Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 23:00:05 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xye_10649/12_2021/6xye_10649.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xye_10649/12_2021/6xye_10649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xye_10649/12_2021/6xye_10649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xye_10649/12_2021/6xye_10649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xye_10649/12_2021/6xye_10649.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xye_10649/12_2021/6xye_10649.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 9834 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 588 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2690 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 13, 'TRANS': 343} Chain: "C" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 588 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2690 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 13, 'TRANS': 343} Chain: "E" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 588 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2690 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 13, 'TRANS': 343} Time building chain proxies: 5.92, per 1000 atoms: 0.60 Number of scatterers: 9834 At special positions: 0 Unit cell: (102.1, 106.184, 101.079, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1902 8.00 N 1656 7.00 C 6219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS B 307 " distance=2.06 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 455 " distance=2.04 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 478 " distance=2.02 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 532 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS D 307 " distance=2.06 Simple disulfide: pdb=" SG CYS D 446 " - pdb=" SG CYS D 455 " distance=2.04 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 478 " distance=2.02 Simple disulfide: pdb=" SG CYS D 502 " - pdb=" SG CYS D 507 " distance=2.03 Simple disulfide: pdb=" SG CYS D 509 " - pdb=" SG CYS D 532 " distance=2.04 Simple disulfide: pdb=" SG CYS E 180 " - pdb=" SG CYS F 307 " distance=2.06 Simple disulfide: pdb=" SG CYS F 446 " - pdb=" SG CYS F 455 " distance=2.04 Simple disulfide: pdb=" SG CYS F 470 " - pdb=" SG CYS F 478 " distance=2.02 Simple disulfide: pdb=" SG CYS F 502 " - pdb=" SG CYS F 507 " distance=2.03 Simple disulfide: pdb=" SG CYS F 509 " - pdb=" SG CYS F 532 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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: 3.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 24 sheets defined 29.2% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 182 through 207 removed outlier: 3.689A pdb=" N LYS A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Proline residue: A 198 - end of helix Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 240 through 251 Processing helix chain 'B' and resid 260 through 268 removed outlier: 3.670A pdb=" N GLU B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 307 through 328 Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 465 through 473 removed outlier: 5.344A pdb=" N CYS B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG B 472 " --> pdb=" O GLN B 468 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 582 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 182 through 207 removed outlier: 3.690A pdb=" N LYS C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Proline residue: C 198 - end of helix Processing helix chain 'D' and resid 232 through 235 No H-bonds generated for 'chain 'D' and resid 232 through 235' Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 260 through 268 removed outlier: 3.670A pdb=" N GLU D 267 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 307 through 328 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 465 through 473 removed outlier: 5.344A pdb=" N CYS D 470 " --> pdb=" O LEU D 466 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE D 471 " --> pdb=" O LEU D 467 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG D 472 " --> pdb=" O GLN D 468 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY D 473 " --> pdb=" O GLN D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 582 Processing helix chain 'E' and resid 139 through 142 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 182 through 207 removed outlier: 3.689A pdb=" N LYS E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) Proline residue: E 198 - end of helix Processing helix chain 'F' and resid 232 through 235 No H-bonds generated for 'chain 'F' and resid 232 through 235' Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 260 through 268 removed outlier: 3.670A pdb=" N GLU F 267 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLN F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 307 through 328 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 368 through 372 Processing helix chain 'F' and resid 465 through 473 removed outlier: 5.343A pdb=" N CYS F 470 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG F 472 " --> pdb=" O GLN F 468 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY F 473 " --> pdb=" O GLN F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 582 Processing sheet with id= A, first strand: chain 'B' and resid 446 through 448 removed outlier: 7.862A pdb=" N ALA B 453 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS A 154 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N CYS B 455 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS A 156 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP A 151 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 155 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 406 " --> pdb=" O TYR A 155 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 156 through 159 Processing sheet with id= C, first strand: chain 'A' and resid 163 through 169 removed outlier: 6.275A pdb=" N SER B 394 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE B 381 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER B 396 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR B 379 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.190A pdb=" N ILE B 273 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 287 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU B 275 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 285 " --> pdb=" O GLU B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 416 through 418 Processing sheet with id= F, first strand: chain 'B' and resid 424 through 425 Processing sheet with id= G, first strand: chain 'B' and resid 491 through 494 Processing sheet with id= H, first strand: chain 'B' and resid 507 through 509 Processing sheet with id= I, first strand: chain 'D' and resid 446 through 448 removed outlier: 7.861A pdb=" N ALA D 453 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS C 154 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N CYS D 455 " --> pdb=" O HIS C 154 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS C 156 " --> pdb=" O CYS D 455 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP C 151 " --> pdb=" O ARG D 410 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 155 " --> pdb=" O VAL D 406 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL D 406 " --> pdb=" O TYR C 155 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 156 through 159 Processing sheet with id= K, first strand: chain 'C' and resid 163 through 169 removed outlier: 6.275A pdb=" N SER D 394 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE D 381 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER D 396 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR D 379 " --> pdb=" O SER D 396 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 273 through 276 removed outlier: 6.190A pdb=" N ILE D 273 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL D 287 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU D 275 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE D 285 " --> pdb=" O GLU D 275 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 416 through 418 Processing sheet with id= N, first strand: chain 'D' and resid 424 through 425 Processing sheet with id= O, first strand: chain 'D' and resid 491 through 494 Processing sheet with id= P, first strand: chain 'D' and resid 507 through 509 Processing sheet with id= Q, first strand: chain 'F' and resid 446 through 448 removed outlier: 7.862A pdb=" N ALA F 453 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS E 154 " --> pdb=" O ALA F 453 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N CYS F 455 " --> pdb=" O HIS E 154 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS E 156 " --> pdb=" O CYS F 455 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP E 151 " --> pdb=" O ARG F 410 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR E 155 " --> pdb=" O VAL F 406 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL F 406 " --> pdb=" O TYR E 155 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 156 through 159 Processing sheet with id= S, first strand: chain 'E' and resid 163 through 169 removed outlier: 6.276A pdb=" N SER F 394 " --> pdb=" O ILE F 381 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE F 381 " --> pdb=" O SER F 394 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER F 396 " --> pdb=" O THR F 379 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR F 379 " --> pdb=" O SER F 396 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 273 through 276 removed outlier: 6.190A pdb=" N ILE F 273 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL F 287 " --> pdb=" O ILE F 273 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU F 275 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE F 285 " --> pdb=" O GLU F 275 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 416 through 418 Processing sheet with id= V, first strand: chain 'F' and resid 424 through 425 Processing sheet with id= W, first strand: chain 'F' and resid 491 through 494 Processing sheet with id= X, first strand: chain 'F' and resid 507 through 509 330 hydrogen bonds defined for protein. 891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2890 1.34 - 1.46: 1651 1.46 - 1.58: 5353 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 9978 Sorted by residual: bond pdb=" N VAL B 427 " pdb=" CA VAL B 427 " ideal model delta sigma weight residual 1.462 1.494 -0.032 9.10e-03 1.21e+04 1.21e+01 bond pdb=" N VAL F 427 " pdb=" CA VAL F 427 " ideal model delta sigma weight residual 1.462 1.494 -0.031 9.10e-03 1.21e+04 1.17e+01 bond pdb=" N VAL D 427 " pdb=" CA VAL D 427 " ideal model delta sigma weight residual 1.462 1.493 -0.031 9.10e-03 1.21e+04 1.16e+01 bond pdb=" CA SER B 459 " pdb=" CB SER B 459 " ideal model delta sigma weight residual 1.537 1.492 0.045 1.38e-02 5.25e+03 1.06e+01 bond pdb=" CA SER D 459 " pdb=" CB SER D 459 " ideal model delta sigma weight residual 1.537 1.492 0.045 1.38e-02 5.25e+03 1.05e+01 ... (remaining 9973 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.46: 216 105.46 - 112.59: 5339 112.59 - 119.73: 3797 119.73 - 126.87: 4130 126.87 - 134.01: 66 Bond angle restraints: 13548 Sorted by residual: angle pdb=" N GLY B 365 " pdb=" CA GLY B 365 " pdb=" C GLY B 365 " ideal model delta sigma weight residual 115.36 109.42 5.94 1.33e+00 5.65e-01 1.99e+01 angle pdb=" N GLY D 365 " pdb=" CA GLY D 365 " pdb=" C GLY D 365 " ideal model delta sigma weight residual 115.36 109.42 5.94 1.33e+00 5.65e-01 1.99e+01 angle pdb=" N GLY F 365 " pdb=" CA GLY F 365 " pdb=" C GLY F 365 " ideal model delta sigma weight residual 115.36 109.45 5.91 1.33e+00 5.65e-01 1.98e+01 angle pdb=" CA GLY F 561 " pdb=" C GLY F 561 " pdb=" O GLY F 561 " ideal model delta sigma weight residual 122.46 118.49 3.97 9.70e-01 1.06e+00 1.68e+01 angle pdb=" CA GLY B 561 " pdb=" C GLY B 561 " pdb=" O GLY B 561 " ideal model delta sigma weight residual 122.46 118.55 3.91 9.70e-01 1.06e+00 1.62e+01 ... (remaining 13543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 5653 14.85 - 29.69: 426 29.69 - 44.53: 47 44.53 - 59.38: 3 59.38 - 74.22: 3 Dihedral angle restraints: 6132 sinusoidal: 2394 harmonic: 3738 Sorted by residual: dihedral pdb=" CA ILE F 418 " pdb=" C ILE F 418 " pdb=" N GLY F 419 " pdb=" CA GLY F 419 " ideal model delta harmonic sigma weight residual -180.00 -150.29 -29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ILE D 418 " pdb=" C ILE D 418 " pdb=" N GLY D 419 " pdb=" CA GLY D 419 " ideal model delta harmonic sigma weight residual -180.00 -150.29 -29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ILE B 418 " pdb=" C ILE B 418 " pdb=" N GLY B 419 " pdb=" CA GLY B 419 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 6129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 891 0.058 - 0.115: 467 0.115 - 0.173: 173 0.173 - 0.231: 107 0.231 - 0.288: 9 Chirality restraints: 1647 Sorted by residual: chirality pdb=" CA TYR F 397 " pdb=" N TYR F 397 " pdb=" C TYR F 397 " pdb=" CB TYR F 397 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA TYR D 397 " pdb=" N TYR D 397 " pdb=" C TYR D 397 " pdb=" CB TYR D 397 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA TYR B 397 " pdb=" N TYR B 397 " pdb=" C TYR B 397 " pdb=" CB TYR B 397 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 1644 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 302 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C MET F 302 " -0.056 2.00e-02 2.50e+03 pdb=" O MET F 302 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN F 303 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 302 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C MET B 302 " -0.056 2.00e-02 2.50e+03 pdb=" O MET B 302 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN B 303 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 302 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C MET D 302 " -0.055 2.00e-02 2.50e+03 pdb=" O MET D 302 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN D 303 " 0.019 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2897 2.83 - 3.35: 9343 3.35 - 3.87: 15826 3.87 - 4.38: 17131 4.38 - 4.90: 28703 Nonbonded interactions: 73900 Sorted by model distance: nonbonded pdb=" OG1 THR F 382 " pdb=" O ILE F 392 " model vdw 2.315 2.440 nonbonded pdb=" OG1 THR D 382 " pdb=" O ILE D 392 " model vdw 2.315 2.440 nonbonded pdb=" OG1 THR B 382 " pdb=" O ILE B 392 " model vdw 2.315 2.440 nonbonded pdb=" O GLN B 543 " pdb=" N GLY F 232 " model vdw 2.360 2.520 nonbonded pdb=" OH TYR F 321 " pdb=" O ALA F 349 " model vdw 2.366 2.440 ... (remaining 73895 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 6219 2.51 5 N 1656 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.840 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 28.770 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 34.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 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 : 0.010 0.051 9978 Z= 0.664 Angle : 1.295 7.767 13548 Z= 0.911 Chirality : 0.087 0.288 1647 Planarity : 0.007 0.042 1716 Dihedral : 10.030 74.225 3687 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.21), residues: 1281 helix: -1.87 (0.25), residues: 342 sheet: -3.21 (0.41), residues: 105 loop : -2.05 (0.20), residues: 834 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.209 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 outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.1803 time to fit residues: 93.8355 Evaluate side-chains 242 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 173 ASN B 296 ASN B 304 HIS ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS C 209 ASN D 296 ASN D 304 HIS D 497 ASN D 518 GLN E 138 HIS E 209 ASN F 260 GLN F 295 ASN F 296 ASN F 304 HIS F 497 ASN F 518 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 9978 Z= 0.205 Angle : 0.667 7.468 13548 Z= 0.352 Chirality : 0.047 0.335 1647 Planarity : 0.005 0.095 1716 Dihedral : 6.439 36.115 1377 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.22), residues: 1281 helix: -0.68 (0.25), residues: 363 sheet: -2.56 (0.43), residues: 105 loop : -1.73 (0.21), residues: 813 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.2072 time to fit residues: 88.8387 Evaluate side-chains 229 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 95 optimal weight: 0.2980 chunk 77 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 440 ASN ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS D 295 ASN D 312 GLN D 440 ASN D 497 ASN E 138 HIS E 209 ASN F 312 GLN F 440 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 9978 Z= 0.263 Angle : 0.673 6.765 13548 Z= 0.356 Chirality : 0.047 0.219 1647 Planarity : 0.004 0.032 1716 Dihedral : 6.231 29.567 1377 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 0.27 % 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: -1.88 (0.23), residues: 1281 helix: 0.12 (0.28), residues: 336 sheet: -2.07 (0.41), residues: 117 loop : -1.80 (0.22), residues: 828 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 280 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 283 average time/residue: 0.1992 time to fit residues: 79.9265 Evaluate side-chains 219 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN D 383 HIS ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN F 312 GLN ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 9978 Z= 0.385 Angle : 0.786 7.439 13548 Z= 0.413 Chirality : 0.050 0.230 1647 Planarity : 0.005 0.067 1716 Dihedral : 6.753 34.612 1377 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.98 (0.23), residues: 1281 helix: 0.25 (0.29), residues: 327 sheet: -2.64 (0.44), residues: 87 loop : -1.92 (0.21), residues: 867 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1771 time to fit residues: 69.3345 Evaluate side-chains 206 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 ASN B 458 ASN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9978 Z= 0.219 Angle : 0.657 6.953 13548 Z= 0.345 Chirality : 0.047 0.250 1647 Planarity : 0.006 0.100 1716 Dihedral : 6.126 28.884 1377 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.23), residues: 1281 helix: 0.87 (0.30), residues: 306 sheet: -2.26 (0.46), residues: 87 loop : -1.84 (0.21), residues: 888 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.1890 time to fit residues: 74.8816 Evaluate side-chains 213 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.190 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.2980 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 121 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 497 ASN ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS E 138 HIS E 209 ASN F 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9978 Z= 0.188 Angle : 0.636 9.220 13548 Z= 0.331 Chirality : 0.047 0.305 1647 Planarity : 0.004 0.035 1716 Dihedral : 5.843 25.133 1377 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.23), residues: 1281 helix: 0.61 (0.29), residues: 330 sheet: -2.02 (0.42), residues: 117 loop : -1.73 (0.22), residues: 834 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1831 time to fit residues: 72.7825 Evaluate side-chains 224 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN C 138 HIS D 440 ASN ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 209 ASN ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9978 Z= 0.264 Angle : 0.704 9.264 13548 Z= 0.365 Chirality : 0.048 0.284 1647 Planarity : 0.004 0.043 1716 Dihedral : 6.132 25.518 1377 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.23), residues: 1281 helix: 0.79 (0.30), residues: 324 sheet: -2.12 (0.41), residues: 117 loop : -1.81 (0.22), residues: 840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1838 time to fit residues: 69.1288 Evaluate side-chains 207 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS D 344 GLN ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9978 Z= 0.180 Angle : 0.655 9.704 13548 Z= 0.336 Chirality : 0.048 0.276 1647 Planarity : 0.004 0.035 1716 Dihedral : 5.806 25.117 1377 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1281 helix: 0.78 (0.30), residues: 321 sheet: -1.94 (0.42), residues: 117 loop : -1.71 (0.21), residues: 843 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1783 time to fit residues: 69.8732 Evaluate side-chains 222 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 0.3980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS D 344 GLN ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 209 ASN F 344 GLN F 458 ASN ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9978 Z= 0.193 Angle : 0.653 9.811 13548 Z= 0.337 Chirality : 0.048 0.269 1647 Planarity : 0.004 0.034 1716 Dihedral : 5.775 24.951 1377 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.23), residues: 1281 helix: 0.71 (0.29), residues: 330 sheet: -1.92 (0.42), residues: 117 loop : -1.73 (0.21), residues: 834 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.170 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 outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1771 time to fit residues: 68.7505 Evaluate side-chains 214 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 7.9990 chunk 56 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 209 ASN F 468 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9978 Z= 0.208 Angle : 0.668 9.448 13548 Z= 0.344 Chirality : 0.048 0.311 1647 Planarity : 0.004 0.035 1716 Dihedral : 5.834 26.434 1377 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.23), residues: 1281 helix: 0.72 (0.30), residues: 321 sheet: -1.95 (0.41), residues: 117 loop : -1.68 (0.21), residues: 843 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1846 time to fit residues: 71.1828 Evaluate side-chains 218 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 0.0270 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS D 344 GLN ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 ASN E 138 HIS E 140 ASN E 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.162749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.141010 restraints weight = 20595.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.144189 restraints weight = 13761.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.146505 restraints weight = 10093.801| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 9978 Z= 0.155 Angle : 0.624 9.674 13548 Z= 0.322 Chirality : 0.047 0.342 1647 Planarity : 0.004 0.040 1716 Dihedral : 5.412 22.473 1377 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.23), residues: 1281 helix: 0.50 (0.28), residues: 342 sheet: -1.74 (0.42), residues: 117 loop : -1.75 (0.21), residues: 822 =============================================================================== Job complete usr+sys time: 1989.94 seconds wall clock time: 41 minutes 47.76 seconds (2507.76 seconds total)