Starting phenix.real_space_refine on Tue Jan 14 05:25:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8q_19006/01_2025/8r8q_19006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8q_19006/01_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_19006/01_2025/8r8q_19006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8q_19006/01_2025/8r8q_19006.map" model { file = "/net/cci-nas-00/data/ceres_data/8r8q_19006/01_2025/8r8q_19006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8q_19006/01_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-5571/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: 3.74, per 1000 atoms: 0.66 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: 1.27 Conformation dependent library (CDL) restraints added in 718.8 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: 0.59 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: 1.58 Time building geometry restraints manager: 1.49 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.020 Find NCS groups from input model: 0.250 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.150 ------------------------------------------------------------------------------- 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 5855 Z= 0.221 Angle : 0.687 10.222 7971 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 *********************** 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 : 0.571 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: 0.1294 time to fit residues: 22.8920 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 : 0.611 ------------------------------------------------------------------------------- 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 = 0.132293 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 = 8783.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131939 restraints weight = 8437.089| |-----------------------------------------------------------------------------| 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 5855 Z= 0.242 Angle : 0.618 6.024 7971 Z= 0.317 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 *********************** 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 : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9298 (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: 0.8849 (t) cc_final: 0.8570 (p) REVERT: A 282 PHE cc_start: 0.8354 (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: 0.7428 (m-70) cc_final: 0.7143 (m-70) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1391 time to fit residues: 25.2369 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 : 0.599 ------------------------------------------------------------------------------- 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: 0.0370 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.166217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132126 restraints weight = 9009.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132594 restraints weight = 9165.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134029 restraints weight = 8986.262| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5855 Z= 0.302 Angle : 0.668 7.247 7971 Z= 0.343 Chirality : 0.043 0.151 922 Planarity : 0.005 0.058 988 Dihedral : 5.281 50.470 876 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % 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: -1.15 (0.32), residues: 720 helix: 1.03 (0.29), residues: 338 sheet: -1.15 (0.51), residues: 119 loop : -3.06 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 136 HIS 0.003 0.001 HIS B 68 PHE 0.016 0.002 PHE A 280 TYR 0.009 0.001 TYR A 275 ARG 0.007 0.001 ARG B 59 *********************** 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 132 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8062 (tpp) cc_final: 0.7849 (tpp) REVERT: A 197 LYS cc_start: 0.8929 (tptp) cc_final: 0.8722 (tptt) REVERT: A 282 PHE cc_start: 0.8431 (t80) cc_final: 0.8145 (t80) REVERT: A 315 MET cc_start: 0.8243 (tpp) cc_final: 0.7751 (tpp) REVERT: B 304 HIS cc_start: 0.7500 (m-70) cc_final: 0.7198 (m-70) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1373 time to fit residues: 24.9677 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 : 0.569 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.0020 overall best weight: 0.5346 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.170349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134110 restraints weight = 8990.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134779 restraints weight = 9729.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136639 restraints weight = 8479.704| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5855 Z= 0.203 Angle : 0.619 7.639 7971 Z= 0.311 Chirality : 0.041 0.147 922 Planarity : 0.004 0.047 988 Dihedral : 5.083 52.114 876 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: -1.01 (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 0.014 0.001 PHE B 117 TYR 0.010 0.001 TYR B 347 ARG 0.003 0.000 ARG B 59 *********************** 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 142 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 197 LYS cc_start: 0.9059 (tptp) cc_final: 0.8817 (tptt) REVERT: A 315 MET cc_start: 0.8090 (tpp) cc_final: 0.7798 (tpp) REVERT: B 269 LEU cc_start: 0.9137 (mm) cc_final: 0.8621 (pt) REVERT: B 304 HIS cc_start: 0.7520 (m-70) cc_final: 0.7159 (m-70) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1407 time to fit residues: 27.2718 Evaluate side-chains 109 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.167984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131987 restraints weight = 8824.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131226 restraints weight = 8197.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131879 restraints weight = 7779.422| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5855 Z= 0.255 Angle : 0.651 7.586 7971 Z= 0.330 Chirality : 0.042 0.144 922 Planarity : 0.005 0.051 988 Dihedral : 5.156 51.093 876 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: -0.96 (0.33), residues: 720 helix: 1.21 (0.29), residues: 339 sheet: -1.06 (0.52), residues: 113 loop : -2.99 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 136 HIS 0.005 0.001 HIS B 229 PHE 0.014 0.001 PHE B 117 TYR 0.011 0.001 TYR B 347 ARG 0.003 0.000 ARG B 200 *********************** 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 126 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 282 PHE cc_start: 0.8410 (t80) cc_final: 0.8141 (t80) REVERT: B 269 LEU cc_start: 0.9229 (mm) cc_final: 0.8679 (pt) REVERT: B 304 HIS cc_start: 0.7497 (m-70) cc_final: 0.7116 (m-70) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1411 time to fit residues: 25.6638 Evaluate side-chains 106 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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: 0.5980 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.169702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134989 restraints weight = 8890.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133080 restraints weight = 8989.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133911 restraints weight = 7726.357| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5855 Z= 0.208 Angle : 0.624 8.177 7971 Z= 0.311 Chirality : 0.041 0.145 922 Planarity : 0.004 0.051 988 Dihedral : 5.033 52.144 876 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -0.95 (0.33), residues: 720 helix: 1.17 (0.29), residues: 345 sheet: -1.05 (0.51), residues: 119 loop : -3.04 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 136 HIS 0.004 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 59 *********************** 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 : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8767 (tp) cc_final: 0.8531 (tt) REVERT: A 282 PHE cc_start: 0.8408 (t80) cc_final: 0.7883 (t80) REVERT: A 315 MET cc_start: 0.8081 (tpp) cc_final: 0.7772 (tpp) REVERT: B 269 LEU cc_start: 0.9207 (mm) cc_final: 0.8623 (pt) REVERT: B 304 HIS cc_start: 0.7441 (m-70) cc_final: 0.7055 (m-70) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1367 time to fit residues: 25.9063 Evaluate side-chains 118 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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: 5.9990 chunk 59 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.161886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127001 restraints weight = 8988.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.126485 restraints weight = 9755.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127376 restraints weight = 10164.901| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 5855 Z= 0.437 Angle : 0.773 8.161 7971 Z= 0.397 Chirality : 0.046 0.181 922 Planarity : 0.005 0.064 988 Dihedral : 5.617 49.301 876 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % 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: -1.34 (0.32), residues: 720 helix: 0.69 (0.29), residues: 336 sheet: -1.03 (0.53), residues: 109 loop : -2.89 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 136 HIS 0.005 0.001 HIS B 229 PHE 0.021 0.002 PHE A 280 TYR 0.013 0.002 TYR A 275 ARG 0.005 0.001 ARG B 200 *********************** 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 121 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8545 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 202 LEU cc_start: 0.8685 (tp) cc_final: 0.8473 (tt) REVERT: A 225 LEU cc_start: 0.9408 (tp) cc_final: 0.9188 (tp) REVERT: A 233 TYR cc_start: 0.8346 (t80) cc_final: 0.8040 (t80) REVERT: A 346 MET cc_start: 0.8365 (ttm) cc_final: 0.8117 (ttm) REVERT: B 304 HIS cc_start: 0.7542 (m-70) cc_final: 0.7068 (m-70) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1214 time to fit residues: 21.3242 Evaluate side-chains 100 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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: 6.9990 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.169535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134540 restraints weight = 8722.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132999 restraints weight = 8187.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133245 restraints weight = 8319.525| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5855 Z= 0.210 Angle : 0.662 9.118 7971 Z= 0.329 Chirality : 0.042 0.147 922 Planarity : 0.005 0.059 988 Dihedral : 5.239 52.561 876 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 0.98 (0.29), residues: 345 sheet: -1.02 (0.51), residues: 121 loop : -3.03 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.005 0.001 HIS A 344 PHE 0.015 0.001 PHE B 117 TYR 0.011 0.001 TYR B 347 ARG 0.006 0.001 ARG B 59 *********************** 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 135 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8077 (tm-30) REVERT: A 202 LEU cc_start: 0.8733 (tp) cc_final: 0.8500 (tt) REVERT: B 269 LEU cc_start: 0.9211 (mm) cc_final: 0.8634 (pt) REVERT: B 304 HIS cc_start: 0.7577 (m-70) cc_final: 0.7059 (m-70) REVERT: B 382 MET cc_start: 0.7315 (tmm) cc_final: 0.7052 (tmm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1230 time to fit residues: 23.5969 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 : 0.630 ------------------------------------------------------------------------------- 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: 4.9990 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.168900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134007 restraints weight = 8821.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132446 restraints weight = 8031.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132800 restraints weight = 8077.289| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5855 Z= 0.230 Angle : 0.684 11.731 7971 Z= 0.335 Chirality : 0.041 0.139 922 Planarity : 0.004 0.057 988 Dihedral : 5.181 51.638 876 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.61 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 1.04 (0.29), residues: 343 sheet: -0.90 (0.52), residues: 121 loop : -3.00 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.005 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 B 39 *********************** 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 128 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 TYR cc_start: 0.8410 (t80) cc_final: 0.8170 (t80) REVERT: A 375 MET cc_start: 0.7873 (mmt) cc_final: 0.7354 (mmp) REVERT: B 269 LEU cc_start: 0.9225 (mm) cc_final: 0.8663 (pt) REVERT: B 304 HIS cc_start: 0.7598 (m-70) cc_final: 0.7089 (m-70) REVERT: B 382 MET cc_start: 0.7197 (tmm) cc_final: 0.6977 (tmm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1174 time to fit residues: 21.7965 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 : 0.586 ------------------------------------------------------------------------------- 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: 0.9990 chunk 63 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 68 optimal weight: 0.0040 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.172276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.138669 restraints weight = 8805.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138105 restraints weight = 8380.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.138530 restraints weight = 8727.355| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5855 Z= 0.196 Angle : 0.656 12.842 7971 Z= 0.321 Chirality : 0.041 0.160 922 Planarity : 0.004 0.056 988 Dihedral : 5.029 52.918 876 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.64 % Favored : 92.22 % 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: -0.88 (0.33), residues: 720 helix: 1.24 (0.29), residues: 343 sheet: -1.03 (0.52), residues: 121 loop : -3.00 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.006 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 A 41 ********************** 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 138 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8639 (mm) cc_final: 0.8416 (mm) REVERT: A 315 MET cc_start: 0.7844 (tpp) cc_final: 0.7615 (tpp) REVERT: A 375 MET cc_start: 0.7927 (mmt) cc_final: 0.7223 (mmp) REVERT: B 269 LEU cc_start: 0.9234 (mm) cc_final: 0.8667 (pt) REVERT: B 304 HIS cc_start: 0.7609 (m-70) cc_final: 0.7080 (m-70) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1144 time to fit residues: 22.8871 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 : 0.619 ------------------------------------------------------------------------------- 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: 0.7980 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.0010 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.170994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135132 restraints weight = 8816.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134891 restraints weight = 7837.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.135547 restraints weight = 7096.393| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5855 Z= 0.223 Angle : 0.685 14.454 7971 Z= 0.336 Chirality : 0.042 0.149 922 Planarity : 0.004 0.055 988 Dihedral : 5.045 51.658 876 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.61 % Favored : 91.25 % 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: -0.89 (0.33), residues: 720 helix: 1.20 (0.29), residues: 342 sheet: -0.97 (0.52), residues: 121 loop : -2.97 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 344 PHE 0.018 0.001 PHE A 118 TYR 0.009 0.001 TYR B 347 ARG 0.002 0.000 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.22 seconds wall clock time: 32 minutes 53.20 seconds (1973.20 seconds total)