Dihedral : 9.388 143.941 1511 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.15 % Allowed : 16.48 % Favored : 81.37 % 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: 0.48 (0.24), residues: 1224 helix: 1.52 (0.24), residues: 497 sheet: 0.39 (0.33), residues: 224 loop : -0.93 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.012 0.001 TYR B 59 PHE 0.015 0.002 PHE A 255 TRP 0.013 0.002 TRP A 21 HIS 0.007 0.002 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00551 (10040) covalent geometry : angle 0.60703 (13637) hydrogen bonds : bond 0.04671 ( 448) hydrogen bonds : angle 4.31237 ( 1276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.376 Fit side-chains REVERT: A 258 ASN cc_start: 0.8603 (m110) cc_final: 0.8280 (m-40) REVERT: A 275 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8159 (t) REVERT: A 302 MET cc_start: 0.8431 (mtp) cc_final: 0.7927 (mtt) REVERT: A 411 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7820 (mm-30) REVERT: B 125 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7663 (mp0) REVERT: B 128 ASP cc_start: 0.8160 (t0) cc_final: 0.7923 (t0) REVERT: B 280 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: K 244 ASN cc_start: 0.8271 (t0) cc_final: 0.7909 (t0) REVERT: K 269 ARG cc_start: 0.7586 (ttp80) cc_final: 0.7214 (tpp80) REVERT: K 349 ARG cc_start: 0.6889 (mmm-85) cc_final: 0.6406 (mtt-85) outliers start: 23 outliers final: 19 residues processed: 223 average time/residue: 0.5490 time to fit residues: 131.8969 Evaluate side-chains 232 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 312 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 8 optimal weight: 0.0030 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 71 optimal weight: 0.0470 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 overall best weight: 0.3286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN B 43 GLN B 52 ASN B 307 HIS K 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108685 restraints weight = 26648.186| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.76 r_work: 0.3279 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10040 Z= 0.105 Angle : 0.534 15.093 13637 Z= 0.261 Chirality : 0.044 0.214 1514 Planarity : 0.004 0.041 1770 Dihedral : 8.936 139.397 1511 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.40 % Allowed : 17.70 % Favored : 80.90 % 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: 0.66 (0.24), residues: 1224 helix: 1.64 (0.24), residues: 507 sheet: 0.44 (0.33), residues: 225 loop : -0.83 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.007 0.001 TYR B 310 PHE 0.014 0.001 PHE A 149 TRP 0.016 0.001 TRP A 21 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00235 (10040) covalent geometry : angle 0.53430 (13637) hydrogen bonds : bond 0.03530 ( 448) hydrogen bonds : angle 4.14590 ( 1276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.416 Fit side-chains REVERT: A 258 ASN cc_start: 0.8503 (m110) cc_final: 0.8120 (m-40) REVERT: A 275 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8137 (t) REVERT: B 125 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7627 (mp0) REVERT: B 128 ASP cc_start: 0.8101 (t0) cc_final: 0.7861 (t0) REVERT: B 280 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: B 323 MET cc_start: 0.8108 (mmm) cc_final: 0.7721 (mmm) REVERT: K 269 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7196 (tpp80) outliers start: 15 outliers final: 12 residues processed: 214 average time/residue: 0.5603 time to fit residues: 128.9731 Evaluate side-chains 212 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 288 ASN Chi-restraints excluded: chain K residue 312 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 0.0030 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 0.0010 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 88 optimal weight: 0.0570 chunk 100 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN B 307 HIS B 416 ASN K 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109068 restraints weight = 25104.795| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.66 r_work: 0.3287 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10040 Z= 0.139 Angle : 0.890 59.200 13637 Z= 0.520 Chirality : 0.044 0.214 1514 Planarity : 0.004 0.047 1770 Dihedral : 8.989 139.412 1511 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.40 % Allowed : 17.98 % Favored : 80.62 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.66 (0.24), residues: 1224 helix: 1.62 (0.24), residues: 509 sheet: 0.45 (0.33), residues: 225 loop : -0.82 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 79 TYR 0.008 0.001 TYR A 103 PHE 0.013 0.001 PHE A 149 TRP 0.015 0.001 TRP A 21 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00277 (10040) covalent geometry : angle 0.89024 (13637) hydrogen bonds : bond 0.03533 ( 448) hydrogen bonds : angle 4.14861 ( 1276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4091.08 seconds wall clock time: 70 minutes 28.21 seconds (4228.21 seconds total)