Starting phenix.real_space_refine on Fri Feb 23 12:36:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/02_2024/8j1h_35922_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/02_2024/8j1h_35922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/02_2024/8j1h_35922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/02_2024/8j1h_35922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/02_2024/8j1h_35922_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1h_35922/02_2024/8j1h_35922_trim_updated.pdb" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 6 Type Number sf(0) Gaussians S 96 5.16 5 C 12480 2.51 5 N 3168 2.21 5 O 3388 1.98 5 F 8 1.80 5 H 19324 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 457": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38464 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 9583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 9583 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 4 Chain: "D" Number of atoms: 9583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 9583 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 4 Chain: "B" Number of atoms: 9583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 9583 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 4 Chain: "A" Number of atoms: 9583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 9583 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 4 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'9QM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'9QM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'9QM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'9QM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.02, per 1000 atoms: 0.44 Number of scatterers: 38464 At special positions: 0 Unit cell: (160.89, 160.89, 119.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 F 8 9.00 O 3388 8.00 N 3168 7.00 C 12480 6.00 H 19324 1.00 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 - 3.50 Amino acid : False - 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: 33.18 Conformation dependent library (CDL) restraints added in 4.1 seconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 4 sheets defined 55.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.22 Creating SS restraints... Processing helix chain 'C' and resid 151 through 159 Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.200A pdb=" N GLY C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 194 through 200 Processing helix chain 'C' and resid 210 through 220 Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.958A pdb=" N GLU C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 323 through 330 Processing helix chain 'C' and resid 337 through 356 removed outlier: 3.801A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 373 through 380 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.095A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 399 No H-bonds generated for 'chain 'C' and resid 397 through 399' Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 446 through 451 removed outlier: 3.660A pdb=" N LEU C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA C 451 " --> pdb=" O HIS C 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 446 through 451' Processing helix chain 'C' and resid 454 through 466 removed outlier: 3.672A pdb=" N ARG C 460 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 489 Processing helix chain 'C' and resid 505 through 530 Processing helix chain 'C' and resid 550 through 568 Processing helix chain 'C' and resid 577 through 592 Processing helix chain 'C' and resid 602 through 609 Processing helix chain 'C' and resid 612 through 635 removed outlier: 3.798A pdb=" N ARG C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 676 Processing helix chain 'C' and resid 696 through 723 removed outlier: 3.816A pdb=" N THR C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 747 Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 164 through 176 removed outlier: 4.199A pdb=" N GLY D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 241 through 247 Processing helix chain 'D' and resid 251 through 259 removed outlier: 3.957A pdb=" N GLU D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 337 through 356 removed outlier: 3.800A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 373 through 380 Processing helix chain 'D' and resid 383 through 389 removed outlier: 4.095A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 433 through 438 Processing helix chain 'D' and resid 446 through 451 removed outlier: 3.661A pdb=" N LEU D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA D 451 " --> pdb=" O HIS D 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 446 through 451' Processing helix chain 'D' and resid 454 through 466 removed outlier: 3.673A pdb=" N ARG D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 489 Processing helix chain 'D' and resid 505 through 530 Processing helix chain 'D' and resid 550 through 568 Processing helix chain 'D' and resid 577 through 592 Processing helix chain 'D' and resid 602 through 609 Processing helix chain 'D' and resid 612 through 635 removed outlier: 3.798A pdb=" N ARG D 616 " --> pdb=" O LYS D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 676 Processing helix chain 'D' and resid 696 through 723 removed outlier: 3.816A pdb=" N THR D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 747 Processing helix chain 'B' and resid 151 through 159 Processing helix chain 'B' and resid 164 through 176 removed outlier: 4.200A pdb=" N GLY B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 224 through 227 No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 251 through 259 removed outlier: 3.958A pdb=" N GLU B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 273 No H-bonds generated for 'chain 'B' and resid 271 through 273' Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 323 through 330 Processing helix chain 'B' and resid 337 through 356 removed outlier: 3.801A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.095A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 446 through 451 removed outlier: 3.660A pdb=" N LEU B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA B 451 " --> pdb=" O HIS B 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 446 through 451' Processing helix chain 'B' and resid 454 through 466 removed outlier: 3.673A pdb=" N ARG B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 489 Processing helix chain 'B' and resid 505 through 530 Processing helix chain 'B' and resid 550 through 568 Processing helix chain 'B' and resid 577 through 592 Processing helix chain 'B' and resid 602 through 609 Processing helix chain 'B' and resid 612 through 635 removed outlier: 3.798A pdb=" N ARG B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 676 Processing helix chain 'B' and resid 696 through 723 removed outlier: 3.817A pdb=" N THR B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 747 Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 164 through 176 removed outlier: 4.200A pdb=" N GLY A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.958A pdb=" N GLU A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 337 through 356 removed outlier: 3.801A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.095A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 446 through 451 removed outlier: 3.660A pdb=" N LEU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA A 451 " --> pdb=" O HIS A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 446 through 451' Processing helix chain 'A' and resid 454 through 466 removed outlier: 3.673A pdb=" N ARG A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 489 Processing helix chain 'A' and resid 505 through 530 Processing helix chain 'A' and resid 550 through 568 Processing helix chain 'A' and resid 577 through 592 Processing helix chain 'A' and resid 602 through 609 Processing helix chain 'A' and resid 612 through 635 removed outlier: 3.798A pdb=" N ARG A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 676 Processing helix chain 'A' and resid 696 through 723 removed outlier: 3.816A pdb=" N THR A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 747 Processing sheet with id= A, first strand: chain 'C' and resid 780 through 783 removed outlier: 3.942A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 780 through 783 removed outlier: 3.942A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 780 through 783 removed outlier: 3.942A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 780 through 783 removed outlier: 3.943A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2460 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: 13.47 Time building geometry restraints manager: 33.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19292 1.03 - 1.23: 54 1.23 - 1.42: 8234 1.42 - 1.62: 11160 1.62 - 1.82: 160 Bond restraints: 38900 Sorted by residual: bond pdb=" C7 9QM D 901 " pdb=" O1 9QM D 901 " ideal model delta sigma weight residual 1.213 1.398 -0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" C7 9QM B 901 " pdb=" O1 9QM B 901 " ideal model delta sigma weight residual 1.213 1.397 -0.184 2.00e-02 2.50e+03 8.50e+01 bond pdb=" C7 9QM A 901 " pdb=" O1 9QM A 901 " ideal model delta sigma weight residual 1.213 1.397 -0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" C7 9QM C 901 " pdb=" O1 9QM C 901 " ideal model delta sigma weight residual 1.213 1.397 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C23 9QM B 901 " pdb=" C25 9QM B 901 " ideal model delta sigma weight residual 1.382 1.526 -0.144 2.00e-02 2.50e+03 5.15e+01 ... (remaining 38895 not shown) Histogram of bond angle deviations from ideal: 71.51 - 84.05: 36 84.05 - 96.58: 0 96.58 - 109.12: 22377 109.12 - 121.66: 41346 121.66 - 134.19: 6457 Bond angle restraints: 70216 Sorted by residual: angle pdb=" C SER D 688 " pdb=" CA SER D 688 " pdb=" HA SER D 688 " ideal model delta sigma weight residual 109.00 71.51 37.49 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C SER C 688 " pdb=" CA SER C 688 " pdb=" HA SER C 688 " ideal model delta sigma weight residual 109.00 71.51 37.49 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C SER A 688 " pdb=" CA SER A 688 " pdb=" HA SER A 688 " ideal model delta sigma weight residual 109.00 71.53 37.47 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C SER B 688 " pdb=" CA SER B 688 " pdb=" HA SER B 688 " ideal model delta sigma weight residual 109.00 71.55 37.45 3.00e+00 1.11e-01 1.56e+02 angle pdb=" N ILE C 696 " pdb=" CA ILE C 696 " pdb=" HA ILE C 696 " ideal model delta sigma weight residual 110.00 73.76 36.24 3.00e+00 1.11e-01 1.46e+02 ... (remaining 70211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 16306 17.76 - 35.53: 1445 35.53 - 53.29: 377 53.29 - 71.06: 84 71.06 - 88.82: 16 Dihedral angle restraints: 18228 sinusoidal: 9836 harmonic: 8392 Sorted by residual: dihedral pdb=" CA LYS C 727 " pdb=" C LYS C 727 " pdb=" N GLU C 728 " pdb=" CA GLU C 728 " ideal model delta harmonic sigma weight residual 180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LYS B 727 " pdb=" C LYS B 727 " pdb=" N GLU B 728 " pdb=" CA GLU B 728 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LYS A 727 " pdb=" C LYS A 727 " pdb=" N GLU A 728 " pdb=" CA GLU A 728 " ideal model delta harmonic sigma weight residual 180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 18225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 3020 0.276 - 0.552: 8 0.552 - 0.829: 0 0.829 - 1.105: 0 1.105 - 1.381: 4 Chirality restraints: 3032 Sorted by residual: chirality pdb=" CB THR B 701 " pdb=" CA THR B 701 " pdb=" OG1 THR B 701 " pdb=" CG2 THR B 701 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.77e+01 chirality pdb=" CB THR A 701 " pdb=" CA THR A 701 " pdb=" OG1 THR A 701 " pdb=" CG2 THR A 701 " both_signs ideal model delta sigma weight residual False 2.55 1.18 1.38 2.00e-01 2.50e+01 4.74e+01 chirality pdb=" CB THR C 701 " pdb=" CA THR C 701 " pdb=" OG1 THR C 701 " pdb=" CG2 THR C 701 " both_signs ideal model delta sigma weight residual False 2.55 1.18 1.38 2.00e-01 2.50e+01 4.73e+01 ... (remaining 3029 not shown) Planarity restraints: 5540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 9QM B 901 " -1.158 2.00e-02 2.50e+03 3.77e-01 5.69e+03 pdb=" C10 9QM B 901 " 0.015 2.00e-02 2.50e+03 pdb=" C11 9QM B 901 " -0.050 2.00e-02 2.50e+03 pdb=" C12 9QM B 901 " -0.007 2.00e-02 2.50e+03 pdb=" C15 9QM B 901 " -0.068 2.00e-02 2.50e+03 pdb=" C16 9QM B 901 " -0.048 2.00e-02 2.50e+03 pdb=" C2 9QM B 901 " 0.939 2.00e-02 2.50e+03 pdb=" C5 9QM B 901 " 0.052 2.00e-02 2.50e+03 pdb=" C7 9QM B 901 " 0.058 2.00e-02 2.50e+03 pdb=" C8 9QM B 901 " 0.124 2.00e-02 2.50e+03 pdb=" C9 9QM B 901 " -0.008 2.00e-02 2.50e+03 pdb=" F1 9QM B 901 " -0.071 2.00e-02 2.50e+03 pdb=" N1 9QM B 901 " 0.066 2.00e-02 2.50e+03 pdb=" N3 9QM B 901 " 0.070 2.00e-02 2.50e+03 pdb=" N4 9QM B 901 " 0.010 2.00e-02 2.50e+03 pdb=" O1 9QM B 901 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 9QM C 901 " -1.158 2.00e-02 2.50e+03 3.77e-01 5.69e+03 pdb=" C10 9QM C 901 " 0.015 2.00e-02 2.50e+03 pdb=" C11 9QM C 901 " -0.050 2.00e-02 2.50e+03 pdb=" C12 9QM C 901 " -0.007 2.00e-02 2.50e+03 pdb=" C15 9QM C 901 " -0.068 2.00e-02 2.50e+03 pdb=" C16 9QM C 901 " -0.048 2.00e-02 2.50e+03 pdb=" C2 9QM C 901 " 0.939 2.00e-02 2.50e+03 pdb=" C5 9QM C 901 " 0.052 2.00e-02 2.50e+03 pdb=" C7 9QM C 901 " 0.057 2.00e-02 2.50e+03 pdb=" C8 9QM C 901 " 0.123 2.00e-02 2.50e+03 pdb=" C9 9QM C 901 " -0.007 2.00e-02 2.50e+03 pdb=" F1 9QM C 901 " -0.071 2.00e-02 2.50e+03 pdb=" N1 9QM C 901 " 0.067 2.00e-02 2.50e+03 pdb=" N3 9QM C 901 " 0.070 2.00e-02 2.50e+03 pdb=" N4 9QM C 901 " 0.011 2.00e-02 2.50e+03 pdb=" O1 9QM C 901 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 9QM D 901 " 1.158 2.00e-02 2.50e+03 3.77e-01 5.69e+03 pdb=" C10 9QM D 901 " -0.015 2.00e-02 2.50e+03 pdb=" C11 9QM D 901 " 0.050 2.00e-02 2.50e+03 pdb=" C12 9QM D 901 " 0.007 2.00e-02 2.50e+03 pdb=" C15 9QM D 901 " 0.068 2.00e-02 2.50e+03 pdb=" C16 9QM D 901 " 0.048 2.00e-02 2.50e+03 pdb=" C2 9QM D 901 " -0.939 2.00e-02 2.50e+03 pdb=" C5 9QM D 901 " -0.052 2.00e-02 2.50e+03 pdb=" C7 9QM D 901 " -0.057 2.00e-02 2.50e+03 pdb=" C8 9QM D 901 " -0.123 2.00e-02 2.50e+03 pdb=" C9 9QM D 901 " 0.008 2.00e-02 2.50e+03 pdb=" F1 9QM D 901 " 0.070 2.00e-02 2.50e+03 pdb=" N1 9QM D 901 " -0.067 2.00e-02 2.50e+03 pdb=" N3 9QM D 901 " -0.070 2.00e-02 2.50e+03 pdb=" N4 9QM D 901 " -0.010 2.00e-02 2.50e+03 pdb=" O1 9QM D 901 " -0.076 2.00e-02 2.50e+03 ... (remaining 5537 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1868 2.14 - 2.76: 76356 2.76 - 3.37: 113680 3.37 - 3.99: 137914 3.99 - 4.60: 214145 Nonbonded interactions: 543963 Sorted by model distance: nonbonded pdb="HD22 ASN D 474 " pdb=" O1 9QM D 901 " model vdw 1.525 1.850 nonbonded pdb="HD22 ASN A 474 " pdb=" O1 9QM A 901 " model vdw 1.525 1.850 nonbonded pdb="HD22 ASN B 474 " pdb=" O1 9QM B 901 " model vdw 1.525 1.850 nonbonded pdb="HD22 ASN C 474 " pdb=" O1 9QM C 901 " model vdw 1.526 1.850 nonbonded pdb=" OD1 ASP B 318 " pdb=" H ASN B 322 " model vdw 1.543 1.850 ... (remaining 543958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.550 Extract box with map and model: 8.480 Check model and map are aligned: 0.580 Set scattering table: 0.370 Process input model: 123.230 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 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 : 0.009 0.185 19576 Z= 0.567 Angle : 0.757 11.030 26524 Z= 0.414 Chirality : 0.067 1.381 3032 Planarity : 0.014 0.377 3280 Dihedral : 13.707 73.260 7148 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.00 % Favored : 87.48 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % 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: -1.29 (0.18), residues: 2316 helix: 0.33 (0.15), residues: 1264 sheet: -0.17 (0.67), residues: 64 loop : -2.57 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP C 737 HIS 0.003 0.001 HIS C 388 PHE 0.036 0.002 PHE B 524 TYR 0.034 0.002 TYR C 346 ARG 0.004 0.001 ARG D 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 318 time to evaluate : 3.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 271 ARG cc_start: 0.7609 (tpm170) cc_final: 0.7167 (tpp-160) REVERT: D 271 ARG cc_start: 0.7558 (tpm170) cc_final: 0.7113 (tpp-160) REVERT: B 271 ARG cc_start: 0.7727 (tpm170) cc_final: 0.7287 (tpp-160) REVERT: A 271 ARG cc_start: 0.7641 (tpm170) cc_final: 0.7166 (tpp-160) REVERT: A 578 MET cc_start: 0.7695 (tmm) cc_final: 0.7425 (tmm) REVERT: A 742 LEU cc_start: 0.8528 (mm) cc_final: 0.8157 (tp) outliers start: 4 outliers final: 3 residues processed: 318 average time/residue: 0.7332 time to fit residues: 361.0361 Evaluate side-chains 266 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 263 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 93 optimal weight: 0.0040 chunk 181 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 overall best weight: 1.9798 ------------------------------------------------------------------------------- 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: 0.6820 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 19576 Z= 0.244 Angle : 0.707 11.179 26524 Z= 0.362 Chirality : 0.067 1.458 3032 Planarity : 0.004 0.060 3280 Dihedral : 5.949 60.000 2669 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.71 % Favored : 88.77 % Rotamer: Outliers : 1.15 % Allowed : 7.39 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2316 helix: 0.37 (0.15), residues: 1264 sheet: -0.20 (0.67), residues: 64 loop : -2.55 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 737 HIS 0.002 0.001 HIS A 731 PHE 0.019 0.001 PHE B 524 TYR 0.020 0.002 TYR B 553 ARG 0.003 0.000 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 285 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 482 MET cc_start: 0.6762 (mmp) cc_final: 0.6455 (mmt) REVERT: A 578 MET cc_start: 0.7678 (tmm) cc_final: 0.7431 (tmm) REVERT: A 742 LEU cc_start: 0.8545 (mm) cc_final: 0.8194 (tp) outliers start: 24 outliers final: 22 residues processed: 288 average time/residue: 0.7206 time to fit residues: 314.1681 Evaluate side-chains 297 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 275 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 30.0000 chunk 175 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 211 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 209 optimal weight: 0.0570 chunk 71 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 overall best weight: 1.7902 ------------------------------------------------------------------------------- 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: 0.6820 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19576 Z= 0.222 Angle : 0.674 11.285 26524 Z= 0.348 Chirality : 0.067 1.448 3032 Planarity : 0.004 0.062 3280 Dihedral : 5.604 59.796 2669 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.54 % Favored : 88.95 % Rotamer: Outliers : 0.96 % Allowed : 9.21 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.18), residues: 2316 helix: 0.50 (0.15), residues: 1256 sheet: -0.16 (0.67), residues: 64 loop : -2.42 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 737 HIS 0.002 0.001 HIS A 731 PHE 0.021 0.001 PHE B 524 TYR 0.016 0.002 TYR C 346 ARG 0.006 0.000 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 276 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 TYR cc_start: 0.8315 (t80) cc_final: 0.8005 (t80) REVERT: A 482 MET cc_start: 0.6711 (mmp) cc_final: 0.6378 (mmp) outliers start: 20 outliers final: 17 residues processed: 280 average time/residue: 0.7284 time to fit residues: 306.6822 Evaluate side-chains 288 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 271 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 0.2980 chunk 158 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 60 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.6803 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19576 Z= 0.189 Angle : 0.654 11.245 26524 Z= 0.337 Chirality : 0.066 1.446 3032 Planarity : 0.004 0.049 3280 Dihedral : 5.529 59.666 2669 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.02 % Favored : 89.64 % Rotamer: Outliers : 1.06 % Allowed : 9.88 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), residues: 2316 helix: 0.68 (0.15), residues: 1252 sheet: -0.03 (0.68), residues: 64 loop : -2.36 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 737 HIS 0.002 0.000 HIS A 731 PHE 0.018 0.001 PHE B 524 TYR 0.017 0.001 TYR D 553 ARG 0.008 0.000 ARG D 616 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 277 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 616 ARG cc_start: 0.7213 (tpp-160) cc_final: 0.7005 (ttp-170) REVERT: A 482 MET cc_start: 0.6728 (mmp) cc_final: 0.6236 (mmp) outliers start: 22 outliers final: 18 residues processed: 282 average time/residue: 0.7466 time to fit residues: 313.5615 Evaluate side-chains 282 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 264 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 56 optimal weight: 0.0170 overall best weight: 2.1224 ------------------------------------------------------------------------------- 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: 0.6837 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19576 Z= 0.234 Angle : 0.662 11.397 26524 Z= 0.345 Chirality : 0.066 1.445 3032 Planarity : 0.004 0.075 3280 Dihedral : 5.512 59.487 2669 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.15 % Favored : 89.51 % Rotamer: Outliers : 1.06 % Allowed : 11.32 % Favored : 87.62 % 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: -0.91 (0.18), residues: 2316 helix: 0.67 (0.15), residues: 1244 sheet: 0.09 (0.69), residues: 64 loop : -2.39 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 737 HIS 0.002 0.001 HIS A 731 PHE 0.034 0.001 PHE B 524 TYR 0.029 0.001 TYR B 553 ARG 0.007 0.000 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 272 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 482 MET cc_start: 0.6722 (mmp) cc_final: 0.6163 (mmp) REVERT: A 482 MET cc_start: 0.6795 (mmp) cc_final: 0.6269 (mmp) outliers start: 22 outliers final: 18 residues processed: 278 average time/residue: 0.7215 time to fit residues: 302.3186 Evaluate side-chains 283 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 265 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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: 0.6826 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19576 Z= 0.206 Angle : 0.663 11.513 26524 Z= 0.343 Chirality : 0.066 1.455 3032 Planarity : 0.004 0.058 3280 Dihedral : 5.460 59.435 2669 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.32 % Favored : 89.34 % Rotamer: Outliers : 1.06 % Allowed : 12.00 % Favored : 86.95 % 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: -0.86 (0.18), residues: 2316 helix: 0.76 (0.15), residues: 1244 sheet: 0.10 (0.68), residues: 64 loop : -2.42 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 737 HIS 0.002 0.000 HIS A 731 PHE 0.030 0.001 PHE B 524 TYR 0.020 0.001 TYR C 553 ARG 0.007 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 275 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 482 MET cc_start: 0.6757 (mmp) cc_final: 0.6206 (mmp) REVERT: A 482 MET cc_start: 0.6803 (mmp) cc_final: 0.6267 (mmp) outliers start: 22 outliers final: 19 residues processed: 281 average time/residue: 0.7261 time to fit residues: 308.4253 Evaluate side-chains 284 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 265 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 742 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 138 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19576 Z= 0.274 Angle : 0.686 11.443 26524 Z= 0.360 Chirality : 0.067 1.460 3032 Planarity : 0.005 0.081 3280 Dihedral : 5.512 59.129 2669 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.53 % Favored : 88.13 % Rotamer: Outliers : 1.49 % Allowed : 13.05 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2316 helix: 0.64 (0.14), residues: 1252 sheet: -0.10 (0.67), residues: 64 loop : -2.47 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 737 HIS 0.002 0.001 HIS A 401 PHE 0.037 0.002 PHE A 524 TYR 0.023 0.002 TYR A 553 ARG 0.008 0.001 ARG D 616 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 482 MET cc_start: 0.6855 (mmp) cc_final: 0.6288 (mmp) REVERT: B 482 MET cc_start: 0.6882 (mmp) cc_final: 0.6483 (mmt) REVERT: A 482 MET cc_start: 0.6863 (mmp) cc_final: 0.6303 (mmp) outliers start: 31 outliers final: 20 residues processed: 284 average time/residue: 0.7431 time to fit residues: 318.6496 Evaluate side-chains 288 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 268 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 707 PHE Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 142 optimal weight: 0.0870 chunk 152 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 203 optimal weight: 0.6980 chunk 214 optimal weight: 9.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- 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: 0.6834 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19576 Z= 0.199 Angle : 0.666 11.465 26524 Z= 0.345 Chirality : 0.066 1.451 3032 Planarity : 0.004 0.051 3280 Dihedral : 5.438 59.336 2669 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.06 % Favored : 89.59 % Rotamer: Outliers : 1.20 % Allowed : 13.68 % Favored : 85.12 % 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: -0.79 (0.18), residues: 2316 helix: 0.78 (0.15), residues: 1256 sheet: -0.00 (0.68), residues: 64 loop : -2.37 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 737 HIS 0.002 0.000 HIS A 731 PHE 0.050 0.001 PHE A 524 TYR 0.023 0.001 TYR D 553 ARG 0.004 0.000 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 271 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.6683 (mmp) cc_final: 0.6212 (mmp) REVERT: D 482 MET cc_start: 0.6804 (mmp) cc_final: 0.6246 (mmp) REVERT: A 453 GLU cc_start: 0.7822 (tp30) cc_final: 0.7535 (tp30) REVERT: A 482 MET cc_start: 0.6795 (mmp) cc_final: 0.6256 (mmp) outliers start: 25 outliers final: 20 residues processed: 282 average time/residue: 0.7478 time to fit residues: 319.4926 Evaluate side-chains 281 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 261 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.6852 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19576 Z= 0.226 Angle : 0.673 11.416 26524 Z= 0.351 Chirality : 0.066 1.455 3032 Planarity : 0.004 0.050 3280 Dihedral : 5.402 58.764 2669 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.71 % Favored : 88.95 % Rotamer: Outliers : 1.34 % Allowed : 14.49 % Favored : 84.17 % 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: -0.82 (0.18), residues: 2316 helix: 0.76 (0.15), residues: 1256 sheet: 0.07 (0.68), residues: 64 loop : -2.39 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 737 HIS 0.003 0.001 HIS D 265 PHE 0.053 0.002 PHE A 524 TYR 0.019 0.001 TYR B 553 ARG 0.004 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 268 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 453 GLU cc_start: 0.7888 (tp30) cc_final: 0.7591 (tp30) REVERT: C 482 MET cc_start: 0.6712 (mmp) cc_final: 0.6225 (mmp) REVERT: D 453 GLU cc_start: 0.7890 (tp30) cc_final: 0.7595 (tp30) REVERT: D 482 MET cc_start: 0.6828 (mmp) cc_final: 0.6253 (mmp) REVERT: A 482 MET cc_start: 0.6819 (mmp) cc_final: 0.6248 (mmp) REVERT: A 619 LEU cc_start: 0.7859 (tp) cc_final: 0.7589 (tp) outliers start: 28 outliers final: 23 residues processed: 283 average time/residue: 0.7319 time to fit residues: 310.8959 Evaluate side-chains 289 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 266 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 756 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 142 optimal weight: 0.0070 chunk 112 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 overall best weight: 0.7202 ------------------------------------------------------------------------------- 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: 0.6803 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19576 Z= 0.173 Angle : 0.676 11.457 26524 Z= 0.344 Chirality : 0.066 1.442 3032 Planarity : 0.004 0.050 3280 Dihedral : 5.326 59.923 2669 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.63 % Favored : 90.03 % Rotamer: Outliers : 0.91 % Allowed : 14.64 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 2316 helix: 0.91 (0.15), residues: 1256 sheet: 0.34 (0.71), residues: 64 loop : -2.33 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 737 HIS 0.003 0.001 HIS B 326 PHE 0.066 0.001 PHE A 524 TYR 0.021 0.001 TYR D 553 ARG 0.007 0.000 ARG D 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 273 time to evaluate : 3.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 482 MET cc_start: 0.6616 (mmp) cc_final: 0.6138 (mmp) REVERT: C 619 LEU cc_start: 0.7726 (tp) cc_final: 0.7342 (tp) REVERT: D 482 MET cc_start: 0.6793 (mmp) cc_final: 0.6241 (mmp) REVERT: A 482 MET cc_start: 0.6757 (mmp) cc_final: 0.6212 (mmp) outliers start: 19 outliers final: 17 residues processed: 283 average time/residue: 0.7693 time to fit residues: 323.5870 Evaluate side-chains 281 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 264 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 718 MET Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 756 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 184 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 161 optimal weight: 0.0570 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 = 0.4578 r_free = 0.4578 target = 0.170369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.135825 restraints weight = 142092.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.141541 restraints weight = 73079.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.145120 restraints weight = 48780.273| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19576 Z= 0.178 Angle : 0.669 11.405 26524 Z= 0.342 Chirality : 0.066 1.434 3032 Planarity : 0.004 0.049 3280 Dihedral : 5.192 59.514 2669 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.84 % Favored : 89.81 % Rotamer: Outliers : 0.86 % Allowed : 14.88 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2316 helix: 1.03 (0.15), residues: 1260 sheet: 0.56 (0.73), residues: 64 loop : -2.34 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 737 HIS 0.002 0.001 HIS C 731 PHE 0.063 0.001 PHE A 524 TYR 0.018 0.001 TYR B 553 ARG 0.008 0.000 ARG B 616 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7579.34 seconds wall clock time: 135 minutes 51.19 seconds (8151.19 seconds total)