Starting phenix.real_space_refine on Sat Aug 23 01:49:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wr3_37761/08_2025/8wr3_37761_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wr3_37761/08_2025/8wr3_37761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wr3_37761/08_2025/8wr3_37761_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wr3_37761/08_2025/8wr3_37761_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wr3_37761/08_2025/8wr3_37761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wr3_37761/08_2025/8wr3_37761.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 46 5.16 5 C 6064 2.51 5 N 1366 2.21 5 O 1540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9022 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4325 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 21, 'TRANS': 555} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4325 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 21, 'TRANS': 555} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 186 Unusual residues: {'CLR': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 186 Unusual residues: {'CLR': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.65, per 1000 atoms: 0.29 Number of scatterers: 9022 At special positions: 0 Unit cell: (125.19, 96.3, 72.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 6 15.00 O 1540 8.00 N 1366 7.00 C 6064 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 A 804 " - " ASN A 309 " " NAG B 804 " - " ASN B 309 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 408.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 38 through 41 Processing helix chain 'A' and resid 42 through 62 removed outlier: 3.910A pdb=" N VAL A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 92 removed outlier: 3.940A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.674A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.546A pdb=" N LYS A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.675A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 197 removed outlier: 4.260A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.851A pdb=" N PHE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.416A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.835A pdb=" N SER A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 removed outlier: 3.511A pdb=" N LEU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 339 through 366 removed outlier: 4.079A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix removed outlier: 4.032A pdb=" N TYR A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 404 removed outlier: 4.031A pdb=" N TYR A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 435 removed outlier: 3.827A pdb=" N THR A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 473 removed outlier: 3.584A pdb=" N THR A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 503 Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 517 through 545 removed outlier: 3.599A pdb=" N MET A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 682 removed outlier: 3.700A pdb=" N VAL A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU A 660 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 Processing helix chain 'A' and resid 702 through 712 removed outlier: 3.575A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 41 Processing helix chain 'B' and resid 42 through 62 removed outlier: 3.926A pdb=" N VAL B 53 " --> pdb=" O CYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 80 removed outlier: 3.955A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 99 through 125 removed outlier: 3.639A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 129 through 141 removed outlier: 3.655A pdb=" N LYS B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.623A pdb=" N ILE B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 165 Processing helix chain 'B' and resid 166 through 197 removed outlier: 4.371A pdb=" N TYR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Proline residue: B 174 - end of helix Proline residue: B 182 - end of helix removed outlier: 3.692A pdb=" N PHE B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.781A pdb=" N ILE B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.896A pdb=" N PHE B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.427A pdb=" N ASN B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.861A pdb=" N SER B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 removed outlier: 3.520A pdb=" N VAL B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 302 Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.757A pdb=" N GLY B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 322 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 339 through 366 removed outlier: 4.024A pdb=" N PHE B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix removed outlier: 3.962A pdb=" N TYR B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 404 removed outlier: 3.718A pdb=" N ALA B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.045A pdb=" N LYS B 408 " --> pdb=" O LYS B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 409 through 433 removed outlier: 4.805A pdb=" N LEU B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 473 removed outlier: 3.927A pdb=" N GLY B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 503 Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 517 through 545 removed outlier: 3.588A pdb=" N MET B 521 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 682 removed outlier: 3.672A pdb=" N VAL B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 661 " --> pdb=" O ARG B 657 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 665 " --> pdb=" O LEU B 661 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 702 Processing helix chain 'B' and resid 702 through 712 removed outlier: 3.598A pdb=" N ILE B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 2007 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: 1.69 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1435 1.33 - 1.45: 2393 1.45 - 1.57: 5310 1.57 - 1.70: 12 1.70 - 1.82: 74 Bond restraints: 9224 Sorted by residual: bond pdb=" C1 NAG B 804 " pdb=" O5 NAG B 804 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.10e+00 bond pdb=" C1 NAG A 804 " pdb=" O5 NAG A 804 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" C TYR A 151 " pdb=" N PRO A 152 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.23e-02 6.61e+03 4.90e+00 bond pdb=" C ALA B 173 " pdb=" N PRO B 174 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.89e+00 bond pdb=" CA ASN B 337 " pdb=" CB ASN B 337 " ideal model delta sigma weight residual 1.530 1.554 -0.023 1.51e-02 4.39e+03 2.37e+00 ... (remaining 9219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 12323 3.17 - 6.33: 184 6.33 - 9.50: 10 9.50 - 12.67: 3 12.67 - 15.83: 2 Bond angle restraints: 12522 Sorted by residual: angle pdb=" C SER A 200 " pdb=" N GLN A 201 " pdb=" CA GLN A 201 " ideal model delta sigma weight residual 121.54 130.95 -9.41 1.91e+00 2.74e-01 2.43e+01 angle pdb=" C SER B 200 " pdb=" N GLN B 201 " pdb=" CA GLN B 201 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" CA LEU A 209 " pdb=" CB LEU A 209 " pdb=" CG LEU A 209 " ideal model delta sigma weight residual 116.30 132.13 -15.83 3.50e+00 8.16e-02 2.05e+01 angle pdb=" CA LEU B 459 " pdb=" CB LEU B 459 " pdb=" CG LEU B 459 " ideal model delta sigma weight residual 116.30 130.75 -14.45 3.50e+00 8.16e-02 1.70e+01 angle pdb=" N ILE B 219 " pdb=" CA ILE B 219 " pdb=" C ILE B 219 " ideal model delta sigma weight residual 110.62 114.77 -4.15 1.02e+00 9.61e-01 1.66e+01 ... (remaining 12517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.73: 4925 22.73 - 45.46: 479 45.46 - 68.18: 88 68.18 - 90.91: 18 90.91 - 113.64: 34 Dihedral angle restraints: 5544 sinusoidal: 2196 harmonic: 3348 Sorted by residual: dihedral pdb=" CA ASN B 202 " pdb=" C ASN B 202 " pdb=" N LYS B 203 " pdb=" CA LYS B 203 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" N2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C2 NAG A 804 " pdb=" O5 NAG A 804 " ideal model delta sinusoidal sigma weight residual -178.19 -64.55 -113.64 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" C3 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C2 NAG A 804 " pdb=" O5 NAG A 804 " ideal model delta sinusoidal sigma weight residual -55.55 57.74 -113.29 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 5541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1022 0.044 - 0.088: 343 0.088 - 0.132: 100 0.132 - 0.176: 17 0.176 - 0.220: 8 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CG LEU A 463 " pdb=" CB LEU A 463 " pdb=" CD1 LEU A 463 " pdb=" CD2 LEU A 463 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1 NAG A 804 " pdb=" ND2 ASN A 309 " pdb=" C2 NAG A 804 " pdb=" O5 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CG LEU A 209 " pdb=" CB LEU A 209 " pdb=" CD1 LEU A 209 " pdb=" CD2 LEU A 209 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1487 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 205 " 0.026 2.00e-02 2.50e+03 5.15e-02 2.65e+01 pdb=" C LYS A 205 " -0.089 2.00e-02 2.50e+03 pdb=" O LYS A 205 " 0.033 2.00e-02 2.50e+03 pdb=" N ILE A 206 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 348 " 0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C VAL A 348 " -0.085 2.00e-02 2.50e+03 pdb=" O VAL A 348 " 0.032 2.00e-02 2.50e+03 pdb=" N ILE A 349 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 77 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C VAL A 77 " 0.074 2.00e-02 2.50e+03 pdb=" O VAL A 77 " -0.028 2.00e-02 2.50e+03 pdb=" N SER A 78 " -0.025 2.00e-02 2.50e+03 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 159 2.69 - 3.24: 8824 3.24 - 3.79: 14439 3.79 - 4.35: 18997 4.35 - 4.90: 31763 Nonbonded interactions: 74182 Sorted by model distance: nonbonded pdb=" O PRO A 138 " pdb=" OG1 THR A 142 " model vdw 2.136 3.040 nonbonded pdb=" O PRO B 138 " pdb=" OG1 THR B 142 " model vdw 2.213 3.040 nonbonded pdb=" O SER A 251 " pdb=" OG SER A 255 " model vdw 2.220 3.040 nonbonded pdb=" O SER A 383 " pdb=" OG SER A 387 " model vdw 2.234 3.040 nonbonded pdb=" O VAL A 117 " pdb=" OG1 THR A 121 " model vdw 2.237 3.040 ... (remaining 74177 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.450 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9226 Z= 0.219 Angle : 0.920 15.833 12528 Z= 0.521 Chirality : 0.050 0.220 1490 Planarity : 0.007 0.069 1502 Dihedral : 20.754 113.637 3384 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 0.57 % Allowed : 25.63 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.22), residues: 1146 helix: -0.56 (0.15), residues: 910 sheet: None (None), residues: 0 loop : -1.48 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 295 TYR 0.022 0.002 TYR A 104 PHE 0.052 0.002 PHE A 332 TRP 0.009 0.001 TRP B 679 HIS 0.012 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9224) covalent geometry : angle 0.91935 (12522) hydrogen bonds : bond 0.18151 ( 673) hydrogen bonds : angle 6.17420 ( 2007) link_NAG-ASN : bond 0.00793 ( 2) link_NAG-ASN : angle 1.99936 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: B 201 GLN cc_start: 0.4913 (OUTLIER) cc_final: 0.4354 (tp40) REVERT: B 664 LEU cc_start: 0.6180 (mt) cc_final: 0.5980 (mt) outliers start: 5 outliers final: 2 residues processed: 129 average time/residue: 0.0787 time to fit residues: 15.3108 Evaluate side-chains 126 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain B residue 201 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.210455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.153172 restraints weight = 9827.004| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.87 r_work: 0.3533 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9226 Z= 0.169 Angle : 0.655 10.186 12528 Z= 0.331 Chirality : 0.043 0.288 1490 Planarity : 0.005 0.050 1502 Dihedral : 15.790 105.832 1624 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.75 % Allowed : 21.74 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.24), residues: 1146 helix: 1.32 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 295 TYR 0.027 0.002 TYR B 104 PHE 0.031 0.002 PHE A 221 TRP 0.016 0.002 TRP A 679 HIS 0.003 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9224) covalent geometry : angle 0.65227 (12522) hydrogen bonds : bond 0.05298 ( 673) hydrogen bonds : angle 4.34926 ( 2007) link_NAG-ASN : bond 0.01053 ( 2) link_NAG-ASN : angle 2.89863 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.316 Fit side-chains REVERT: A 90 MET cc_start: 0.7266 (mtp) cc_final: 0.6991 (mmm) REVERT: A 332 PHE cc_start: 0.7535 (m-10) cc_final: 0.7328 (m-10) REVERT: A 450 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6758 (tt) REVERT: A 705 PHE cc_start: 0.7514 (t80) cc_final: 0.7302 (t80) REVERT: B 146 ASP cc_start: 0.7729 (m-30) cc_final: 0.7500 (m-30) REVERT: B 201 GLN cc_start: 0.5167 (OUTLIER) cc_final: 0.3805 (tp40) REVERT: B 234 ASP cc_start: 0.8454 (t0) cc_final: 0.8137 (t0) outliers start: 24 outliers final: 15 residues processed: 152 average time/residue: 0.0756 time to fit residues: 17.3634 Evaluate side-chains 139 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 512 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.210720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153719 restraints weight = 9673.106| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.89 r_work: 0.3489 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9226 Z= 0.147 Angle : 0.600 7.420 12528 Z= 0.305 Chirality : 0.042 0.180 1490 Planarity : 0.004 0.043 1502 Dihedral : 14.529 95.620 1623 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.32 % Allowed : 21.62 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.25), residues: 1146 helix: 1.91 (0.17), residues: 926 sheet: None (None), residues: 0 loop : -1.32 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 295 TYR 0.026 0.001 TYR A 104 PHE 0.026 0.001 PHE A 221 TRP 0.010 0.001 TRP A 679 HIS 0.002 0.000 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9224) covalent geometry : angle 0.59063 (12522) hydrogen bonds : bond 0.04699 ( 673) hydrogen bonds : angle 4.16486 ( 2007) link_NAG-ASN : bond 0.01118 ( 2) link_NAG-ASN : angle 4.82619 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.327 Fit side-chains REVERT: A 90 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7133 (mmm) REVERT: A 296 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: A 331 ILE cc_start: 0.8412 (mm) cc_final: 0.8197 (mt) REVERT: A 332 PHE cc_start: 0.7674 (m-10) cc_final: 0.7408 (m-10) REVERT: A 450 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6757 (tt) REVERT: A 705 PHE cc_start: 0.7548 (t80) cc_final: 0.7330 (t80) REVERT: B 90 MET cc_start: 0.7418 (mtp) cc_final: 0.7099 (mmm) REVERT: B 143 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7814 (tt0) REVERT: B 234 ASP cc_start: 0.8426 (t0) cc_final: 0.8103 (t0) REVERT: B 332 PHE cc_start: 0.7576 (m-10) cc_final: 0.7365 (m-10) outliers start: 29 outliers final: 16 residues processed: 147 average time/residue: 0.0764 time to fit residues: 17.0866 Evaluate side-chains 138 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 512 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.213214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.166407 restraints weight = 9803.568| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.58 r_work: 0.3560 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9226 Z= 0.131 Angle : 0.568 8.887 12528 Z= 0.288 Chirality : 0.041 0.196 1490 Planarity : 0.004 0.040 1502 Dihedral : 14.148 100.662 1623 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.86 % Allowed : 23.23 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.25), residues: 1146 helix: 2.20 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.26 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 295 TYR 0.025 0.001 TYR A 104 PHE 0.024 0.001 PHE A 221 TRP 0.010 0.001 TRP B 193 HIS 0.002 0.000 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9224) covalent geometry : angle 0.56098 (12522) hydrogen bonds : bond 0.04255 ( 673) hydrogen bonds : angle 4.06024 ( 2007) link_NAG-ASN : bond 0.01047 ( 2) link_NAG-ASN : angle 4.17024 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.198 Fit side-chains REVERT: A 331 ILE cc_start: 0.8562 (mm) cc_final: 0.8328 (mt) REVERT: A 332 PHE cc_start: 0.7925 (m-10) cc_final: 0.7654 (m-10) REVERT: A 450 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6843 (tt) REVERT: B 90 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7120 (mmm) REVERT: B 143 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7872 (tt0) REVERT: B 234 ASP cc_start: 0.8457 (t0) cc_final: 0.8146 (t0) REVERT: B 332 PHE cc_start: 0.7850 (m-10) cc_final: 0.7623 (m-10) outliers start: 25 outliers final: 17 residues processed: 146 average time/residue: 0.0740 time to fit residues: 16.2739 Evaluate side-chains 143 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 512 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 54 optimal weight: 0.0570 chunk 74 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.213509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.165877 restraints weight = 9736.736| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.37 r_work: 0.3612 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9226 Z= 0.132 Angle : 0.569 9.396 12528 Z= 0.288 Chirality : 0.041 0.187 1490 Planarity : 0.004 0.038 1502 Dihedral : 13.830 97.620 1620 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.86 % Allowed : 23.46 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.25), residues: 1146 helix: 2.32 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.17 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.025 0.001 TYR A 104 PHE 0.024 0.001 PHE A 221 TRP 0.009 0.001 TRP B 193 HIS 0.003 0.000 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9224) covalent geometry : angle 0.56130 (12522) hydrogen bonds : bond 0.04178 ( 673) hydrogen bonds : angle 4.03641 ( 2007) link_NAG-ASN : bond 0.00911 ( 2) link_NAG-ASN : angle 4.36314 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.7502 (m-80) cc_final: 0.7225 (m-80) REVERT: A 332 PHE cc_start: 0.8025 (m-10) cc_final: 0.7743 (m-10) REVERT: A 450 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6735 (tt) REVERT: B 90 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.7005 (mmm) REVERT: B 143 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7870 (tt0) REVERT: B 234 ASP cc_start: 0.8479 (t0) cc_final: 0.8190 (t0) REVERT: B 332 PHE cc_start: 0.7959 (m-10) cc_final: 0.7709 (m-10) outliers start: 25 outliers final: 19 residues processed: 146 average time/residue: 0.0626 time to fit residues: 14.0843 Evaluate side-chains 147 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 512 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.210620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.152761 restraints weight = 9793.038| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.95 r_work: 0.3413 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9226 Z= 0.167 Angle : 0.598 9.422 12528 Z= 0.301 Chirality : 0.042 0.190 1490 Planarity : 0.004 0.039 1502 Dihedral : 13.740 95.713 1620 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.66 % Allowed : 22.88 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.25), residues: 1146 helix: 2.28 (0.17), residues: 920 sheet: None (None), residues: 0 loop : -1.14 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 295 TYR 0.026 0.002 TYR A 104 PHE 0.027 0.002 PHE A 221 TRP 0.009 0.001 TRP B 679 HIS 0.003 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9224) covalent geometry : angle 0.59030 (12522) hydrogen bonds : bond 0.04482 ( 673) hydrogen bonds : angle 4.11796 ( 2007) link_NAG-ASN : bond 0.00849 ( 2) link_NAG-ASN : angle 4.29818 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.223 Fit side-chains REVERT: A 90 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6832 (mmm) REVERT: A 131 PHE cc_start: 0.7522 (m-80) cc_final: 0.7126 (m-80) REVERT: A 279 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7739 (mp) REVERT: A 450 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6625 (tt) REVERT: B 90 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.7064 (mmm) REVERT: B 143 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7729 (tt0) REVERT: B 234 ASP cc_start: 0.8403 (t0) cc_final: 0.8087 (t0) outliers start: 32 outliers final: 20 residues processed: 147 average time/residue: 0.0678 time to fit residues: 15.2060 Evaluate side-chains 144 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.210912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.154008 restraints weight = 9770.141| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.90 r_work: 0.3518 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9226 Z= 0.130 Angle : 0.588 9.385 12528 Z= 0.295 Chirality : 0.041 0.187 1490 Planarity : 0.004 0.038 1502 Dihedral : 13.438 93.646 1620 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.20 % Allowed : 23.34 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.25), residues: 1146 helix: 2.39 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.17 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.025 0.001 TYR A 104 PHE 0.024 0.001 PHE B 221 TRP 0.008 0.001 TRP B 396 HIS 0.002 0.000 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9224) covalent geometry : angle 0.58120 (12522) hydrogen bonds : bond 0.04084 ( 673) hydrogen bonds : angle 4.02791 ( 2007) link_NAG-ASN : bond 0.00863 ( 2) link_NAG-ASN : angle 4.25573 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.327 Fit side-chains REVERT: A 131 PHE cc_start: 0.7376 (m-80) cc_final: 0.7006 (m-80) REVERT: A 279 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7985 (mp) REVERT: A 295 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.7511 (ttt-90) REVERT: A 409 GLN cc_start: 0.6441 (OUTLIER) cc_final: 0.5958 (mt0) REVERT: A 413 MET cc_start: 0.6586 (mtt) cc_final: 0.6095 (tpt) REVERT: B 90 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7169 (mmm) REVERT: B 143 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7750 (tt0) REVERT: B 146 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: B 234 ASP cc_start: 0.8424 (t0) cc_final: 0.8061 (t0) REVERT: B 332 PHE cc_start: 0.7758 (m-10) cc_final: 0.7483 (m-10) outliers start: 28 outliers final: 18 residues processed: 141 average time/residue: 0.0858 time to fit residues: 17.5195 Evaluate side-chains 143 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 0.0980 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.211936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155513 restraints weight = 9707.568| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.86 r_work: 0.3477 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9226 Z= 0.124 Angle : 0.577 9.424 12528 Z= 0.290 Chirality : 0.040 0.191 1490 Planarity : 0.004 0.037 1502 Dihedral : 13.104 90.454 1620 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.86 % Allowed : 24.26 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.26), residues: 1146 helix: 2.47 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.20 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 295 TYR 0.026 0.001 TYR A 316 PHE 0.024 0.001 PHE B 115 TRP 0.008 0.001 TRP B 396 HIS 0.003 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9224) covalent geometry : angle 0.56995 (12522) hydrogen bonds : bond 0.03929 ( 673) hydrogen bonds : angle 3.97789 ( 2007) link_NAG-ASN : bond 0.00829 ( 2) link_NAG-ASN : angle 4.26951 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.305 Fit side-chains REVERT: A 131 PHE cc_start: 0.7427 (m-80) cc_final: 0.7060 (m-80) REVERT: A 295 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7625 (ttt-90) REVERT: A 331 ILE cc_start: 0.8445 (mm) cc_final: 0.8229 (mt) REVERT: A 409 GLN cc_start: 0.6476 (OUTLIER) cc_final: 0.5715 (mt0) REVERT: A 413 MET cc_start: 0.6396 (mtt) cc_final: 0.5991 (tpt) REVERT: A 450 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6714 (tt) REVERT: B 143 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7795 (tt0) REVERT: B 234 ASP cc_start: 0.8517 (t0) cc_final: 0.8129 (t0) REVERT: B 295 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7570 (ttt-90) REVERT: B 332 PHE cc_start: 0.7821 (m-10) cc_final: 0.7605 (m-10) REVERT: B 413 MET cc_start: 0.6330 (mtt) cc_final: 0.5877 (tpt) outliers start: 25 outliers final: 18 residues processed: 143 average time/residue: 0.0802 time to fit residues: 16.6594 Evaluate side-chains 145 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 71 optimal weight: 0.0980 chunk 48 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.211723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155600 restraints weight = 9740.795| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.87 r_work: 0.3532 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9226 Z= 0.129 Angle : 0.598 9.383 12528 Z= 0.295 Chirality : 0.041 0.188 1490 Planarity : 0.004 0.036 1502 Dihedral : 12.990 89.300 1618 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.52 % Allowed : 24.37 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.26), residues: 1146 helix: 2.50 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.18 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 295 TYR 0.024 0.001 TYR A 104 PHE 0.028 0.001 PHE A 332 TRP 0.008 0.001 TRP B 396 HIS 0.004 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9224) covalent geometry : angle 0.59092 (12522) hydrogen bonds : bond 0.03948 ( 673) hydrogen bonds : angle 3.97079 ( 2007) link_NAG-ASN : bond 0.00807 ( 2) link_NAG-ASN : angle 4.29525 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.226 Fit side-chains REVERT: A 203 LYS cc_start: 0.6141 (mmtm) cc_final: 0.5907 (mmtm) REVERT: A 295 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.7675 (ttt-90) REVERT: A 331 ILE cc_start: 0.8386 (mm) cc_final: 0.8161 (mt) REVERT: A 409 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.5972 (mt0) REVERT: A 413 MET cc_start: 0.6453 (mtt) cc_final: 0.6077 (tpt) REVERT: A 450 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6662 (tt) REVERT: B 143 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7734 (tt0) REVERT: B 234 ASP cc_start: 0.8476 (t0) cc_final: 0.8079 (t0) REVERT: B 332 PHE cc_start: 0.7721 (m-10) cc_final: 0.7500 (m-10) outliers start: 22 outliers final: 19 residues processed: 138 average time/residue: 0.0658 time to fit residues: 13.7278 Evaluate side-chains 143 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 90 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4311 r_free = 0.4311 target = 0.210934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.154317 restraints weight = 9798.312| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.88 r_work: 0.3480 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9226 Z= 0.140 Angle : 0.611 9.417 12528 Z= 0.300 Chirality : 0.041 0.185 1490 Planarity : 0.004 0.036 1502 Dihedral : 12.922 88.850 1618 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.63 % Allowed : 24.37 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.25), residues: 1146 helix: 2.43 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.18 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 295 TYR 0.025 0.001 TYR A 316 PHE 0.028 0.001 PHE A 332 TRP 0.016 0.001 TRP A 193 HIS 0.004 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9224) covalent geometry : angle 0.60326 (12522) hydrogen bonds : bond 0.04072 ( 673) hydrogen bonds : angle 4.00299 ( 2007) link_NAG-ASN : bond 0.00780 ( 2) link_NAG-ASN : angle 4.33702 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.255 Fit side-chains REVERT: A 203 LYS cc_start: 0.6038 (mmtm) cc_final: 0.5821 (mmtm) REVERT: A 295 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7673 (ttt-90) REVERT: A 316 TYR cc_start: 0.8314 (t80) cc_final: 0.7876 (t80) REVERT: A 409 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.5802 (mt0) REVERT: A 413 MET cc_start: 0.6393 (mtt) cc_final: 0.6092 (tpt) REVERT: A 450 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6668 (tt) REVERT: B 143 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7912 (mt0) REVERT: B 234 ASP cc_start: 0.8473 (t0) cc_final: 0.8063 (t0) REVERT: B 332 PHE cc_start: 0.7819 (m-10) cc_final: 0.7526 (m-10) outliers start: 23 outliers final: 20 residues processed: 136 average time/residue: 0.0625 time to fit residues: 13.0554 Evaluate side-chains 143 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 46 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 4 optimal weight: 0.0470 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.214235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.158934 restraints weight = 9591.722| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.84 r_work: 0.3505 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9226 Z= 0.115 Angle : 0.588 9.624 12528 Z= 0.288 Chirality : 0.040 0.185 1490 Planarity : 0.004 0.036 1502 Dihedral : 12.705 86.816 1618 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.17 % Allowed : 24.83 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.26), residues: 1146 helix: 2.55 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -1.35 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 295 TYR 0.024 0.001 TYR B 104 PHE 0.024 0.001 PHE B 115 TRP 0.013 0.001 TRP A 193 HIS 0.003 0.000 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9224) covalent geometry : angle 0.58001 (12522) hydrogen bonds : bond 0.03665 ( 673) hydrogen bonds : angle 3.89814 ( 2007) link_NAG-ASN : bond 0.00792 ( 2) link_NAG-ASN : angle 4.40091 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2535.66 seconds wall clock time: 43 minutes 59.96 seconds (2639.96 seconds total)