Starting phenix.real_space_refine on Sun Apr 27 12:49:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8q_19006/04_2025/8r8q_19006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8q_19006/04_2025/8r8q_19006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r8q_19006/04_2025/8r8q_19006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8q_19006/04_2025/8r8q_19006.map" model { file = "/net/cci-nas-00/data/ceres_data/8r8q_19006/04_2025/8r8q_19006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8q_19006/04_2025/8r8q_19006.cif" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 3743 2.51 5 N 917 2.21 5 O 999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5702 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3041 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 9, 'TRANS': 381} Chain breaks: 1 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2591 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 28, 'TRANS': 312} Chain breaks: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.30, per 1000 atoms: 0.75 Number of scatterers: 5702 At special positions: 0 Unit cell: (70.4, 91.3, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 999 8.00 N 917 7.00 C 3743 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 NAG-ASN " NAG B 501 " - " ASN B 85 " " NAG B 502 " - " ASN B 157 " " NAG B 503 " - " ASN B 228 " " NAG B 504 " - " ASN B 331 " " NAG B 505 " - " ASN B 94 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 647.3 milliseconds 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1342 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 4 sheets defined 53.4% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.653A pdb=" N CYS A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.501A pdb=" N PHE A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.603A pdb=" N MET A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.636A pdb=" N TRP A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 105 Processing helix chain 'A' and resid 106 through 132 removed outlier: 4.437A pdb=" N TRP A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 114 " --> pdb=" O TRP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.677A pdb=" N MET A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 164 removed outlier: 4.727A pdb=" N ILE A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 203 removed outlier: 4.208A pdb=" N PHE A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 192 " --> pdb=" O MET A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 240 removed outlier: 3.552A pdb=" N ILE A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N CYS A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 222 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 286 removed outlier: 4.270A pdb=" N ILE A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 286 through 293 removed outlier: 3.752A pdb=" N PHE A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.635A pdb=" N ASN A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 removed outlier: 4.012A pdb=" N ILE A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 325 removed outlier: 3.828A pdb=" N ASP A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 350 removed outlier: 3.653A pdb=" N THR A 350 " --> pdb=" O MET A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 367 removed outlier: 3.658A pdb=" N ALA A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 363 " --> pdb=" O CYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 380 removed outlier: 3.682A pdb=" N PHE A 378 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 415 removed outlier: 3.981A pdb=" N GLY A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 445 removed outlier: 4.205A pdb=" N ALA A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 157 through 162 removed outlier: 4.242A pdb=" N SER B 161 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 321 Processing helix chain 'B' and resid 365 through 391 removed outlier: 3.750A pdb=" N ALA B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Proline residue: B 379 - end of helix removed outlier: 3.720A pdb=" N MET B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 383 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 45 removed outlier: 3.589A pdb=" N THR B 84 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL B 82 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 72 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 83 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE B 117 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 126 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU B 128 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 45 removed outlier: 3.589A pdb=" N THR B 84 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL B 82 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 72 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 83 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE B 117 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 121 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU B 239 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N PHE B 123 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA B 237 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG B 125 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE B 232 " --> pdb=" O PHE B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 168 through 171 removed outlier: 3.550A pdb=" N VAL B 192 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 217 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 354 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 279 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 355 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 275 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 268 " --> pdb=" O MET B 278 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 251 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 267 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN B 249 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 269 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 247 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 171 removed outlier: 3.550A pdb=" N VAL B 192 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 217 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 220 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 348 " --> pdb=" O LEU B 220 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 876 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: 1.66 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1345 1.33 - 1.45: 1294 1.45 - 1.58: 3149 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 5855 Sorted by residual: bond pdb=" CA TYR B 347 " pdb=" C TYR B 347 " ideal model delta sigma weight residual 1.521 1.554 -0.032 1.28e-02 6.10e+03 6.38e+00 bond pdb=" CZ TYR B 347 " pdb=" OH TYR B 347 " ideal model delta sigma weight residual 1.376 1.325 0.051 2.10e-02 2.27e+03 5.92e+00 bond pdb=" CB TYR B 347 " pdb=" CG TYR B 347 " ideal model delta sigma weight residual 1.512 1.461 0.051 2.20e-02 2.07e+03 5.44e+00 bond pdb=" N TYR B 347 " pdb=" CA TYR B 347 " ideal model delta sigma weight residual 1.455 1.435 0.021 1.18e-02 7.18e+03 3.06e+00 bond pdb=" C TYR B 347 " pdb=" O TYR B 347 " ideal model delta sigma weight residual 1.234 1.213 0.021 1.30e-02 5.92e+03 2.60e+00 ... (remaining 5850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 7787 2.04 - 4.09: 154 4.09 - 6.13: 22 6.13 - 8.18: 6 8.18 - 10.22: 2 Bond angle restraints: 7971 Sorted by residual: angle pdb=" N TYR B 347 " pdb=" CA TYR B 347 " pdb=" CB TYR B 347 " ideal model delta sigma weight residual 110.99 101.80 9.19 1.77e+00 3.19e-01 2.70e+01 angle pdb=" C VAL B 361 " pdb=" N ASP B 362 " pdb=" CA ASP B 362 " ideal model delta sigma weight residual 122.19 132.41 -10.22 2.30e+00 1.89e-01 1.98e+01 angle pdb=" C TYR B 347 " pdb=" CA TYR B 347 " pdb=" CB TYR B 347 " ideal model delta sigma weight residual 109.86 116.56 -6.70 1.80e+00 3.09e-01 1.39e+01 angle pdb=" N TYR B 347 " pdb=" CA TYR B 347 " pdb=" C TYR B 347 " ideal model delta sigma weight residual 108.55 114.37 -5.82 1.62e+00 3.81e-01 1.29e+01 angle pdb=" CB MET A 208 " pdb=" CG MET A 208 " pdb=" SD MET A 208 " ideal model delta sigma weight residual 112.70 120.48 -7.78 3.00e+00 1.11e-01 6.72e+00 ... (remaining 7966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 3063 17.29 - 34.58: 309 34.58 - 51.87: 60 51.87 - 69.16: 4 69.16 - 86.45: 5 Dihedral angle restraints: 3441 sinusoidal: 1351 harmonic: 2090 Sorted by residual: dihedral pdb=" CA GLY A 286 " pdb=" C GLY A 286 " pdb=" N LYS A 287 " pdb=" CA LYS A 287 " ideal model delta harmonic sigma weight residual -180.00 -162.59 -17.41 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PRO B 76 " pdb=" C PRO B 76 " pdb=" N PRO B 77 " pdb=" CA PRO B 77 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA LYS A 287 " pdb=" C LYS A 287 " pdb=" N VAL A 288 " pdb=" CA VAL A 288 " ideal model delta harmonic sigma weight residual 180.00 -164.12 -15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 3438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 616 0.036 - 0.071: 214 0.071 - 0.107: 79 0.107 - 0.142: 12 0.142 - 0.177: 1 Chirality restraints: 922 Sorted by residual: chirality pdb=" CG LEU A 171 " pdb=" CB LEU A 171 " pdb=" CD1 LEU A 171 " pdb=" CD2 LEU A 171 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" C1 NAG B 505 " pdb=" ND2 ASN B 94 " pdb=" C2 NAG B 505 " pdb=" O5 NAG B 505 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA VAL B 79 " pdb=" N VAL B 79 " pdb=" C VAL B 79 " pdb=" CB VAL B 79 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 919 not shown) Planarity restraints: 993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 347 " 0.010 2.00e-02 2.50e+03 1.47e-02 4.31e+00 pdb=" CG TYR B 347 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR B 347 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 347 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 347 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 347 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 347 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR B 347 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 313 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 314 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 314 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 314 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 75 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO B 76 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " 0.022 5.00e-02 4.00e+02 ... (remaining 990 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 590 2.75 - 3.29: 5762 3.29 - 3.82: 8889 3.82 - 4.36: 9552 4.36 - 4.90: 16711 Nonbonded interactions: 41504 Sorted by model distance: nonbonded pdb=" OG1 THR A 340 " pdb=" OG SER A 364 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR B 66 " pdb=" OG1 THR B 84 " model vdw 2.229 3.040 nonbonded pdb=" O PHE A 57 " pdb=" ND2 ASN A 187 " model vdw 2.230 3.120 nonbonded pdb=" OG SER B 131 " pdb=" O ALA B 134 " model vdw 2.299 3.040 nonbonded pdb=" OG SER A 343 " pdb=" O ALA A 357 " model vdw 2.305 3.040 ... (remaining 41499 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: 1.940 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.590 Find NCS groups from input model: 0.070 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.003 0.051 5860 Z= 0.162 Angle : 0.688 10.222 7986 Z= 0.340 Chirality : 0.041 0.177 922 Planarity : 0.004 0.045 988 Dihedral : 13.963 86.451 2099 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.17 % Allowed : 0.33 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.32), residues: 720 helix: 1.02 (0.29), residues: 329 sheet: -1.33 (0.52), residues: 114 loop : -3.00 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.007 0.001 HIS B 229 PHE 0.014 0.001 PHE B 117 TYR 0.027 0.001 TYR B 347 ARG 0.004 0.001 ARG A 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 5) link_NAG-ASN : angle 1.00339 ( 15) hydrogen bonds : bond 0.20626 ( 275) hydrogen bonds : angle 7.20078 ( 876) covalent geometry : bond 0.00337 ( 5855) covalent geometry : angle 0.68698 ( 7971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 GLU cc_start: 0.6666 (tm-30) cc_final: 0.6345 (tm-30) REVERT: B 304 HIS cc_start: 0.7324 (m-70) cc_final: 0.7055 (m-70) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1301 time to fit residues: 22.8886 Evaluate side-chains 112 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.168612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132292 restraints weight = 8886.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131380 restraints weight = 8783.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131946 restraints weight = 8433.167| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5860 Z= 0.156 Angle : 0.619 6.024 7986 Z= 0.318 Chirality : 0.041 0.149 922 Planarity : 0.004 0.042 988 Dihedral : 5.099 50.944 876 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.32), residues: 720 helix: 1.00 (0.29), residues: 344 sheet: -1.26 (0.50), residues: 115 loop : -3.03 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.003 0.001 HIS B 229 PHE 0.015 0.001 PHE A 422 TYR 0.009 0.001 TYR A 159 ARG 0.003 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 5) link_NAG-ASN : angle 1.03009 ( 15) hydrogen bonds : bond 0.04880 ( 275) hydrogen bonds : angle 4.84385 ( 876) covalent geometry : bond 0.00365 ( 5855) covalent geometry : angle 0.61801 ( 7971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9297 (mp) cc_final: 0.9088 (mp) REVERT: A 176 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7878 (tm-30) REVERT: A 193 TRP cc_start: 0.7543 (t60) cc_final: 0.7330 (t60) REVERT: A 212 VAL cc_start: 0.8850 (t) cc_final: 0.8571 (p) REVERT: A 282 PHE cc_start: 0.8355 (t80) cc_final: 0.8049 (t80) REVERT: A 346 MET cc_start: 0.8289 (ttm) cc_final: 0.8074 (ttm) REVERT: B 269 LEU cc_start: 0.9195 (mm) cc_final: 0.8673 (pt) REVERT: B 304 HIS cc_start: 0.7429 (m-70) cc_final: 0.7143 (m-70) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1567 time to fit residues: 28.3036 Evaluate side-chains 102 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 55 optimal weight: 0.0060 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.167621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130119 restraints weight = 8980.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131326 restraints weight = 8866.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132563 restraints weight = 7216.075| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5860 Z= 0.177 Angle : 0.650 7.347 7986 Z= 0.332 Chirality : 0.042 0.147 922 Planarity : 0.005 0.052 988 Dihedral : 5.185 50.863 876 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.32), residues: 720 helix: 1.07 (0.29), residues: 339 sheet: -1.13 (0.51), residues: 119 loop : -3.05 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 136 HIS 0.003 0.001 HIS B 229 PHE 0.015 0.002 PHE A 422 TYR 0.008 0.001 TYR A 275 ARG 0.007 0.001 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 5) link_NAG-ASN : angle 0.95021 ( 15) hydrogen bonds : bond 0.04837 ( 275) hydrogen bonds : angle 4.58442 ( 876) covalent geometry : bond 0.00416 ( 5855) covalent geometry : angle 0.64941 ( 7971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6674 (mm-30) REVERT: A 191 MET cc_start: 0.8115 (tpp) cc_final: 0.7872 (tpp) REVERT: A 193 TRP cc_start: 0.7328 (t60) cc_final: 0.7101 (t60) REVERT: A 282 PHE cc_start: 0.8383 (t80) cc_final: 0.8063 (t80) REVERT: A 315 MET cc_start: 0.8302 (tpp) cc_final: 0.7772 (tpp) REVERT: B 89 SER cc_start: 0.8113 (p) cc_final: 0.7857 (p) REVERT: B 304 HIS cc_start: 0.7422 (m-70) cc_final: 0.7107 (m-70) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1372 time to fit residues: 25.4434 Evaluate side-chains 110 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 71 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.170547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134854 restraints weight = 8986.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136184 restraints weight = 9051.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137660 restraints weight = 7477.384| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5860 Z= 0.136 Angle : 0.617 7.519 7986 Z= 0.311 Chirality : 0.041 0.146 922 Planarity : 0.004 0.048 988 Dihedral : 5.052 52.015 876 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.33), residues: 720 helix: 1.14 (0.30), residues: 339 sheet: -1.06 (0.51), residues: 119 loop : -3.00 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 136 HIS 0.006 0.001 HIS B 229 PHE 0.013 0.001 PHE B 117 TYR 0.009 0.001 TYR B 347 ARG 0.002 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 5) link_NAG-ASN : angle 0.88336 ( 15) hydrogen bonds : bond 0.04109 ( 275) hydrogen bonds : angle 4.39116 ( 876) covalent geometry : bond 0.00314 ( 5855) covalent geometry : angle 0.61628 ( 7971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 191 MET cc_start: 0.8054 (tpp) cc_final: 0.7818 (tpp) REVERT: A 315 MET cc_start: 0.8130 (tpp) cc_final: 0.7585 (tpp) REVERT: B 269 LEU cc_start: 0.9180 (mm) cc_final: 0.8630 (pt) REVERT: B 304 HIS cc_start: 0.7448 (m-70) cc_final: 0.7117 (m-70) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1631 time to fit residues: 30.4819 Evaluate side-chains 107 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 60 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.170207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134380 restraints weight = 8821.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132832 restraints weight = 9003.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133578 restraints weight = 9000.658| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5860 Z= 0.139 Angle : 0.627 7.671 7986 Z= 0.314 Chirality : 0.041 0.148 922 Planarity : 0.004 0.049 988 Dihedral : 5.017 51.745 876 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.33), residues: 720 helix: 1.28 (0.29), residues: 340 sheet: -1.02 (0.51), residues: 119 loop : -2.98 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.005 0.001 HIS B 229 PHE 0.014 0.001 PHE B 117 TYR 0.010 0.001 TYR B 347 ARG 0.002 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 5) link_NAG-ASN : angle 0.92138 ( 15) hydrogen bonds : bond 0.04044 ( 275) hydrogen bonds : angle 4.30393 ( 876) covalent geometry : bond 0.00325 ( 5855) covalent geometry : angle 0.62618 ( 7971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 282 PHE cc_start: 0.8427 (t80) cc_final: 0.7994 (t80) REVERT: A 315 MET cc_start: 0.8214 (tpp) cc_final: 0.7623 (tpp) REVERT: B 269 LEU cc_start: 0.9214 (mm) cc_final: 0.8676 (pt) REVERT: B 304 HIS cc_start: 0.7451 (m-70) cc_final: 0.7079 (m-70) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1258 time to fit residues: 22.9378 Evaluate side-chains 108 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 62 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.169620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133135 restraints weight = 8893.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132417 restraints weight = 8553.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133680 restraints weight = 7597.098| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5860 Z= 0.136 Angle : 0.622 7.972 7986 Z= 0.309 Chirality : 0.041 0.147 922 Planarity : 0.004 0.051 988 Dihedral : 4.987 51.899 876 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.33), residues: 720 helix: 1.37 (0.29), residues: 340 sheet: -1.03 (0.51), residues: 119 loop : -3.04 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 136 HIS 0.004 0.001 HIS B 229 PHE 0.013 0.001 PHE B 117 TYR 0.010 0.001 TYR B 347 ARG 0.002 0.000 ARG B 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 5) link_NAG-ASN : angle 0.91946 ( 15) hydrogen bonds : bond 0.03934 ( 275) hydrogen bonds : angle 4.26906 ( 876) covalent geometry : bond 0.00322 ( 5855) covalent geometry : angle 0.62130 ( 7971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8805 (tp) cc_final: 0.8560 (tt) REVERT: A 282 PHE cc_start: 0.8394 (t80) cc_final: 0.7996 (t80) REVERT: B 269 LEU cc_start: 0.9220 (mm) cc_final: 0.8655 (pt) REVERT: B 304 HIS cc_start: 0.7424 (m-70) cc_final: 0.7040 (m-70) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1191 time to fit residues: 22.7372 Evaluate side-chains 114 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.164068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130284 restraints weight = 9013.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128324 restraints weight = 10846.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129319 restraints weight = 10315.379| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5860 Z= 0.232 Angle : 0.728 8.040 7986 Z= 0.370 Chirality : 0.045 0.172 922 Planarity : 0.005 0.059 988 Dihedral : 5.422 49.907 876 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.32), residues: 720 helix: 0.88 (0.29), residues: 344 sheet: -0.98 (0.53), residues: 115 loop : -3.00 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 136 HIS 0.005 0.001 HIS B 229 PHE 0.019 0.002 PHE A 280 TYR 0.012 0.002 TYR A 275 ARG 0.004 0.001 ARG B 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 5) link_NAG-ASN : angle 1.12727 ( 15) hydrogen bonds : bond 0.05185 ( 275) hydrogen bonds : angle 4.61273 ( 876) covalent geometry : bond 0.00558 ( 5855) covalent geometry : angle 0.72680 ( 7971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8443 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 202 LEU cc_start: 0.8663 (tp) cc_final: 0.8455 (tt) REVERT: A 225 LEU cc_start: 0.9350 (tp) cc_final: 0.9123 (tp) REVERT: A 315 MET cc_start: 0.8178 (tpp) cc_final: 0.7937 (tpp) REVERT: B 304 HIS cc_start: 0.7591 (m-70) cc_final: 0.7089 (m-70) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1348 time to fit residues: 24.3843 Evaluate side-chains 108 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 48 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.170517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135259 restraints weight = 8831.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135770 restraints weight = 9084.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137139 restraints weight = 7794.556| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5860 Z= 0.123 Angle : 0.644 9.037 7986 Z= 0.316 Chirality : 0.041 0.148 922 Planarity : 0.004 0.054 988 Dihedral : 5.056 53.123 876 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.33), residues: 720 helix: 1.13 (0.29), residues: 344 sheet: -1.11 (0.51), residues: 121 loop : -2.84 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 136 HIS 0.004 0.001 HIS A 344 PHE 0.013 0.001 PHE B 117 TYR 0.010 0.001 TYR B 347 ARG 0.002 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 5) link_NAG-ASN : angle 0.98810 ( 15) hydrogen bonds : bond 0.03688 ( 275) hydrogen bonds : angle 4.30083 ( 876) covalent geometry : bond 0.00283 ( 5855) covalent geometry : angle 0.64341 ( 7971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8651 (tp) cc_final: 0.8447 (tt) REVERT: A 315 MET cc_start: 0.7951 (tpp) cc_final: 0.7423 (tpp) REVERT: A 375 MET cc_start: 0.7889 (mmt) cc_final: 0.7320 (mmp) REVERT: B 269 LEU cc_start: 0.9169 (mm) cc_final: 0.8605 (pt) REVERT: B 304 HIS cc_start: 0.7567 (m-70) cc_final: 0.7056 (m-70) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1646 time to fit residues: 31.3720 Evaluate side-chains 110 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 24 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.167932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132665 restraints weight = 8874.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133370 restraints weight = 9836.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.134530 restraints weight = 8706.970| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5860 Z= 0.165 Angle : 0.693 10.945 7986 Z= 0.340 Chirality : 0.042 0.142 922 Planarity : 0.005 0.058 988 Dihedral : 5.184 50.841 876 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.33), residues: 720 helix: 0.99 (0.29), residues: 348 sheet: -0.98 (0.52), residues: 119 loop : -3.10 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 86 HIS 0.006 0.001 HIS A 344 PHE 0.015 0.001 PHE B 117 TYR 0.010 0.001 TYR B 347 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 5) link_NAG-ASN : angle 0.97221 ( 15) hydrogen bonds : bond 0.04395 ( 275) hydrogen bonds : angle 4.35705 ( 876) covalent geometry : bond 0.00395 ( 5855) covalent geometry : angle 0.69248 ( 7971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 LEU cc_start: 0.9388 (tp) cc_final: 0.9115 (tp) REVERT: A 375 MET cc_start: 0.7870 (mmt) cc_final: 0.7373 (mmp) REVERT: B 256 ASP cc_start: 0.7784 (t0) cc_final: 0.7472 (t0) REVERT: B 269 LEU cc_start: 0.9230 (mm) cc_final: 0.8672 (pt) REVERT: B 304 HIS cc_start: 0.7621 (m-70) cc_final: 0.7085 (m-70) REVERT: B 382 MET cc_start: 0.7363 (tmm) cc_final: 0.7134 (tmm) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1134 time to fit residues: 21.4495 Evaluate side-chains 110 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 57 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.171851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.136277 restraints weight = 8875.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137162 restraints weight = 9083.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138901 restraints weight = 7741.684| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5860 Z= 0.123 Angle : 0.661 13.938 7986 Z= 0.321 Chirality : 0.041 0.158 922 Planarity : 0.004 0.057 988 Dihedral : 5.022 52.900 876 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.33), residues: 720 helix: 1.18 (0.29), residues: 347 sheet: -0.98 (0.51), residues: 121 loop : -3.03 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.007 0.001 HIS B 229 PHE 0.017 0.001 PHE A 118 TYR 0.010 0.001 TYR B 347 ARG 0.002 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 5) link_NAG-ASN : angle 0.96492 ( 15) hydrogen bonds : bond 0.03600 ( 275) hydrogen bonds : angle 4.21941 ( 876) covalent geometry : bond 0.00287 ( 5855) covalent geometry : angle 0.66022 ( 7971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.7733 (tt0) cc_final: 0.7461 (tp30) REVERT: A 315 MET cc_start: 0.7804 (tpp) cc_final: 0.7604 (tpp) REVERT: A 375 MET cc_start: 0.7774 (mmt) cc_final: 0.7232 (mmp) REVERT: B 269 LEU cc_start: 0.9215 (mm) cc_final: 0.8626 (pt) REVERT: B 304 HIS cc_start: 0.7663 (m-70) cc_final: 0.7139 (m-70) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1196 time to fit residues: 23.4124 Evaluate side-chains 119 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 21 optimal weight: 0.5980 chunk 70 optimal weight: 0.0370 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.0270 chunk 25 optimal weight: 0.0570 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.173995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141057 restraints weight = 8799.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.140834 restraints weight = 7158.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141029 restraints weight = 6229.014| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5860 Z= 0.120 Angle : 0.653 12.707 7986 Z= 0.318 Chirality : 0.041 0.148 922 Planarity : 0.004 0.052 988 Dihedral : 4.879 52.754 876 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.33), residues: 720 helix: 1.34 (0.29), residues: 343 sheet: -0.85 (0.52), residues: 121 loop : -3.09 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.005 0.001 HIS B 229 PHE 0.012 0.001 PHE B 117 TYR 0.009 0.001 TYR B 347 ARG 0.002 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 5) link_NAG-ASN : angle 0.91379 ( 15) hydrogen bonds : bond 0.03298 ( 275) hydrogen bonds : angle 4.15908 ( 876) covalent geometry : bond 0.00275 ( 5855) covalent geometry : angle 0.65223 ( 7971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.99 seconds wall clock time: 40 minutes 59.55 seconds (2459.55 seconds total)