Starting phenix.real_space_refine on Tue Jan 21 02:48:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2k_50149/01_2025/9f2k_50149_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2k_50149/01_2025/9f2k_50149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f2k_50149/01_2025/9f2k_50149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2k_50149/01_2025/9f2k_50149.map" model { file = "/net/cci-nas-00/data/ceres_data/9f2k_50149/01_2025/9f2k_50149_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2k_50149/01_2025/9f2k_50149_neut.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 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 8 5.49 5 S 72 5.16 5 C 10220 2.51 5 N 2788 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16184 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 513, 3986 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 24, 'TRANS': 488} Conformer: "B" Number of residues, atoms: 513, 3986 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 24, 'TRANS': 488} bond proxies already assigned to first conformer: 4049 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS A 167 " occ=0.75 ... (18 atoms not shown) pdb=" NE2BHIS A 167 " occ=0.25 residue: pdb=" N AHIS B 167 " occ=0.75 ... (18 atoms not shown) pdb=" NE2BHIS B 167 " occ=0.25 residue: pdb=" N AHIS C 167 " occ=0.75 ... (18 atoms not shown) pdb=" NE2BHIS C 167 " occ=0.25 residue: pdb=" N AHIS D 167 " occ=0.75 ... (18 atoms not shown) pdb=" NE2BHIS D 167 " occ=0.25 Time building chain proxies: 13.78, per 1000 atoms: 0.85 Number of scatterers: 16184 At special positions: 0 Unit cell: (105.61, 136.29, 99.71, 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 72 16.00 P 8 15.00 O 3096 8.00 N 2788 7.00 C 10220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.70 Conformation dependent library (CDL) restraints added in 4.0 seconds 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 20 sheets defined 41.1% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 103 through 119 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 194 through 206 removed outlier: 3.541A pdb=" N LEU A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.702A pdb=" N GLU A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 257 removed outlier: 3.969A pdb=" N VAL A 242 " --> pdb=" O CYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 removed outlier: 3.599A pdb=" N LYS A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.509A pdb=" N ASP A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 384 through 397 removed outlier: 4.377A pdb=" N SER A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 406 removed outlier: 3.555A pdb=" N ASN A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 458 through 477 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.533A pdb=" N TRP A 493 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 removed outlier: 3.719A pdb=" N LEU A 503 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR A 505 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'B' and resid 103 through 119 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 182 through 191 Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.541A pdb=" N LEU B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.702A pdb=" N GLU B 225 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 257 removed outlier: 3.969A pdb=" N VAL B 242 " --> pdb=" O CYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 removed outlier: 3.599A pdb=" N LYS B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 326 through 335 Processing helix chain 'B' and resid 346 through 360 removed outlier: 3.509A pdb=" N ASP B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 382 Processing helix chain 'B' and resid 384 through 397 removed outlier: 4.377A pdb=" N SER B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS B 391 " --> pdb=" O GLN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 406 removed outlier: 3.555A pdb=" N ASN B 406 " --> pdb=" O MET B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 458 through 477 Proline residue: B 464 - end of helix Processing helix chain 'B' and resid 489 through 493 removed outlier: 3.533A pdb=" N TRP B 493 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.719A pdb=" N LEU B 503 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR B 505 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 536 Processing helix chain 'C' and resid 103 through 119 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 182 through 191 Processing helix chain 'C' and resid 194 through 206 removed outlier: 3.541A pdb=" N LEU C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.702A pdb=" N GLU C 225 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 257 removed outlier: 3.969A pdb=" N VAL C 242 " --> pdb=" O CYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 293 removed outlier: 3.599A pdb=" N LYS C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 346 through 360 removed outlier: 3.509A pdb=" N ASP C 356 " --> pdb=" O SER C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 382 Processing helix chain 'C' and resid 384 through 397 removed outlier: 4.377A pdb=" N SER C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 406 removed outlier: 3.555A pdb=" N ASN C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 445 No H-bonds generated for 'chain 'C' and resid 443 through 445' Processing helix chain 'C' and resid 458 through 477 Proline residue: C 464 - end of helix Processing helix chain 'C' and resid 489 through 493 removed outlier: 3.533A pdb=" N TRP C 493 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.719A pdb=" N LEU C 503 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR C 505 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 536 Processing helix chain 'D' and resid 103 through 119 Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 194 through 206 removed outlier: 3.541A pdb=" N LEU D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 225 removed outlier: 3.702A pdb=" N GLU D 225 " --> pdb=" O ALA D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 257 removed outlier: 3.969A pdb=" N VAL D 242 " --> pdb=" O CYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 293 removed outlier: 3.599A pdb=" N LYS D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 326 through 335 Processing helix chain 'D' and resid 346 through 360 removed outlier: 3.509A pdb=" N ASP D 356 " --> pdb=" O SER D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 382 Processing helix chain 'D' and resid 384 through 397 removed outlier: 4.377A pdb=" N SER D 390 " --> pdb=" O ARG D 386 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 406 removed outlier: 3.555A pdb=" N ASN D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 445 No H-bonds generated for 'chain 'D' and resid 443 through 445' Processing helix chain 'D' and resid 458 through 477 Proline residue: D 464 - end of helix Processing helix chain 'D' and resid 489 through 493 removed outlier: 3.533A pdb=" N TRP D 493 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.719A pdb=" N LEU D 503 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR D 505 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 536 Processing sheet with id=1, first strand: chain 'A' and resid 57 through 68 Processing sheet with id=2, first strand: chain 'A' and resid 172 through 176 Processing sheet with id=3, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=4, first strand: chain 'A' and resid 142 through 147 removed outlier: 5.237A pdb=" N LYS A 144 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 157 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 146 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 417 through 424 removed outlier: 5.585A pdb=" N LEU A 365 " --> pdb=" O GLU A 441 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLU A 441 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 57 through 68 Processing sheet with id=7, first strand: chain 'B' and resid 172 through 176 Processing sheet with id=8, first strand: chain 'B' and resid 121 through 124 Processing sheet with id=9, first strand: chain 'B' and resid 142 through 147 removed outlier: 5.237A pdb=" N LYS B 144 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE B 157 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 146 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 417 through 424 removed outlier: 5.585A pdb=" N LEU B 365 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLU B 441 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 57 through 68 Processing sheet with id=12, first strand: chain 'C' and resid 172 through 176 Processing sheet with id=13, first strand: chain 'C' and resid 121 through 124 Processing sheet with id=14, first strand: chain 'C' and resid 142 through 147 removed outlier: 5.237A pdb=" N LYS C 144 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 157 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 146 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 417 through 424 removed outlier: 5.585A pdb=" N LEU C 365 " --> pdb=" O GLU C 441 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLU C 441 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 57 through 68 Processing sheet with id=17, first strand: chain 'D' and resid 172 through 176 Processing sheet with id=18, first strand: chain 'D' and resid 121 through 124 Processing sheet with id=19, first strand: chain 'D' and resid 142 through 147 removed outlier: 5.237A pdb=" N LYS D 144 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE D 157 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 146 " --> pdb=" O ILE D 155 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 417 through 424 removed outlier: 5.585A pdb=" N LEU D 365 " --> pdb=" O GLU D 441 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLU D 441 " --> pdb=" O LEU D 365 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2052 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: 5.86 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5368 1.34 - 1.46: 3376 1.46 - 1.58: 7652 1.58 - 1.69: 16 1.69 - 1.81: 128 Bond restraints: 16540 Sorted by residual: bond pdb=" N ILE D 109 " pdb=" CA ILE D 109 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N ILE A 109 " pdb=" CA ILE A 109 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N ILE C 109 " pdb=" CA ILE C 109 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N ILE B 109 " pdb=" CA ILE B 109 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" O3 NAD D 601 " pdb=" PA NAD D 601 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 7.05e+00 ... (remaining 16535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 22004 1.91 - 3.82: 404 3.82 - 5.74: 68 5.74 - 7.65: 12 7.65 - 9.56: 4 Bond angle restraints: 22492 Sorted by residual: angle pdb=" PA NAD A 601 " pdb=" O3 NAD A 601 " pdb=" PN NAD A 601 " ideal model delta sigma weight residual 126.50 136.06 -9.56 3.00e+00 1.11e-01 1.02e+01 angle pdb=" PA NAD C 601 " pdb=" O3 NAD C 601 " pdb=" PN NAD C 601 " ideal model delta sigma weight residual 126.50 136.06 -9.56 3.00e+00 1.11e-01 1.02e+01 angle pdb=" PA NAD D 601 " pdb=" O3 NAD D 601 " pdb=" PN NAD D 601 " ideal model delta sigma weight residual 126.50 136.06 -9.56 3.00e+00 1.11e-01 1.02e+01 angle pdb=" PA NAD B 601 " pdb=" O3 NAD B 601 " pdb=" PN NAD B 601 " ideal model delta sigma weight residual 126.50 136.06 -9.56 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CA ILE D 109 " pdb=" C ILE D 109 " pdb=" O ILE D 109 " ideal model delta sigma weight residual 121.17 118.15 3.02 1.06e+00 8.90e-01 8.14e+00 ... (remaining 22487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 8744 17.56 - 35.13: 988 35.13 - 52.69: 296 52.69 - 70.26: 48 70.26 - 87.82: 20 Dihedral angle restraints: 10096 sinusoidal: 4140 harmonic: 5956 Sorted by residual: dihedral pdb=" CB GLU A 225 " pdb=" CG GLU A 225 " pdb=" CD GLU A 225 " pdb=" OE1 GLU A 225 " ideal model delta sinusoidal sigma weight residual 0.00 -87.82 87.82 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU D 225 " pdb=" CG GLU D 225 " pdb=" CD GLU D 225 " pdb=" OE1 GLU D 225 " ideal model delta sinusoidal sigma weight residual 0.00 -87.82 87.82 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU C 225 " pdb=" CG GLU C 225 " pdb=" CD GLU C 225 " pdb=" OE1 GLU C 225 " ideal model delta sinusoidal sigma weight residual 0.00 -87.82 87.82 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 10093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1968 0.045 - 0.090: 368 0.090 - 0.135: 204 0.135 - 0.179: 0 0.179 - 0.224: 4 Chirality restraints: 2544 Sorted by residual: chirality pdb=" CA ILE D 109 " pdb=" N ILE D 109 " pdb=" C ILE D 109 " pdb=" CB ILE D 109 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE A 109 " pdb=" N ILE A 109 " pdb=" C ILE A 109 " pdb=" CB ILE A 109 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE B 109 " pdb=" N ILE B 109 " pdb=" C ILE B 109 " pdb=" CB ILE B 109 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2541 not shown) Planarity restraints: 2896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 110 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C THR D 110 " -0.038 2.00e-02 2.50e+03 pdb=" O THR D 110 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA D 111 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 110 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C THR C 110 " -0.038 2.00e-02 2.50e+03 pdb=" O THR C 110 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA C 111 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 110 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C THR B 110 " 0.038 2.00e-02 2.50e+03 pdb=" O THR B 110 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA B 111 " -0.013 2.00e-02 2.50e+03 ... (remaining 2893 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 144 2.60 - 3.18: 13076 3.18 - 3.75: 25460 3.75 - 4.33: 38548 4.33 - 4.90: 62840 Nonbonded interactions: 140068 Sorted by model distance: nonbonded pdb=" OE1 GLN D 347 " pdb=" OD1 ASP D 436 " model vdw 2.026 3.040 nonbonded pdb=" OE1 GLN B 347 " pdb=" OD1 ASP B 436 " model vdw 2.026 3.040 nonbonded pdb=" OE1 GLN C 347 " pdb=" OD1 ASP C 436 " model vdw 2.026 3.040 nonbonded pdb=" OE1 GLN A 347 " pdb=" OD1 ASP A 436 " model vdw 2.026 3.040 nonbonded pdb=" OG SER C 136 " pdb=" OD1 ASP C 468 " model vdw 2.131 3.040 ... (remaining 140063 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 19.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 45.080 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.004 0.053 16540 Z= 0.272 Angle : 0.638 9.559 22492 Z= 0.327 Chirality : 0.044 0.224 2544 Planarity : 0.005 0.041 2896 Dihedral : 16.420 87.819 6264 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.14 % Allowed : 21.00 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2060 helix: -0.22 (0.18), residues: 748 sheet: 0.88 (0.27), residues: 376 loop : -0.15 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 122 HIS 0.003 0.001 HIS C 373 PHE 0.008 0.001 PHE D 219 TYR 0.006 0.001 TYR A 50 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 1.946 Fit side-chains outliers start: 20 outliers final: 20 residues processed: 208 average time/residue: 1.4357 time to fit residues: 329.9294 Evaluate side-chains 208 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 436 ASP Chi-restraints excluded: chain C residue 456 CYS Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 436 ASP Chi-restraints excluded: chain D residue 456 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 316 ASN A 347 GLN A 372 ASN B 288 ASN B 316 ASN B 347 GLN B 372 ASN C 288 ASN C 316 ASN C 347 GLN C 372 ASN D 288 ASN D 316 ASN D 347 GLN D 372 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141615 restraints weight = 53398.716| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.26 r_work: 0.3516 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16540 Z= 0.379 Angle : 0.713 8.113 22492 Z= 0.380 Chirality : 0.049 0.208 2544 Planarity : 0.006 0.040 2896 Dihedral : 9.126 57.904 2464 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.97 % Allowed : 17.12 % Favored : 79.91 % 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: 0.27 (0.18), residues: 2060 helix: 0.12 (0.18), residues: 728 sheet: 1.04 (0.26), residues: 392 loop : 0.02 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 101 HIS 0.008 0.002 HIS B 549 PHE 0.015 0.002 PHE D 552 TYR 0.013 0.002 TYR B 134 ARG 0.004 0.001 ARG D 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 2.071 Fit side-chains REVERT: A 79 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7899 (mpt180) REVERT: A 125 ARG cc_start: 0.7363 (ptm-80) cc_final: 0.7158 (ptm-80) REVERT: A 223 ASN cc_start: 0.8000 (p0) cc_final: 0.7701 (p0) REVERT: A 432 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7970 (tmmm) REVERT: A 490 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: B 79 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7886 (mpt180) REVERT: B 125 ARG cc_start: 0.7371 (ptm-80) cc_final: 0.7166 (ptm-80) REVERT: B 223 ASN cc_start: 0.8013 (p0) cc_final: 0.7681 (p0) REVERT: B 432 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.7982 (tmmm) REVERT: B 490 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: C 79 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7899 (mpt180) REVERT: C 125 ARG cc_start: 0.7358 (ptm-80) cc_final: 0.7156 (ptm-80) REVERT: C 223 ASN cc_start: 0.8002 (p0) cc_final: 0.7696 (p0) REVERT: C 432 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.7969 (tmmm) REVERT: C 490 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: D 79 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7889 (mpt180) REVERT: D 125 ARG cc_start: 0.7367 (ptm-80) cc_final: 0.7161 (ptm-80) REVERT: D 223 ASN cc_start: 0.8014 (p0) cc_final: 0.7684 (p0) REVERT: D 432 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.7976 (tmmm) REVERT: D 490 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7142 (mp0) outliers start: 52 outliers final: 20 residues processed: 236 average time/residue: 1.4749 time to fit residues: 383.0166 Evaluate side-chains 196 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 456 CYS Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 432 LYS Chi-restraints excluded: chain D residue 456 CYS Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 387 GLN B 288 ASN B 387 GLN C 288 ASN C 387 GLN D 288 ASN D 387 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.160922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142167 restraints weight = 51033.443| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.23 r_work: 0.3519 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16540 Z= 0.316 Angle : 0.647 8.006 22492 Z= 0.345 Chirality : 0.046 0.161 2544 Planarity : 0.005 0.040 2896 Dihedral : 8.899 59.553 2436 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.11 % Allowed : 15.07 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2060 helix: 0.12 (0.18), residues: 756 sheet: 0.97 (0.24), residues: 432 loop : -0.05 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 176 HIS 0.006 0.002 HIS B 373 PHE 0.013 0.002 PHE D 552 TYR 0.009 0.002 TYR D 134 ARG 0.003 0.001 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 184 time to evaluate : 1.845 Fit side-chains REVERT: A 79 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7877 (mpt180) REVERT: A 125 ARG cc_start: 0.7376 (ptm-80) cc_final: 0.7173 (ptm-80) REVERT: A 194 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: A 218 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7304 (p0) REVERT: A 240 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6524 (mm-30) REVERT: A 432 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.7988 (tmmm) REVERT: A 490 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: B 79 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7892 (mpt180) REVERT: B 125 ARG cc_start: 0.7385 (ptm-80) cc_final: 0.7180 (ptm-80) REVERT: B 194 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: B 218 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7309 (p0) REVERT: B 240 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6562 (mm-30) REVERT: B 432 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8004 (tmmm) REVERT: B 490 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: C 79 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7883 (mpt180) REVERT: C 125 ARG cc_start: 0.7367 (ptm-80) cc_final: 0.7162 (ptm-80) REVERT: C 194 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7262 (mm-30) REVERT: C 218 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7308 (p0) REVERT: C 240 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6565 (mm-30) REVERT: C 432 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7988 (tmmm) REVERT: C 490 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: D 79 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7888 (mpt180) REVERT: D 125 ARG cc_start: 0.7375 (ptm-80) cc_final: 0.7168 (ptm-80) REVERT: D 194 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7254 (mm-30) REVERT: D 218 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7313 (p0) REVERT: D 240 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6589 (mm-30) REVERT: D 432 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.7999 (tmmm) REVERT: D 490 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7251 (mp0) outliers start: 72 outliers final: 28 residues processed: 236 average time/residue: 1.4351 time to fit residues: 372.2898 Evaluate side-chains 236 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 456 CYS Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 432 LYS Chi-restraints excluded: chain D residue 456 CYS Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 191 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 5 optimal weight: 0.0370 chunk 20 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 10 optimal weight: 8.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.167612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149360 restraints weight = 49864.326| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.17 r_work: 0.3604 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16540 Z= 0.159 Angle : 0.512 5.359 22492 Z= 0.272 Chirality : 0.042 0.124 2544 Planarity : 0.004 0.035 2896 Dihedral : 8.090 61.802 2436 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.20 % Allowed : 14.38 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2060 helix: 0.71 (0.18), residues: 756 sheet: 1.35 (0.27), residues: 356 loop : 0.16 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.006 0.001 HIS B 373 PHE 0.006 0.001 PHE B 552 TYR 0.004 0.001 TYR C 216 ARG 0.001 0.000 ARG D 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 2.018 Fit side-chains REVERT: A 218 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7247 (p0) REVERT: A 350 MET cc_start: 0.8795 (ttm) cc_final: 0.8481 (ttp) REVERT: A 354 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7988 (tt) REVERT: A 378 ASP cc_start: 0.8332 (t70) cc_final: 0.8103 (t70) REVERT: A 437 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: B 218 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7244 (p0) REVERT: B 350 MET cc_start: 0.8800 (ttm) cc_final: 0.8484 (ttp) REVERT: B 354 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7981 (tt) REVERT: B 378 ASP cc_start: 0.8338 (t70) cc_final: 0.8108 (t70) REVERT: B 437 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: C 218 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7250 (p0) REVERT: C 350 MET cc_start: 0.8796 (ttm) cc_final: 0.8482 (ttp) REVERT: C 354 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7989 (tt) REVERT: C 378 ASP cc_start: 0.8327 (t70) cc_final: 0.8100 (t70) REVERT: C 437 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: D 194 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: D 218 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7238 (p0) REVERT: D 350 MET cc_start: 0.8805 (ttm) cc_final: 0.8488 (ttp) REVERT: D 354 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7974 (tt) REVERT: D 378 ASP cc_start: 0.8342 (t70) cc_final: 0.8108 (t70) REVERT: D 437 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7582 (tm-30) outliers start: 56 outliers final: 20 residues processed: 252 average time/residue: 1.5577 time to fit residues: 429.0454 Evaluate side-chains 236 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 437 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 387 GLN B 256 ASN B 387 GLN C 256 ASN C 387 GLN D 256 ASN D 387 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144276 restraints weight = 56856.543| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.38 r_work: 0.3536 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16540 Z= 0.236 Angle : 0.572 6.894 22492 Z= 0.304 Chirality : 0.044 0.123 2544 Planarity : 0.004 0.035 2896 Dihedral : 8.441 60.302 2432 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.25 % Allowed : 15.70 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2060 helix: 0.55 (0.18), residues: 772 sheet: 1.12 (0.26), residues: 364 loop : 0.35 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 176 HIS 0.006 0.001 HIS C 373 PHE 0.009 0.001 PHE A 552 TYR 0.006 0.001 TYR D 505 ARG 0.003 0.000 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 183 time to evaluate : 2.034 Fit side-chains REVERT: A 79 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7760 (mpt180) REVERT: A 218 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7250 (p0) REVERT: A 350 MET cc_start: 0.8802 (ttm) cc_final: 0.8488 (ttp) REVERT: A 354 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8045 (tt) REVERT: A 437 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: A 490 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: A 542 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7042 (tp30) REVERT: B 79 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7767 (mpt180) REVERT: B 218 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7248 (p0) REVERT: B 350 MET cc_start: 0.8802 (ttm) cc_final: 0.8486 (ttp) REVERT: B 354 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8038 (tt) REVERT: B 437 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: B 490 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: B 542 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7032 (tp30) REVERT: C 79 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7753 (mpt180) REVERT: C 218 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7247 (p0) REVERT: C 350 MET cc_start: 0.8797 (ttm) cc_final: 0.8482 (ttp) REVERT: C 354 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8048 (tt) REVERT: C 437 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: C 490 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: C 542 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7044 (tp30) REVERT: D 79 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7761 (mpt180) REVERT: D 194 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6978 (mm-30) REVERT: D 218 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7243 (p0) REVERT: D 350 MET cc_start: 0.8803 (ttm) cc_final: 0.8485 (ttp) REVERT: D 354 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8037 (tt) REVERT: D 437 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: D 490 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: D 542 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6984 (mm-30) outliers start: 57 outliers final: 20 residues processed: 224 average time/residue: 1.4883 time to fit residues: 367.1001 Evaluate side-chains 213 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 490 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 116 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 198 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.161512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142570 restraints weight = 52341.136| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.30 r_work: 0.3522 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16540 Z= 0.300 Angle : 0.625 7.487 22492 Z= 0.333 Chirality : 0.045 0.131 2544 Planarity : 0.005 0.036 2896 Dihedral : 8.679 59.499 2432 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.11 % Allowed : 15.30 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2060 helix: 0.39 (0.18), residues: 772 sheet: 1.00 (0.25), residues: 404 loop : 0.24 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 176 HIS 0.006 0.001 HIS C 373 PHE 0.011 0.002 PHE C 552 TYR 0.007 0.001 TYR B 505 ARG 0.003 0.001 ARG D 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 172 time to evaluate : 2.066 Fit side-chains REVERT: A 79 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7885 (mpt180) REVERT: A 218 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7367 (p0) REVERT: A 240 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6539 (mm-30) REVERT: A 350 MET cc_start: 0.8899 (ttm) cc_final: 0.8582 (ttp) REVERT: A 354 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8108 (tt) REVERT: A 437 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: A 490 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: B 79 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7889 (mpt180) REVERT: B 218 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7363 (p0) REVERT: B 240 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6567 (mm-30) REVERT: B 350 MET cc_start: 0.8907 (ttm) cc_final: 0.8589 (ttp) REVERT: B 354 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8104 (tt) REVERT: B 437 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: B 490 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: C 79 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7869 (mpt180) REVERT: C 218 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7365 (p0) REVERT: C 240 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6570 (mm-30) REVERT: C 350 MET cc_start: 0.8902 (ttm) cc_final: 0.8581 (ttp) REVERT: C 354 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8103 (tt) REVERT: C 437 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: C 490 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: D 79 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7884 (mpt180) REVERT: D 194 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: D 218 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7360 (p0) REVERT: D 240 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6567 (mm-30) REVERT: D 350 MET cc_start: 0.8916 (ttm) cc_final: 0.8592 (ttp) REVERT: D 354 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8091 (tt) REVERT: D 437 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: D 490 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7323 (mp0) outliers start: 72 outliers final: 28 residues processed: 216 average time/residue: 1.3908 time to fit residues: 332.4372 Evaluate side-chains 229 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 36 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 121 optimal weight: 0.0470 chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.163049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144505 restraints weight = 46746.169| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.11 r_work: 0.3558 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16540 Z= 0.241 Angle : 0.581 6.659 22492 Z= 0.310 Chirality : 0.044 0.124 2544 Planarity : 0.004 0.036 2896 Dihedral : 8.555 60.666 2432 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.88 % Allowed : 15.53 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2060 helix: 0.47 (0.18), residues: 772 sheet: 1.01 (0.25), residues: 404 loop : 0.29 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 176 HIS 0.006 0.001 HIS A 373 PHE 0.009 0.001 PHE C 443 TYR 0.006 0.001 TYR C 505 ARG 0.002 0.000 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 176 time to evaluate : 1.974 Fit side-chains REVERT: A 79 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7853 (mpt180) REVERT: A 194 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: A 218 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7325 (p0) REVERT: A 240 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6459 (mm-30) REVERT: A 350 MET cc_start: 0.8873 (ttm) cc_final: 0.8549 (ttp) REVERT: A 354 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 411 LYS cc_start: 0.7685 (mmpt) cc_final: 0.7484 (mmmt) REVERT: A 437 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: A 490 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: B 79 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7850 (mpt180) REVERT: B 194 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: B 218 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7324 (p0) REVERT: B 240 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6466 (mm-30) REVERT: B 350 MET cc_start: 0.8875 (ttm) cc_final: 0.8552 (ttp) REVERT: B 354 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8094 (tt) REVERT: B 411 LYS cc_start: 0.7687 (mmpt) cc_final: 0.7486 (mmmt) REVERT: B 437 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: B 490 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: C 79 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7848 (mpt180) REVERT: C 194 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7211 (mm-30) REVERT: C 218 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7316 (p0) REVERT: C 240 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6463 (mm-30) REVERT: C 350 MET cc_start: 0.8877 (ttm) cc_final: 0.8550 (ttp) REVERT: C 354 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8077 (tt) REVERT: C 411 LYS cc_start: 0.7696 (mmpt) cc_final: 0.7493 (mmmt) REVERT: C 437 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: C 490 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: D 79 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7828 (mpt180) REVERT: D 194 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: D 218 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7331 (p0) REVERT: D 240 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6452 (mm-30) REVERT: D 350 MET cc_start: 0.8879 (ttm) cc_final: 0.8554 (ttp) REVERT: D 354 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8089 (tt) REVERT: D 411 LYS cc_start: 0.7696 (mmpt) cc_final: 0.7493 (mmmt) REVERT: D 437 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: D 490 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7356 (mp0) outliers start: 68 outliers final: 28 residues processed: 216 average time/residue: 1.4060 time to fit residues: 335.3067 Evaluate side-chains 228 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 88 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 200 optimal weight: 0.4980 chunk 172 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.165952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147726 restraints weight = 55732.060| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.29 r_work: 0.3575 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16540 Z= 0.179 Angle : 0.527 5.946 22492 Z= 0.281 Chirality : 0.042 0.123 2544 Planarity : 0.004 0.033 2896 Dihedral : 8.182 61.760 2432 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.82 % Allowed : 15.35 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2060 helix: 0.81 (0.18), residues: 760 sheet: 1.28 (0.26), residues: 356 loop : 0.35 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 176 HIS 0.006 0.001 HIS D 373 PHE 0.007 0.001 PHE D 443 TYR 0.004 0.001 TYR D 216 ARG 0.001 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 188 time to evaluate : 1.734 Fit side-chains REVERT: A 79 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7755 (mpt180) REVERT: A 194 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: A 218 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7213 (p0) REVERT: A 240 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6195 (mm-30) REVERT: A 350 MET cc_start: 0.8752 (ttm) cc_final: 0.8386 (ttp) REVERT: A 437 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: A 490 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: B 79 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7746 (mpt180) REVERT: B 194 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: B 218 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7210 (p0) REVERT: B 240 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6207 (mm-30) REVERT: B 350 MET cc_start: 0.8752 (ttm) cc_final: 0.8387 (ttp) REVERT: B 437 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: B 490 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: C 79 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7748 (mpt180) REVERT: C 194 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6991 (mm-30) REVERT: C 218 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7214 (p0) REVERT: C 240 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6184 (mm-30) REVERT: C 350 MET cc_start: 0.8759 (ttm) cc_final: 0.8396 (ttp) REVERT: C 437 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: C 490 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: D 79 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7736 (mpt180) REVERT: D 194 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6941 (mm-30) REVERT: D 218 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7209 (p0) REVERT: D 240 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6217 (mm-30) REVERT: D 350 MET cc_start: 0.8756 (ttm) cc_final: 0.8388 (ttp) REVERT: D 437 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: D 490 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7393 (mp0) outliers start: 67 outliers final: 23 residues processed: 232 average time/residue: 1.4381 time to fit residues: 368.3870 Evaluate side-chains 224 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 490 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 99 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.159998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139682 restraints weight = 56584.332| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.73 r_work: 0.3428 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16540 Z= 0.255 Angle : 0.599 8.740 22492 Z= 0.317 Chirality : 0.044 0.128 2544 Planarity : 0.004 0.035 2896 Dihedral : 8.538 60.139 2432 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.20 % Allowed : 15.75 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2060 helix: 0.53 (0.18), residues: 772 sheet: 1.02 (0.25), residues: 404 loop : 0.36 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 176 HIS 0.006 0.001 HIS B 373 PHE 0.009 0.002 PHE C 443 TYR 0.006 0.001 TYR D 505 ARG 0.002 0.000 ARG D 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 1.919 Fit side-chains REVERT: A 79 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7736 (mpt180) REVERT: A 194 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6892 (mm-30) REVERT: A 218 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7184 (p0) REVERT: A 240 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6197 (mm-30) REVERT: A 350 MET cc_start: 0.8788 (ttm) cc_final: 0.8366 (ttp) REVERT: A 436 ASP cc_start: 0.7703 (m-30) cc_final: 0.7502 (m-30) REVERT: A 437 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: A 490 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: B 79 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7749 (mpt180) REVERT: B 194 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: B 218 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7180 (p0) REVERT: B 240 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6189 (mm-30) REVERT: B 350 MET cc_start: 0.8791 (ttm) cc_final: 0.8369 (ttp) REVERT: B 437 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: B 490 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: C 79 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7742 (mpt180) REVERT: C 194 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: C 218 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7181 (p0) REVERT: C 240 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6203 (mm-30) REVERT: C 350 MET cc_start: 0.8786 (ttm) cc_final: 0.8364 (ttp) REVERT: C 437 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: C 490 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: D 79 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7746 (mpt180) REVERT: D 194 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6880 (mm-30) REVERT: D 218 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7181 (p0) REVERT: D 240 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6191 (mm-30) REVERT: D 350 MET cc_start: 0.8787 (ttm) cc_final: 0.8362 (ttp) REVERT: D 437 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: D 490 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7255 (mp0) outliers start: 56 outliers final: 28 residues processed: 216 average time/residue: 1.5030 time to fit residues: 356.2169 Evaluate side-chains 236 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 182 optimal weight: 0.0570 chunk 140 optimal weight: 0.2980 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.163944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144083 restraints weight = 53420.640| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.68 r_work: 0.3485 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16540 Z= 0.168 Angle : 0.540 10.338 22492 Z= 0.283 Chirality : 0.042 0.127 2544 Planarity : 0.004 0.031 2896 Dihedral : 8.185 60.771 2432 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.28 % Allowed : 17.07 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2060 helix: 0.86 (0.18), residues: 760 sheet: 1.10 (0.27), residues: 364 loop : 0.46 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 176 HIS 0.006 0.001 HIS C 373 PHE 0.006 0.001 PHE A 443 TYR 0.004 0.001 TYR A 216 ARG 0.002 0.000 ARG C 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 2.104 Fit side-chains REVERT: A 79 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7743 (mpt180) REVERT: A 194 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: A 240 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6095 (mm-30) REVERT: A 350 MET cc_start: 0.8768 (ttm) cc_final: 0.8328 (ttp) REVERT: B 79 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7741 (mpt180) REVERT: B 194 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6869 (mm-30) REVERT: B 240 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6095 (mm-30) REVERT: B 350 MET cc_start: 0.8765 (ttm) cc_final: 0.8316 (ttp) REVERT: B 437 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: C 79 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7741 (mpt180) REVERT: C 194 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: C 240 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6101 (mm-30) REVERT: C 350 MET cc_start: 0.8770 (ttm) cc_final: 0.8323 (ttp) REVERT: C 437 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: D 79 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7738 (mpt180) REVERT: D 194 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: D 240 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6093 (mm-30) REVERT: D 350 MET cc_start: 0.8772 (ttm) cc_final: 0.8325 (ttp) REVERT: D 437 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7483 (tm-30) outliers start: 40 outliers final: 21 residues processed: 216 average time/residue: 1.4455 time to fit residues: 344.3113 Evaluate side-chains 212 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 489 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 33 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 98 optimal weight: 0.0070 chunk 29 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 166 optimal weight: 6.9990 chunk 37 optimal weight: 0.0980 chunk 151 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.164941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145569 restraints weight = 39952.159| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.24 r_work: 0.3529 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16540 Z= 0.159 Angle : 0.524 7.858 22492 Z= 0.277 Chirality : 0.042 0.122 2544 Planarity : 0.004 0.031 2896 Dihedral : 8.031 61.687 2432 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.17 % Allowed : 17.12 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.18), residues: 2060 helix: 0.95 (0.18), residues: 764 sheet: 1.19 (0.27), residues: 364 loop : 0.58 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 176 HIS 0.005 0.001 HIS B 373 PHE 0.005 0.001 PHE D 552 TYR 0.004 0.001 TYR D 216 ARG 0.002 0.000 ARG B 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12430.49 seconds wall clock time: 221 minutes 28.27 seconds (13288.27 seconds total)