Starting phenix.real_space_refine on Fri Sep 27 14:02:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f2k_50149/09_2024/9f2k_50149_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f2k_50149/09_2024/9f2k_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f2k_50149/09_2024/9f2k_50149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f2k_50149/09_2024/9f2k_50149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f2k_50149/09_2024/9f2k_50149_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f2k_50149/09_2024/9f2k_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 12.92, per 1000 atoms: 0.80 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: 3.64 Conformation dependent library (CDL) restraints added in 3.7 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: 1.64 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: 5.79 Time building geometry restraints manager: 4.31 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 166 or resid 168 through 456 or resid 458 throu \ gh 552 or resid 601)) selection = (chain 'B' and (resid 40 through 166 or resid 168 through 456 or resid 458 throu \ gh 552 or resid 601)) selection = (chain 'C' and (resid 40 through 166 or resid 168 through 456 or resid 458 throu \ gh 552 or resid 601)) selection = (chain 'D' and (resid 40 through 166 or resid 168 through 456 or resid 458 throu \ gh 552 or resid 601)) } 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: 20.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.220 Check model and map are aligned: 0.000 Set scattering table: 0.110 Process input model: 42.590 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.660 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.911 Fit side-chains outliers start: 20 outliers final: 20 residues processed: 208 average time/residue: 1.3965 time to fit residues: 321.2607 Evaluate side-chains 208 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 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 fitting. rotamer outliers: 52 poor density : 192 time to evaluate : 1.730 Fit side-chains REVERT: A 79 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7479 (mpt180) REVERT: A 125 ARG cc_start: 0.7352 (ptm-80) cc_final: 0.7142 (ptm-80) REVERT: A 332 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7516 (mt-10) REVERT: A 432 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7998 (tmmm) REVERT: A 490 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: B 79 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7477 (mpt180) REVERT: B 125 ARG cc_start: 0.7353 (ptm-80) cc_final: 0.7141 (ptm-80) REVERT: B 332 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7517 (mt-10) REVERT: B 432 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7999 (tmmm) REVERT: B 490 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: C 79 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7476 (mpt180) REVERT: C 125 ARG cc_start: 0.7345 (ptm-80) cc_final: 0.7137 (ptm-80) REVERT: C 332 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7516 (mt-10) REVERT: C 432 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.7999 (tmmm) REVERT: C 490 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: D 79 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7476 (mpt180) REVERT: D 125 ARG cc_start: 0.7352 (ptm-80) cc_final: 0.7140 (ptm-80) REVERT: D 332 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7517 (mt-10) REVERT: D 432 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7999 (tmmm) REVERT: D 490 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7011 (mp0) outliers start: 52 outliers final: 20 residues processed: 236 average time/residue: 1.3812 time to fit residues: 359.5902 Evaluate side-chains 200 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 1.882 ------------------------------------------------------------------------------- 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 102 optimal weight: 0.0060 chunk 57 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 148 optimal weight: 0.4980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 288 ASN A 387 GLN B 223 ASN B 288 ASN B 387 GLN C 223 ASN C 288 ASN C 387 GLN D 223 ASN D 288 ASN D 387 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16540 Z= 0.175 Angle : 0.532 6.234 22492 Z= 0.283 Chirality : 0.043 0.126 2544 Planarity : 0.004 0.036 2896 Dihedral : 8.184 62.680 2436 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.97 % Allowed : 15.75 % Favored : 81.28 % 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: 0.61 (0.18), residues: 2060 helix: 0.50 (0.18), residues: 764 sheet: 1.32 (0.26), residues: 384 loop : 0.06 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 176 HIS 0.006 0.001 HIS C 373 PHE 0.008 0.001 PHE D 552 TYR 0.005 0.001 TYR B 134 ARG 0.001 0.000 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 264 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 212 time to evaluate : 1.797 Fit side-chains REVERT: A 79 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7498 (mpt180) REVERT: A 194 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6809 (mm-30) REVERT: A 218 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.7098 (p0) REVERT: A 350 MET cc_start: 0.8400 (ttm) cc_final: 0.8023 (ttp) REVERT: A 354 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7790 (tp) REVERT: B 79 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7497 (mpt180) REVERT: B 194 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: B 218 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7096 (p0) REVERT: B 350 MET cc_start: 0.8399 (ttm) cc_final: 0.8021 (ttp) REVERT: B 354 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7791 (tp) REVERT: C 79 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7497 (mpt180) REVERT: C 194 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6809 (mm-30) REVERT: C 218 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7096 (p0) REVERT: C 332 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7452 (mt-10) REVERT: C 350 MET cc_start: 0.8399 (ttm) cc_final: 0.8020 (ttp) REVERT: C 354 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7789 (tp) REVERT: D 79 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7498 (mpt180) REVERT: D 194 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6808 (mm-30) REVERT: D 218 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7097 (p0) REVERT: D 350 MET cc_start: 0.8398 (ttm) cc_final: 0.8020 (ttp) REVERT: D 354 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7790 (tp) outliers start: 52 outliers final: 12 residues processed: 248 average time/residue: 1.5308 time to fit residues: 414.0404 Evaluate side-chains 209 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 16540 Z= 0.434 Angle : 0.734 8.877 22492 Z= 0.389 Chirality : 0.050 0.211 2544 Planarity : 0.005 0.040 2896 Dihedral : 8.919 60.334 2432 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.74 % Allowed : 15.35 % 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: 0.36 (0.18), residues: 2060 helix: 0.25 (0.18), residues: 736 sheet: 0.94 (0.24), residues: 432 loop : 0.05 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 176 HIS 0.007 0.002 HIS B 549 PHE 0.016 0.002 PHE B 552 TYR 0.010 0.002 TYR C 134 ARG 0.004 0.001 ARG D 189 *********************** 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 260 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 177 time to evaluate : 1.699 Fit side-chains REVERT: A 79 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7506 (mpt180) REVERT: A 125 ARG cc_start: 0.7415 (ptm-80) cc_final: 0.7162 (ptm-80) REVERT: A 194 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: A 218 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7253 (p0) REVERT: A 240 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6245 (mm-30) REVERT: A 432 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8031 (tmmm) REVERT: A 437 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: A 490 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: B 79 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7503 (mpt180) REVERT: B 125 ARG cc_start: 0.7418 (ptm-80) cc_final: 0.7165 (ptm-80) REVERT: B 194 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: B 218 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7255 (p0) REVERT: B 240 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6242 (mm-30) REVERT: B 432 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8029 (tmmm) REVERT: B 437 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: B 490 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: C 79 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7500 (mpt180) REVERT: C 125 ARG cc_start: 0.7416 (ptm-80) cc_final: 0.7162 (ptm-80) REVERT: C 194 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: C 218 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7254 (p0) REVERT: C 240 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6246 (mm-30) REVERT: C 332 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7454 (mt-10) REVERT: C 432 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8032 (tmmm) REVERT: C 437 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: C 490 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: D 79 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7501 (mpt180) REVERT: D 125 ARG cc_start: 0.7414 (ptm-80) cc_final: 0.7163 (ptm-80) REVERT: D 194 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6942 (mm-30) REVERT: D 218 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7257 (p0) REVERT: D 240 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6244 (mm-30) REVERT: D 432 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8030 (tmmm) REVERT: D 437 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: D 490 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7039 (mp0) outliers start: 83 outliers final: 32 residues processed: 237 average time/residue: 1.2917 time to fit residues: 339.6908 Evaluate side-chains 233 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 173 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 432 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 100 optimal weight: 0.0870 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16540 Z= 0.190 Angle : 0.543 6.294 22492 Z= 0.288 Chirality : 0.043 0.124 2544 Planarity : 0.004 0.037 2896 Dihedral : 8.364 61.984 2432 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.74 % Allowed : 16.89 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2060 helix: 0.52 (0.18), residues: 764 sheet: 1.26 (0.26), residues: 356 loop : 0.18 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 176 HIS 0.006 0.001 HIS B 373 PHE 0.007 0.001 PHE C 443 TYR 0.005 0.001 TYR D 505 ARG 0.002 0.000 ARG C 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 245 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 197 time to evaluate : 1.765 Fit side-chains REVERT: A 79 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7436 (mpt180) REVERT: A 194 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: A 218 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7235 (p0) REVERT: A 350 MET cc_start: 0.8439 (ttm) cc_final: 0.8052 (ttp) REVERT: A 354 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7820 (tp) REVERT: A 437 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: A 490 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: B 79 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7435 (mpt180) REVERT: B 194 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: B 218 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7233 (p0) REVERT: B 350 MET cc_start: 0.8442 (ttm) cc_final: 0.8052 (ttp) REVERT: B 354 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7821 (tp) REVERT: B 437 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: B 490 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: C 79 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7434 (mpt180) REVERT: C 194 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: C 218 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7233 (p0) REVERT: C 332 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7415 (mt-10) REVERT: C 350 MET cc_start: 0.8440 (ttm) cc_final: 0.8051 (ttp) REVERT: C 354 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7821 (tp) REVERT: C 437 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: C 490 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: D 79 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7434 (mpt180) REVERT: D 194 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: D 218 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7234 (p0) REVERT: D 350 MET cc_start: 0.8438 (ttm) cc_final: 0.8050 (ttp) REVERT: D 354 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7819 (tp) REVERT: D 437 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: D 490 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7192 (mp0) outliers start: 48 outliers final: 16 residues processed: 229 average time/residue: 1.5579 time to fit residues: 388.4767 Evaluate side-chains 225 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 185 time to evaluate : 1.849 ------------------------------------------------------------------------------- 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 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 194 GLU Chi-restraints excluded: chain B residue 218 ASP 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 194 GLU Chi-restraints excluded: chain C residue 218 ASP 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 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 66 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN B 387 GLN C 387 GLN D 387 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16540 Z= 0.215 Angle : 0.562 7.601 22492 Z= 0.299 Chirality : 0.043 0.123 2544 Planarity : 0.004 0.034 2896 Dihedral : 8.397 61.733 2432 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.20 % Allowed : 16.44 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2060 helix: 0.55 (0.18), residues: 772 sheet: 1.06 (0.26), residues: 364 loop : 0.31 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 176 HIS 0.006 0.001 HIS C 373 PHE 0.008 0.001 PHE D 443 TYR 0.006 0.001 TYR C 505 ARG 0.003 0.000 ARG D 125 *********************** 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 241 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 185 time to evaluate : 1.759 Fit side-chains REVERT: A 79 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7459 (mpt180) REVERT: A 125 ARG cc_start: 0.7298 (ptm-80) cc_final: 0.7078 (ptm-80) REVERT: A 194 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: A 218 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7194 (p0) REVERT: A 240 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6052 (mm-30) REVERT: A 347 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: A 350 MET cc_start: 0.8448 (ttm) cc_final: 0.8064 (ttp) REVERT: A 354 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7900 (tt) REVERT: A 437 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: A 490 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: B 79 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7457 (mpt180) REVERT: B 125 ARG cc_start: 0.7301 (ptm-80) cc_final: 0.7083 (ptm-80) REVERT: B 194 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6843 (mm-30) REVERT: B 218 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7194 (p0) REVERT: B 240 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6052 (mm-30) REVERT: B 347 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: B 350 MET cc_start: 0.8449 (ttm) cc_final: 0.8065 (ttp) REVERT: B 354 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7902 (tt) REVERT: B 437 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: B 490 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: C 79 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7455 (mpt180) REVERT: C 125 ARG cc_start: 0.7299 (ptm-80) cc_final: 0.7081 (ptm-80) REVERT: C 194 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6843 (mm-30) REVERT: C 218 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7194 (p0) REVERT: C 240 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6051 (mm-30) REVERT: C 332 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7438 (mt-10) REVERT: C 347 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: C 350 MET cc_start: 0.8451 (ttm) cc_final: 0.8066 (ttp) REVERT: C 354 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7901 (tt) REVERT: C 437 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: C 490 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: D 79 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7457 (mpt180) REVERT: D 125 ARG cc_start: 0.7301 (ptm-80) cc_final: 0.7082 (ptm-80) REVERT: D 194 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: D 218 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7194 (p0) REVERT: D 240 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6048 (mm-30) REVERT: D 347 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: D 350 MET cc_start: 0.8448 (ttm) cc_final: 0.8064 (ttp) REVERT: D 354 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7901 (tt) REVERT: D 437 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: D 490 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7180 (mp0) outliers start: 56 outliers final: 20 residues processed: 217 average time/residue: 1.4517 time to fit residues: 345.2428 Evaluate side-chains 229 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 177 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 240 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 347 GLN 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 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 347 GLN 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 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 347 GLN 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 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 347 GLN 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 190 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 0.0020 chunk 144 optimal weight: 0.3980 chunk 111 optimal weight: 0.7980 chunk 166 optimal weight: 0.4980 chunk 110 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN B 256 ASN C 256 ASN D 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16540 Z= 0.146 Angle : 0.490 5.312 22492 Z= 0.261 Chirality : 0.042 0.125 2544 Planarity : 0.004 0.031 2896 Dihedral : 7.876 62.043 2432 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.83 % Allowed : 17.58 % 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: 1.02 (0.18), residues: 2060 helix: 0.93 (0.18), residues: 764 sheet: 1.15 (0.27), residues: 364 loop : 0.43 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 176 HIS 0.006 0.001 HIS C 373 PHE 0.005 0.001 PHE C 443 TYR 0.004 0.001 TYR C 216 ARG 0.001 0.000 ARG D 125 *********************** 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 233 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 1.961 Fit side-chains REVERT: A 194 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: A 218 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7220 (p0) REVERT: A 347 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: A 350 MET cc_start: 0.8419 (ttm) cc_final: 0.7962 (ttp) REVERT: B 194 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: B 218 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7220 (p0) REVERT: B 347 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: B 350 MET cc_start: 0.8419 (ttm) cc_final: 0.7961 (ttp) REVERT: C 194 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6793 (mm-30) REVERT: C 218 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7223 (p0) REVERT: C 332 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7383 (mt-10) REVERT: C 347 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: C 350 MET cc_start: 0.8418 (ttm) cc_final: 0.7961 (ttp) REVERT: D 194 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: D 218 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7221 (p0) REVERT: D 347 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: D 350 MET cc_start: 0.8420 (ttm) cc_final: 0.7963 (ttp) outliers start: 32 outliers final: 16 residues processed: 221 average time/residue: 1.2915 time to fit residues: 316.7381 Evaluate side-chains 217 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 264 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 398 VAL 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 264 LEU Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 398 VAL 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 264 LEU Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 398 VAL 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 347 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.0870 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16540 Z= 0.222 Angle : 0.555 5.727 22492 Z= 0.297 Chirality : 0.043 0.123 2544 Planarity : 0.004 0.032 2896 Dihedral : 8.350 60.321 2432 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.74 % Allowed : 17.12 % Favored : 80.14 % 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: 0.92 (0.18), residues: 2060 helix: 0.77 (0.18), residues: 760 sheet: 1.16 (0.27), residues: 364 loop : 0.42 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 176 HIS 0.006 0.001 HIS B 373 PHE 0.008 0.001 PHE C 552 TYR 0.006 0.001 TYR D 505 ARG 0.003 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 229 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 181 time to evaluate : 1.923 Fit side-chains REVERT: A 79 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7460 (mpt180) REVERT: A 194 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6826 (mm-30) REVERT: A 218 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7182 (p0) REVERT: A 240 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6048 (mm-30) REVERT: A 350 MET cc_start: 0.8500 (ttm) cc_final: 0.8076 (ttp) REVERT: A 437 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: A 490 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: B 79 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7460 (mpt180) REVERT: B 194 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: B 218 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7181 (p0) REVERT: B 240 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6042 (mm-30) REVERT: B 350 MET cc_start: 0.8500 (ttm) cc_final: 0.8078 (ttp) REVERT: B 437 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: B 490 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: C 79 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7458 (mpt180) REVERT: C 194 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6824 (mm-30) REVERT: C 218 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7184 (p0) REVERT: C 240 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6056 (mm-30) REVERT: C 332 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7430 (mt-10) REVERT: C 350 MET cc_start: 0.8499 (ttm) cc_final: 0.8075 (ttp) REVERT: C 437 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: C 490 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: D 79 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7458 (mpt180) REVERT: D 194 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: D 218 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7183 (p0) REVERT: D 240 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6043 (mm-30) REVERT: D 350 MET cc_start: 0.8499 (ttm) cc_final: 0.8076 (ttp) REVERT: D 437 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: D 490 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7231 (mp0) outliers start: 48 outliers final: 20 residues processed: 209 average time/residue: 1.5287 time to fit residues: 349.6176 Evaluate side-chains 221 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 177 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 489 THR 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 188 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16540 Z= 0.279 Angle : 0.604 6.128 22492 Z= 0.324 Chirality : 0.045 0.124 2544 Planarity : 0.004 0.035 2896 Dihedral : 8.631 59.817 2432 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: 0.66 (0.18), residues: 2060 helix: 0.46 (0.18), residues: 772 sheet: 1.08 (0.25), residues: 404 loop : 0.29 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 176 HIS 0.006 0.001 HIS A 373 PHE 0.010 0.002 PHE C 443 TYR 0.007 0.001 TYR A 505 ARG 0.005 0.001 ARG A 125 *********************** 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 225 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 173 time to evaluate : 1.852 Fit side-chains REVERT: A 79 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7464 (mpt180) REVERT: A 194 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6884 (mm-30) REVERT: A 218 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7268 (p0) REVERT: A 240 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6094 (mm-30) REVERT: A 350 MET cc_start: 0.8523 (ttm) cc_final: 0.8116 (ttp) REVERT: A 437 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: A 490 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: B 79 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7463 (mpt180) REVERT: B 194 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: B 218 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7268 (p0) REVERT: B 240 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6089 (mm-30) REVERT: B 350 MET cc_start: 0.8523 (ttm) cc_final: 0.8117 (ttp) REVERT: B 437 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: B 490 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: C 79 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7461 (mpt180) REVERT: C 194 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: C 218 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7269 (p0) REVERT: C 240 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6091 (mm-30) REVERT: C 332 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7391 (mt-10) REVERT: C 350 MET cc_start: 0.8523 (ttm) cc_final: 0.8115 (ttp) REVERT: C 437 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: C 490 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: D 79 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7462 (mpt180) REVERT: D 194 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6881 (mm-30) REVERT: D 218 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7269 (p0) REVERT: D 240 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6090 (mm-30) REVERT: D 350 MET cc_start: 0.8522 (ttm) cc_final: 0.8115 (ttp) REVERT: D 437 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: D 490 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7200 (mp0) outliers start: 52 outliers final: 20 residues processed: 201 average time/residue: 1.4682 time to fit residues: 326.0538 Evaluate side-chains 213 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 193 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 203 optimal weight: 0.4980 chunk 187 optimal weight: 0.9990 chunk 161 optimal weight: 0.0040 chunk 16 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2312 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= 0.154 Angle : 0.510 5.533 22492 Z= 0.271 Chirality : 0.042 0.125 2544 Planarity : 0.004 0.032 2896 Dihedral : 8.075 60.717 2432 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.94 % Allowed : 18.15 % 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: 1.02 (0.18), residues: 2060 helix: 0.85 (0.18), residues: 764 sheet: 1.18 (0.27), residues: 364 loop : 0.50 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 176 HIS 0.005 0.001 HIS B 373 PHE 0.005 0.001 PHE D 552 TYR 0.004 0.001 TYR A 216 ARG 0.003 0.000 ARG B 125 ********************** 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 215 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 181 time to evaluate : 1.831 Fit side-chains REVERT: A 194 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6763 (mm-30) REVERT: A 218 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7246 (p0) REVERT: A 350 MET cc_start: 0.8476 (ttm) cc_final: 0.8032 (ttp) REVERT: A 437 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: B 194 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6762 (mm-30) REVERT: B 218 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7245 (p0) REVERT: B 350 MET cc_start: 0.8477 (ttm) cc_final: 0.8032 (ttp) REVERT: B 437 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: C 194 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6761 (mm-30) REVERT: C 218 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7249 (p0) REVERT: C 332 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7364 (mt-10) REVERT: C 350 MET cc_start: 0.8476 (ttm) cc_final: 0.8032 (ttp) REVERT: C 437 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: D 194 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6761 (mm-30) REVERT: D 218 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7247 (p0) REVERT: D 350 MET cc_start: 0.8476 (ttm) cc_final: 0.8032 (ttp) REVERT: D 437 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7622 (tm-30) outliers start: 34 outliers final: 20 residues processed: 209 average time/residue: 1.2648 time to fit residues: 295.2332 Evaluate side-chains 205 residues out of total 1736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 456 CYS 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 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 456 CYS 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 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 456 CYS 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 370 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 456 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.157894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137295 restraints weight = 60604.535| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.78 r_work: 0.3396 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16540 Z= 0.346 Angle : 0.650 6.489 22492 Z= 0.348 Chirality : 0.046 0.147 2544 Planarity : 0.005 0.036 2896 Dihedral : 8.754 59.326 2432 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.40 % Allowed : 17.24 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2060 helix: 0.37 (0.18), residues: 772 sheet: 1.06 (0.25), residues: 404 loop : 0.25 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 176 HIS 0.005 0.002 HIS C 549 PHE 0.012 0.002 PHE C 552 TYR 0.008 0.002 TYR D 505 ARG 0.005 0.001 ARG B 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.08 seconds wall clock time: 114 minutes 23.28 seconds (6863.28 seconds total)