Starting phenix.real_space_refine on Mon May 12 13:57:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wr3_37761/05_2025/8wr3_37761_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wr3_37761/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wr3_37761/05_2025/8wr3_37761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wr3_37761/05_2025/8wr3_37761.map" model { file = "/net/cci-nas-00/data/ceres_data/8wr3_37761/05_2025/8wr3_37761_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wr3_37761/05_2025/8wr3_37761_neut.cif" } resolution = 3.1 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= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} 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, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} 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: 5.82, per 1000 atoms: 0.65 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: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.82 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: 2.43 Time building geometry restraints manager: 2.98 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: 0.04 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: 0.970 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.410 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- 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 (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: -1.31 (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 TRP 0.009 0.001 TRP B 679 HIS 0.012 0.001 HIS A 658 PHE 0.052 0.002 PHE A 332 TYR 0.022 0.002 TYR A 104 ARG 0.012 0.001 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00793 ( 2) link_NAG-ASN : angle 1.99936 ( 6) hydrogen bonds : bond 0.18151 ( 673) hydrogen bonds : angle 6.17420 ( 2007) covalent geometry : bond 0.00481 ( 9224) covalent geometry : angle 0.91935 (12522) *********************** 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 : 0.867 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: 0.1732 time to fit residues: 32.9715 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 : 0.868 ------------------------------------------------------------------------------- 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 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.213708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156883 restraints weight = 9693.575| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.89 r_work: 0.3592 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9226 Z= 0.141 Angle : 0.628 9.891 12528 Z= 0.319 Chirality : 0.042 0.281 1490 Planarity : 0.005 0.051 1502 Dihedral : 15.902 106.446 1624 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.06 % Allowed : 22.31 % Favored : 75.63 % 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: 1.21 (0.24), residues: 1146 helix: 1.30 (0.17), residues: 928 sheet: None (None), residues: 0 loop : -1.21 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 679 HIS 0.002 0.001 HIS A 658 PHE 0.028 0.001 PHE B 221 TYR 0.026 0.001 TYR B 104 ARG 0.007 0.001 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.01037 ( 2) link_NAG-ASN : angle 2.61168 ( 6) hydrogen bonds : bond 0.05211 ( 673) hydrogen bonds : angle 4.29369 ( 2007) covalent geometry : bond 0.00291 ( 9224) covalent geometry : angle 0.62535 (12522) *********************** 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 154 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.853 Fit side-chains REVERT: B 146 ASP cc_start: 0.7699 (m-30) cc_final: 0.7449 (m-30) REVERT: B 201 GLN cc_start: 0.5101 (OUTLIER) cc_final: 0.3803 (tp40) REVERT: B 234 ASP cc_start: 0.8412 (t0) cc_final: 0.8083 (t0) outliers start: 18 outliers final: 13 residues processed: 150 average time/residue: 0.1578 time to fit residues: 35.4670 Evaluate side-chains 139 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 B residue 201 GLN 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 366 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 0.0070 chunk 111 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.213046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.160508 restraints weight = 9776.960| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.26 r_work: 0.3557 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9226 Z= 0.131 Angle : 0.584 7.869 12528 Z= 0.296 Chirality : 0.041 0.157 1490 Planarity : 0.004 0.044 1502 Dihedral : 14.375 94.763 1623 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.63 % Allowed : 23.00 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.04 (0.25), residues: 1146 helix: 1.94 (0.17), residues: 932 sheet: None (None), residues: 0 loop : -1.31 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 679 HIS 0.002 0.000 HIS A 658 PHE 0.025 0.001 PHE B 221 TYR 0.026 0.001 TYR B 104 ARG 0.004 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.01131 ( 2) link_NAG-ASN : angle 4.90875 ( 6) hydrogen bonds : bond 0.04490 ( 673) hydrogen bonds : angle 4.10141 ( 2007) covalent geometry : bond 0.00282 ( 9224) covalent geometry : angle 0.57433 (12522) *********************** 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 149 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.890 Fit side-chains REVERT: A 90 MET cc_start: 0.7276 (mtp) cc_final: 0.7067 (mmm) REVERT: A 450 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6660 (tt) REVERT: B 90 MET cc_start: 0.7361 (mtp) cc_final: 0.7039 (mmm) REVERT: B 143 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7826 (tt0) REVERT: B 146 ASP cc_start: 0.7724 (m-30) cc_final: 0.7503 (m-30) REVERT: B 227 ILE cc_start: 0.7394 (pt) cc_final: 0.7145 (mp) REVERT: B 234 ASP cc_start: 0.8412 (t0) cc_final: 0.8088 (t0) outliers start: 23 outliers final: 12 residues processed: 147 average time/residue: 0.1638 time to fit residues: 36.3791 Evaluate side-chains 135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU 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 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 366 THR 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 84 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.213843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.166493 restraints weight = 9709.183| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.41 r_work: 0.3565 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9226 Z= 0.133 Angle : 0.575 9.576 12528 Z= 0.292 Chirality : 0.041 0.203 1490 Planarity : 0.004 0.040 1502 Dihedral : 14.164 99.177 1623 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.97 % Allowed : 23.11 % 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 (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: 2.43 (0.25), residues: 1146 helix: 2.26 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.24 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 679 HIS 0.003 0.001 HIS B 658 PHE 0.025 0.001 PHE B 221 TYR 0.025 0.001 TYR A 104 ARG 0.005 0.000 ARG A 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00999 ( 2) link_NAG-ASN : angle 4.06297 ( 6) hydrogen bonds : bond 0.04262 ( 673) hydrogen bonds : angle 4.02623 ( 2007) covalent geometry : bond 0.00300 ( 9224) covalent geometry : angle 0.56836 (12522) *********************** 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 152 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.877 Fit side-chains REVERT: A 450 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6713 (tt) REVERT: B 90 MET cc_start: 0.7273 (mtp) cc_final: 0.6992 (mmm) REVERT: B 143 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7808 (tt0) REVERT: B 201 GLN cc_start: 0.4902 (OUTLIER) cc_final: 0.4421 (mt0) REVERT: B 234 ASP cc_start: 0.8444 (t0) cc_final: 0.8108 (t0) outliers start: 26 outliers final: 19 residues processed: 147 average time/residue: 0.1671 time to fit residues: 36.5037 Evaluate side-chains 144 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 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 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 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 449 LEU 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 72 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.213164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.164834 restraints weight = 9692.912| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.42 r_work: 0.3606 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9226 Z= 0.140 Angle : 0.574 9.632 12528 Z= 0.290 Chirality : 0.041 0.186 1490 Planarity : 0.004 0.038 1502 Dihedral : 13.778 97.501 1623 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.55 % Allowed : 22.20 % Favored : 74.26 % 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: 2.55 (0.25), residues: 1146 helix: 2.33 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.12 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 679 HIS 0.003 0.001 HIS B 658 PHE 0.025 0.002 PHE B 221 TYR 0.024 0.001 TYR A 104 ARG 0.003 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00898 ( 2) link_NAG-ASN : angle 4.45057 ( 6) hydrogen bonds : bond 0.04246 ( 673) hydrogen bonds : angle 4.03063 ( 2007) covalent geometry : bond 0.00325 ( 9224) covalent geometry : angle 0.56562 (12522) *********************** 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 152 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.966 Fit side-chains REVERT: A 450 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6783 (tt) REVERT: B 90 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.7044 (mmm) REVERT: B 143 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7865 (tt0) REVERT: B 234 ASP cc_start: 0.8499 (t0) cc_final: 0.8183 (t0) REVERT: B 347 MET cc_start: 0.8754 (tmm) cc_final: 0.8478 (ttp) outliers start: 31 outliers final: 22 residues processed: 145 average time/residue: 0.1632 time to fit residues: 35.5274 Evaluate side-chains 147 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 379 ILE 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 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 449 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 45 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.212109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.163357 restraints weight = 9668.935| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.43 r_work: 0.3562 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9226 Z= 0.149 Angle : 0.594 8.890 12528 Z= 0.299 Chirality : 0.042 0.188 1490 Planarity : 0.004 0.038 1502 Dihedral : 13.592 95.292 1620 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.20 % Allowed : 23.11 % 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 (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: 2.55 (0.25), residues: 1146 helix: 2.33 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.13 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 193 HIS 0.003 0.000 HIS B 658 PHE 0.029 0.002 PHE B 332 TYR 0.025 0.001 TYR A 104 ARG 0.002 0.000 ARG A 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 2) link_NAG-ASN : angle 4.23713 ( 6) hydrogen bonds : bond 0.04305 ( 673) hydrogen bonds : angle 4.05621 ( 2007) covalent geometry : bond 0.00350 ( 9224) covalent geometry : angle 0.58644 (12522) *********************** 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 150 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.946 Fit side-chains REVERT: A 131 PHE cc_start: 0.7505 (m-80) cc_final: 0.7203 (m-80) REVERT: A 203 LYS cc_start: 0.6632 (mmtt) cc_final: 0.6250 (mmtt) REVERT: A 279 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7794 (mp) REVERT: A 450 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6778 (tt) REVERT: B 90 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7137 (mmm) REVERT: B 143 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7851 (tt0) REVERT: B 234 ASP cc_start: 0.8498 (t0) cc_final: 0.8177 (t0) REVERT: B 347 MET cc_start: 0.8709 (tmm) cc_final: 0.8468 (ttp) outliers start: 28 outliers final: 20 residues processed: 143 average time/residue: 0.1628 time to fit residues: 34.8935 Evaluate side-chains 145 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 379 ILE 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 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 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 Chi-restraints excluded: chain B residue 512 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 49 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.213900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.167851 restraints weight = 9838.922| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.49 r_work: 0.3595 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9226 Z= 0.127 Angle : 0.570 9.738 12528 Z= 0.286 Chirality : 0.041 0.186 1490 Planarity : 0.004 0.037 1502 Dihedral : 13.276 92.962 1620 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.43 % Allowed : 23.23 % Favored : 73.34 % 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: 2.69 (0.25), residues: 1146 helix: 2.44 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.13 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 396 HIS 0.002 0.000 HIS B 658 PHE 0.024 0.001 PHE A 332 TYR 0.024 0.001 TYR A 104 ARG 0.002 0.000 ARG A 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00843 ( 2) link_NAG-ASN : angle 4.24539 ( 6) hydrogen bonds : bond 0.04004 ( 673) hydrogen bonds : angle 3.98099 ( 2007) covalent geometry : bond 0.00283 ( 9224) covalent geometry : angle 0.56289 (12522) *********************** 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 156 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.944 Fit side-chains REVERT: A 131 PHE cc_start: 0.7487 (m-80) cc_final: 0.7200 (m-80) REVERT: A 203 LYS cc_start: 0.6801 (mmtt) cc_final: 0.6535 (mmtm) REVERT: A 295 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.7852 (ttt-90) REVERT: A 413 MET cc_start: 0.6225 (mtt) cc_final: 0.5997 (tpt) REVERT: A 450 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6815 (tt) REVERT: B 234 ASP cc_start: 0.8519 (t0) cc_final: 0.8174 (t0) outliers start: 30 outliers final: 19 residues processed: 148 average time/residue: 0.1839 time to fit residues: 39.5574 Evaluate side-chains 146 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 415 THR 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 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 58 optimal weight: 0.5980 chunk 108 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.213256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.164498 restraints weight = 9897.182| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.46 r_work: 0.3525 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9226 Z= 0.137 Angle : 0.586 9.403 12528 Z= 0.294 Chirality : 0.041 0.186 1490 Planarity : 0.004 0.037 1502 Dihedral : 13.149 91.724 1618 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.75 % Allowed : 23.80 % 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 (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: 2.69 (0.25), residues: 1146 helix: 2.43 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.12 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 679 HIS 0.002 0.000 HIS A 658 PHE 0.027 0.001 PHE A 332 TYR 0.023 0.001 TYR B 104 ARG 0.003 0.000 ARG A 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00794 ( 2) link_NAG-ASN : angle 4.23227 ( 6) hydrogen bonds : bond 0.04112 ( 673) hydrogen bonds : angle 4.00492 ( 2007) covalent geometry : bond 0.00316 ( 9224) covalent geometry : angle 0.57832 (12522) *********************** 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 150 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.870 Fit side-chains REVERT: A 203 LYS cc_start: 0.6778 (mmtt) cc_final: 0.6521 (mmtm) REVERT: A 295 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7555 (ttt-90) REVERT: A 409 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.5783 (mt0) REVERT: A 413 MET cc_start: 0.6315 (mtt) cc_final: 0.6043 (tpt) REVERT: A 450 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6602 (tt) REVERT: B 143 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7763 (tt0) REVERT: B 146 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: B 234 ASP cc_start: 0.8479 (t0) cc_final: 0.8098 (t0) outliers start: 24 outliers final: 18 residues processed: 143 average time/residue: 0.1779 time to fit residues: 37.2053 Evaluate side-chains 148 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 415 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.211425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157661 restraints weight = 9757.726| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.74 r_work: 0.3435 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9226 Z= 0.157 Angle : 0.603 9.410 12528 Z= 0.302 Chirality : 0.042 0.185 1490 Planarity : 0.004 0.037 1502 Dihedral : 13.083 90.306 1618 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.97 % Allowed : 23.80 % Favored : 73.23 % 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: 2.60 (0.25), residues: 1146 helix: 2.37 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.15 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 679 HIS 0.001 0.000 HIS B 658 PHE 0.027 0.002 PHE A 332 TYR 0.023 0.002 TYR B 104 ARG 0.003 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00776 ( 2) link_NAG-ASN : angle 4.31247 ( 6) hydrogen bonds : bond 0.04310 ( 673) hydrogen bonds : angle 4.05630 ( 2007) covalent geometry : bond 0.00374 ( 9224) covalent geometry : angle 0.59590 (12522) *********************** 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 151 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.859 Fit side-chains REVERT: A 203 LYS cc_start: 0.6737 (mmtt) cc_final: 0.6500 (mmtm) REVERT: A 295 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7604 (ttt-90) REVERT: A 409 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.5828 (mt0) REVERT: A 413 MET cc_start: 0.6497 (mtt) cc_final: 0.6160 (tpt) REVERT: A 450 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6602 (tt) REVERT: B 143 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7748 (tt0) REVERT: B 146 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: B 234 ASP cc_start: 0.8474 (t0) cc_final: 0.8081 (t0) REVERT: B 347 MET cc_start: 0.8598 (tmm) cc_final: 0.8377 (ttp) outliers start: 26 outliers final: 19 residues processed: 143 average time/residue: 0.1725 time to fit residues: 36.0617 Evaluate side-chains 148 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU 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 415 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 0.0470 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 50 optimal weight: 20.0000 chunk 33 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 0.0670 overall best weight: 0.3114 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.215992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162572 restraints weight = 9830.621| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.20 r_work: 0.3480 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9226 Z= 0.115 Angle : 0.575 9.488 12528 Z= 0.288 Chirality : 0.040 0.184 1490 Planarity : 0.004 0.036 1502 Dihedral : 12.830 87.670 1618 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.71 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 (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: 2.80 (0.26), residues: 1146 helix: 2.54 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -1.29 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 396 HIS 0.002 0.000 HIS B 658 PHE 0.026 0.001 PHE B 115 TYR 0.024 0.001 TYR B 104 ARG 0.003 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00800 ( 2) link_NAG-ASN : angle 4.32840 ( 6) hydrogen bonds : bond 0.03716 ( 673) hydrogen bonds : angle 3.91376 ( 2007) covalent geometry : bond 0.00237 ( 9224) covalent geometry : angle 0.56772 (12522) ********************** 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 148 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.925 Fit side-chains REVERT: A 203 LYS cc_start: 0.6868 (mmtt) cc_final: 0.6554 (mmtt) REVERT: A 295 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7453 (ttt-90) REVERT: A 409 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.5982 (mt0) REVERT: B 143 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7691 (tt0) REVERT: B 146 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.7031 (m-30) REVERT: B 234 ASP cc_start: 0.8434 (t0) cc_final: 0.8099 (t0) outliers start: 19 outliers final: 17 residues processed: 142 average time/residue: 0.1847 time to fit residues: 37.9374 Evaluate side-chains 145 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL 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 415 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 450 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 0.0000 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.213625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156845 restraints weight = 9855.046| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.85 r_work: 0.3499 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9226 Z= 0.134 Angle : 0.599 9.928 12528 Z= 0.298 Chirality : 0.041 0.184 1490 Planarity : 0.004 0.036 1502 Dihedral : 12.774 88.723 1618 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.29 % Allowed : 25.17 % Favored : 72.54 % 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: 2.73 (0.25), residues: 1146 helix: 2.50 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -1.34 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 396 HIS 0.001 0.000 HIS B 658 PHE 0.026 0.001 PHE B 115 TYR 0.023 0.001 TYR B 104 ARG 0.003 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00755 ( 2) link_NAG-ASN : angle 4.42430 ( 6) hydrogen bonds : bond 0.03973 ( 673) hydrogen bonds : angle 3.93994 ( 2007) covalent geometry : bond 0.00306 ( 9224) covalent geometry : angle 0.59100 (12522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5186.42 seconds wall clock time: 90 minutes 20.47 seconds (5420.47 seconds total)