Starting phenix.real_space_refine on Thu Mar 14 21:37:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xye_10649/03_2024/6xye_10649.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xye_10649/03_2024/6xye_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_10649/03_2024/6xye_10649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xye_10649/03_2024/6xye_10649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xye_10649/03_2024/6xye_10649.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xye_10649/03_2024/6xye_10649.pdb" } resolution = 4.3 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= 0.004 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: 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. Process input model Symmetric amino acids flipped Residue "B ARG 277": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 320": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 429": "NH1" <-> "NH2" Residue "D ARG 472": "NH1" <-> "NH2" Residue "F ARG 277": "NH1" <-> "NH2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F ARG 320": "NH1" <-> "NH2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F ARG 472": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.69, per 1000 atoms: 0.58 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 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: 3.89 Conformation dependent library (CDL) restraints added in 1.9 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: 1.21 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: 2.77 Time building geometry restraints manager: 4.20 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 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.440 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.200 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 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 : 10.029 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 % Allowed : 1.89 % Favored : 98.11 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.006 TRP E 139 HIS 0.012 0.002 HIS F 409 PHE 0.016 0.003 PHE F 448 TYR 0.027 0.004 TYR B 293 ARG 0.005 0.001 ARG F 480 *********************** 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 : 1.259 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: A 142 LEU cc_start: 0.8999 (mt) cc_final: 0.8697 (mt) REVERT: A 173 ASN cc_start: 0.7386 (t0) cc_final: 0.7112 (t0) REVERT: A 193 ASN cc_start: 0.8737 (m-40) cc_final: 0.8248 (m-40) REVERT: B 322 TYR cc_start: 0.7309 (t80) cc_final: 0.5901 (t80) REVERT: B 385 ASP cc_start: 0.6926 (t70) cc_final: 0.6679 (m-30) REVERT: B 389 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7389 (mptt) REVERT: B 411 LEU cc_start: 0.8406 (mt) cc_final: 0.8122 (mp) REVERT: B 412 GLU cc_start: 0.8062 (tp30) cc_final: 0.7503 (tp30) REVERT: B 460 LEU cc_start: 0.9090 (mt) cc_final: 0.8781 (tt) REVERT: B 463 MET cc_start: 0.6900 (ttm) cc_final: 0.5346 (ttm) REVERT: C 142 LEU cc_start: 0.9009 (mt) cc_final: 0.8708 (mt) REVERT: C 173 ASN cc_start: 0.7560 (t0) cc_final: 0.7325 (t0) REVERT: C 193 ASN cc_start: 0.8798 (m-40) cc_final: 0.8162 (m-40) REVERT: D 389 LYS cc_start: 0.8442 (mmtt) cc_final: 0.7525 (mptt) REVERT: D 436 TYR cc_start: 0.6971 (t80) cc_final: 0.6659 (t80) REVERT: D 463 MET cc_start: 0.6952 (ttm) cc_final: 0.5710 (ttm) REVERT: D 551 ASP cc_start: 0.7378 (m-30) cc_final: 0.6743 (t70) REVERT: D 580 LYS cc_start: 0.9178 (tttt) cc_final: 0.8485 (mttm) REVERT: E 142 LEU cc_start: 0.9012 (mt) cc_final: 0.8709 (mt) REVERT: E 173 ASN cc_start: 0.7548 (t0) cc_final: 0.7313 (t0) REVERT: E 193 ASN cc_start: 0.8685 (m-40) cc_final: 0.8469 (m-40) REVERT: F 276 ILE cc_start: 0.8922 (mm) cc_final: 0.8709 (pt) REVERT: F 302 MET cc_start: 0.7249 (mmm) cc_final: 0.6951 (mmt) REVERT: F 389 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7583 (mptt) REVERT: F 422 GLU cc_start: 0.6669 (tt0) cc_final: 0.6319 (mp0) REVERT: F 430 TYR cc_start: 0.8339 (m-80) cc_final: 0.8056 (m-80) REVERT: F 436 TYR cc_start: 0.7039 (t80) cc_final: 0.6799 (t80) REVERT: F 463 MET cc_start: 0.6671 (ttm) cc_final: 0.5420 (ttm) REVERT: F 510 TYR cc_start: 0.7011 (t80) cc_final: 0.6364 (t80) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.2268 time to fit residues: 116.5841 Evaluate side-chains 251 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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: 8.9990 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS B 296 ASN B 304 HIS ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS C 209 ASN D 295 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: 0.6902 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9978 Z= 0.203 Angle : 0.657 7.503 13548 Z= 0.347 Chirality : 0.047 0.333 1647 Planarity : 0.004 0.031 1716 Dihedral : 6.399 34.947 1377 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: -2.11 (0.22), residues: 1281 helix: -0.54 (0.26), residues: 345 sheet: -2.60 (0.43), residues: 105 loop : -1.68 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 423 HIS 0.003 0.001 HIS B 304 PHE 0.011 0.001 PHE D 329 TYR 0.016 0.001 TYR D 424 ARG 0.005 0.001 ARG D 277 *********************** 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 300 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.238 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: A 142 LEU cc_start: 0.8783 (mt) cc_final: 0.8460 (mt) REVERT: A 147 ILE cc_start: 0.8420 (mm) cc_final: 0.8170 (mm) REVERT: A 173 ASN cc_start: 0.7543 (t0) cc_final: 0.7150 (t0) REVERT: A 193 ASN cc_start: 0.8836 (m-40) cc_final: 0.8362 (m-40) REVERT: B 275 GLU cc_start: 0.6960 (pt0) cc_final: 0.6689 (pm20) REVERT: B 322 TYR cc_start: 0.7179 (t80) cc_final: 0.6002 (t80) REVERT: B 385 ASP cc_start: 0.6825 (t70) cc_final: 0.6321 (m-30) REVERT: B 389 LYS cc_start: 0.8388 (mmtt) cc_final: 0.7381 (mptt) REVERT: B 408 VAL cc_start: 0.8413 (t) cc_final: 0.8179 (t) REVERT: B 412 GLU cc_start: 0.8188 (tp30) cc_final: 0.7531 (tp30) REVERT: B 551 ASP cc_start: 0.7356 (m-30) cc_final: 0.6729 (t70) REVERT: C 142 LEU cc_start: 0.8676 (mt) cc_final: 0.8391 (mt) REVERT: C 147 ILE cc_start: 0.8201 (mm) cc_final: 0.7894 (mm) REVERT: C 176 LEU cc_start: 0.7782 (mt) cc_final: 0.7182 (tt) REVERT: C 193 ASN cc_start: 0.8887 (m-40) cc_final: 0.8352 (m-40) REVERT: D 275 GLU cc_start: 0.7106 (pt0) cc_final: 0.6816 (pm20) REVERT: D 389 LYS cc_start: 0.8473 (mmtt) cc_final: 0.7481 (mptt) REVERT: D 436 TYR cc_start: 0.7367 (t80) cc_final: 0.6978 (t80) REVERT: D 551 ASP cc_start: 0.7116 (m-30) cc_final: 0.6607 (t70) REVERT: E 142 LEU cc_start: 0.8688 (mt) cc_final: 0.8433 (mt) REVERT: E 147 ILE cc_start: 0.8463 (mm) cc_final: 0.8212 (mm) REVERT: F 312 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7664 (tp-100) REVERT: F 314 LEU cc_start: 0.9207 (mt) cc_final: 0.8985 (mt) REVERT: F 385 ASP cc_start: 0.8113 (m-30) cc_final: 0.7809 (m-30) REVERT: F 389 LYS cc_start: 0.8482 (mmtt) cc_final: 0.7638 (mptt) REVERT: F 510 TYR cc_start: 0.6795 (t80) cc_final: 0.6366 (t80) REVERT: F 551 ASP cc_start: 0.7507 (m-30) cc_final: 0.6667 (t70) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1912 time to fit residues: 81.0521 Evaluate side-chains 242 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 0.0980 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN B 312 GLN ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS D 383 HIS D 497 ASN E 138 HIS E 209 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9978 Z= 0.264 Angle : 0.661 6.762 13548 Z= 0.352 Chirality : 0.046 0.219 1647 Planarity : 0.004 0.032 1716 Dihedral : 6.319 29.240 1377 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: -1.95 (0.23), residues: 1281 helix: 0.06 (0.28), residues: 333 sheet: -2.31 (0.38), residues: 135 loop : -1.77 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 423 HIS 0.004 0.001 HIS D 250 PHE 0.018 0.002 PHE F 491 TYR 0.019 0.002 TYR D 424 ARG 0.005 0.001 ARG D 547 *********************** 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 286 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8835 (mt) cc_final: 0.8588 (mt) REVERT: A 147 ILE cc_start: 0.8517 (mm) cc_final: 0.8133 (mm) REVERT: A 173 ASN cc_start: 0.7587 (t0) cc_final: 0.7325 (t0) REVERT: A 176 LEU cc_start: 0.7704 (mt) cc_final: 0.7409 (tt) REVERT: A 193 ASN cc_start: 0.8978 (m-40) cc_final: 0.8565 (m-40) REVERT: B 314 LEU cc_start: 0.9176 (mt) cc_final: 0.8957 (mt) REVERT: B 322 TYR cc_start: 0.7278 (t80) cc_final: 0.5703 (t80) REVERT: B 385 ASP cc_start: 0.6882 (t70) cc_final: 0.6602 (m-30) REVERT: B 389 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7439 (mptt) REVERT: B 412 GLU cc_start: 0.8122 (tp30) cc_final: 0.7559 (tp30) REVERT: B 487 MET cc_start: 0.5699 (tmm) cc_final: 0.5403 (tmm) REVERT: B 551 ASP cc_start: 0.7424 (m-30) cc_final: 0.6353 (t70) REVERT: C 142 LEU cc_start: 0.8758 (mt) cc_final: 0.8457 (mt) REVERT: C 147 ILE cc_start: 0.8194 (mm) cc_final: 0.7834 (mm) REVERT: C 176 LEU cc_start: 0.7782 (mt) cc_final: 0.7249 (tt) REVERT: C 193 ASN cc_start: 0.9020 (m-40) cc_final: 0.8282 (m-40) REVERT: D 275 GLU cc_start: 0.7177 (pt0) cc_final: 0.6872 (pm20) REVERT: D 276 ILE cc_start: 0.8927 (mm) cc_final: 0.8683 (pt) REVERT: D 389 LYS cc_start: 0.8553 (mmtt) cc_final: 0.7602 (mptt) REVERT: D 436 TYR cc_start: 0.7350 (t80) cc_final: 0.6993 (t80) REVERT: D 551 ASP cc_start: 0.6977 (m-30) cc_final: 0.6623 (t70) REVERT: E 142 LEU cc_start: 0.8827 (mt) cc_final: 0.8547 (mt) REVERT: E 147 ILE cc_start: 0.8555 (mm) cc_final: 0.8243 (mm) REVERT: E 176 LEU cc_start: 0.7738 (mt) cc_final: 0.7511 (tt) REVERT: F 305 MET cc_start: 0.3322 (mpp) cc_final: 0.3077 (mtm) REVERT: F 312 GLN cc_start: 0.8054 (tp-100) cc_final: 0.7776 (tp-100) REVERT: F 389 LYS cc_start: 0.8484 (mmtt) cc_final: 0.7513 (mptt) REVERT: F 430 TYR cc_start: 0.8546 (m-80) cc_final: 0.8184 (m-80) REVERT: F 446 CYS cc_start: 0.4323 (t) cc_final: 0.4086 (t) REVERT: F 487 MET cc_start: 0.5849 (tmm) cc_final: 0.5592 (tmm) REVERT: F 551 ASP cc_start: 0.7489 (m-30) cc_final: 0.7000 (m-30) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1884 time to fit residues: 76.2966 Evaluate side-chains 226 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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: 6.9990 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 0.1980 chunk 121 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS B 312 GLN B 468 GLN ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS D 312 GLN ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 209 ASN ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9978 Z= 0.289 Angle : 0.674 6.169 13548 Z= 0.358 Chirality : 0.047 0.211 1647 Planarity : 0.005 0.041 1716 Dihedral : 6.294 33.257 1377 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: -1.83 (0.23), residues: 1281 helix: 0.25 (0.28), residues: 336 sheet: -2.54 (0.44), residues: 87 loop : -1.78 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 423 HIS 0.005 0.001 HIS A 138 PHE 0.009 0.002 PHE D 526 TYR 0.019 0.002 TYR D 424 ARG 0.005 0.001 ARG D 277 *********************** 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 281 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.044 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: A 147 ILE cc_start: 0.8519 (mm) cc_final: 0.8047 (mm) REVERT: A 150 THR cc_start: 0.7564 (p) cc_final: 0.7258 (m) REVERT: A 173 ASN cc_start: 0.7479 (t0) cc_final: 0.7214 (t0) REVERT: A 193 ASN cc_start: 0.8947 (m-40) cc_final: 0.8548 (m-40) REVERT: B 314 LEU cc_start: 0.9212 (mt) cc_final: 0.9012 (mt) REVERT: B 389 LYS cc_start: 0.8482 (mmtt) cc_final: 0.7572 (mptt) REVERT: B 412 GLU cc_start: 0.7805 (tp30) cc_final: 0.7295 (tp30) REVERT: B 463 MET cc_start: 0.6844 (ttm) cc_final: 0.6468 (ttm) REVERT: B 551 ASP cc_start: 0.7022 (m-30) cc_final: 0.6302 (t70) REVERT: C 142 LEU cc_start: 0.8753 (mt) cc_final: 0.8519 (mt) REVERT: C 193 ASN cc_start: 0.9020 (m-40) cc_final: 0.8349 (m-40) REVERT: D 275 GLU cc_start: 0.7249 (pt0) cc_final: 0.6989 (pm20) REVERT: D 389 LYS cc_start: 0.8591 (mmtt) cc_final: 0.7639 (mptt) REVERT: D 551 ASP cc_start: 0.7055 (m-30) cc_final: 0.6585 (t70) REVERT: E 142 LEU cc_start: 0.8795 (mt) cc_final: 0.8556 (mt) REVERT: E 147 ILE cc_start: 0.8641 (mm) cc_final: 0.8277 (mm) REVERT: F 305 MET cc_start: 0.3516 (mpp) cc_final: 0.3120 (mtm) REVERT: F 312 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7826 (tp-100) REVERT: F 389 LYS cc_start: 0.8612 (mmtt) cc_final: 0.7786 (mptt) REVERT: F 430 TYR cc_start: 0.8696 (m-80) cc_final: 0.8477 (m-80) REVERT: F 487 MET cc_start: 0.5744 (tmm) cc_final: 0.5386 (tmm) REVERT: F 551 ASP cc_start: 0.7072 (m-30) cc_final: 0.6328 (t70) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1731 time to fit residues: 70.9519 Evaluate side-chains 220 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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: 10.0000 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS B 383 HIS B 458 ASN ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9978 Z= 0.249 Angle : 0.657 6.942 13548 Z= 0.346 Chirality : 0.047 0.249 1647 Planarity : 0.004 0.036 1716 Dihedral : 6.168 29.551 1377 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: -1.75 (0.23), residues: 1281 helix: 0.59 (0.29), residues: 318 sheet: -2.30 (0.46), residues: 87 loop : -1.83 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 423 HIS 0.003 0.001 HIS F 250 PHE 0.026 0.002 PHE F 491 TYR 0.018 0.002 TYR F 293 ARG 0.004 0.001 ARG D 277 *********************** 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 270 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8865 (mt) cc_final: 0.8598 (mt) REVERT: A 147 ILE cc_start: 0.8577 (mm) cc_final: 0.8308 (mm) REVERT: A 150 THR cc_start: 0.7562 (p) cc_final: 0.7281 (m) REVERT: A 173 ASN cc_start: 0.7350 (t0) cc_final: 0.7077 (t0) REVERT: B 322 TYR cc_start: 0.7323 (t80) cc_final: 0.5859 (t80) REVERT: B 412 GLU cc_start: 0.7811 (tp30) cc_final: 0.7294 (tp30) REVERT: B 551 ASP cc_start: 0.7119 (m-30) cc_final: 0.6375 (t70) REVERT: B 567 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6353 (mm-30) REVERT: C 142 LEU cc_start: 0.8692 (mt) cc_final: 0.8455 (mt) REVERT: C 193 ASN cc_start: 0.9022 (m-40) cc_final: 0.8275 (m-40) REVERT: D 275 GLU cc_start: 0.7426 (pt0) cc_final: 0.7164 (pm20) REVERT: D 322 TYR cc_start: 0.7085 (t80) cc_final: 0.5462 (t80) REVERT: D 436 TYR cc_start: 0.7259 (t80) cc_final: 0.6982 (t80) REVERT: D 463 MET cc_start: 0.6657 (ttm) cc_final: 0.6453 (ttm) REVERT: D 487 MET cc_start: 0.5817 (tmm) cc_final: 0.3862 (mtm) REVERT: D 508 LYS cc_start: 0.8384 (ttpt) cc_final: 0.8111 (ttpt) REVERT: D 551 ASP cc_start: 0.7097 (m-30) cc_final: 0.6693 (t70) REVERT: E 147 ILE cc_start: 0.8608 (mm) cc_final: 0.8219 (mm) REVERT: F 305 MET cc_start: 0.3303 (mpp) cc_final: 0.2808 (mtm) REVERT: F 312 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7858 (tp-100) REVERT: F 322 TYR cc_start: 0.7167 (t80) cc_final: 0.6913 (t80) REVERT: F 389 LYS cc_start: 0.8577 (mmtt) cc_final: 0.7719 (mptt) REVERT: F 487 MET cc_start: 0.5918 (tmm) cc_final: 0.5355 (tmm) REVERT: F 551 ASP cc_start: 0.7000 (m-30) cc_final: 0.5926 (t70) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1727 time to fit residues: 68.8353 Evaluate side-chains 218 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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: 0.0970 chunk 109 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 121 optimal weight: 30.0000 chunk 101 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9978 Z= 0.175 Angle : 0.601 6.439 13548 Z= 0.315 Chirality : 0.046 0.252 1647 Planarity : 0.004 0.036 1716 Dihedral : 5.710 24.755 1377 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: 0.60 (0.29), residues: 333 sheet: -1.72 (0.44), residues: 117 loop : -1.70 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 423 HIS 0.003 0.001 HIS F 250 PHE 0.010 0.002 PHE F 491 TYR 0.013 0.001 TYR F 293 ARG 0.004 0.000 ARG D 277 *********************** 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 290 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8785 (mt) cc_final: 0.8541 (mt) REVERT: A 147 ILE cc_start: 0.8584 (mm) cc_final: 0.8352 (mm) REVERT: A 150 THR cc_start: 0.7522 (p) cc_final: 0.7247 (m) REVERT: B 308 GLU cc_start: 0.5205 (mp0) cc_final: 0.4981 (mp0) REVERT: B 322 TYR cc_start: 0.7209 (t80) cc_final: 0.5788 (t80) REVERT: B 412 GLU cc_start: 0.7735 (tp30) cc_final: 0.7276 (tp30) REVERT: B 551 ASP cc_start: 0.7068 (m-30) cc_final: 0.6421 (t70) REVERT: B 567 GLU cc_start: 0.6551 (mm-30) cc_final: 0.6235 (mm-30) REVERT: C 193 ASN cc_start: 0.8994 (m-40) cc_final: 0.8360 (m-40) REVERT: D 322 TYR cc_start: 0.6901 (t80) cc_final: 0.5322 (t80) REVERT: D 463 MET cc_start: 0.6824 (ttm) cc_final: 0.6083 (ttm) REVERT: D 468 GLN cc_start: 0.8476 (mm-40) cc_final: 0.7348 (mm-40) REVERT: D 487 MET cc_start: 0.5875 (tmm) cc_final: 0.5642 (tmm) REVERT: D 508 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7970 (ttpt) REVERT: D 510 TYR cc_start: 0.7055 (t80) cc_final: 0.6342 (t80) REVERT: D 551 ASP cc_start: 0.7018 (m-30) cc_final: 0.6691 (t70) REVERT: E 142 LEU cc_start: 0.8781 (mt) cc_final: 0.8552 (mt) REVERT: F 305 MET cc_start: 0.3214 (mpp) cc_final: 0.2652 (mtm) REVERT: F 389 LYS cc_start: 0.8527 (mmtt) cc_final: 0.7632 (mptt) REVERT: F 487 MET cc_start: 0.5745 (tmm) cc_final: 0.5224 (tmm) REVERT: F 551 ASP cc_start: 0.7110 (m-30) cc_final: 0.5865 (t70) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2070 time to fit residues: 85.8019 Evaluate side-chains 228 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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: 6.9990 chunk 69 optimal weight: 0.0270 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 0.0770 chunk 75 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS B 458 ASN ** B 468 GLN ** 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 F 458 ASN ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9978 Z= 0.226 Angle : 0.655 8.163 13548 Z= 0.340 Chirality : 0.047 0.324 1647 Planarity : 0.004 0.038 1716 Dihedral : 5.872 24.600 1377 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -1.53 (0.23), residues: 1281 helix: 0.65 (0.29), residues: 333 sheet: -1.68 (0.43), residues: 117 loop : -1.71 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 423 HIS 0.002 0.001 HIS B 409 PHE 0.016 0.002 PHE B 491 TYR 0.020 0.002 TYR F 293 ARG 0.006 0.001 ARG D 277 *********************** 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 276 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8794 (mt) cc_final: 0.8560 (mt) REVERT: A 147 ILE cc_start: 0.8617 (mm) cc_final: 0.8352 (mm) REVERT: A 150 THR cc_start: 0.7573 (p) cc_final: 0.7328 (m) REVERT: B 322 TYR cc_start: 0.7293 (t80) cc_final: 0.5852 (t80) REVERT: B 412 GLU cc_start: 0.7789 (tp30) cc_final: 0.7340 (tp30) REVERT: B 551 ASP cc_start: 0.7154 (m-30) cc_final: 0.6518 (t70) REVERT: B 567 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6362 (mm-30) REVERT: C 193 ASN cc_start: 0.8969 (m-40) cc_final: 0.8226 (m-40) REVERT: D 322 TYR cc_start: 0.7049 (t80) cc_final: 0.5358 (t80) REVERT: D 487 MET cc_start: 0.6027 (tmm) cc_final: 0.5787 (tmm) REVERT: D 551 ASP cc_start: 0.7122 (m-30) cc_final: 0.6607 (t70) REVERT: E 142 LEU cc_start: 0.8743 (mt) cc_final: 0.8519 (mt) REVERT: F 305 MET cc_start: 0.3288 (mpp) cc_final: 0.2751 (mtm) REVERT: F 314 LEU cc_start: 0.9126 (mt) cc_final: 0.8905 (mt) REVERT: F 487 MET cc_start: 0.5711 (tmm) cc_final: 0.5207 (tmm) REVERT: F 551 ASP cc_start: 0.6955 (m-30) cc_final: 0.5876 (t70) REVERT: F 570 ASP cc_start: 0.8018 (m-30) cc_final: 0.7749 (m-30) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1716 time to fit residues: 70.6076 Evaluate side-chains 222 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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: 0.0040 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- 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 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9978 Z= 0.226 Angle : 0.677 8.728 13548 Z= 0.351 Chirality : 0.048 0.304 1647 Planarity : 0.004 0.035 1716 Dihedral : 5.936 26.997 1377 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -1.68 (0.23), residues: 1281 helix: 0.48 (0.28), residues: 351 sheet: -1.69 (0.43), residues: 117 loop : -1.86 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 423 HIS 0.002 0.001 HIS F 383 PHE 0.028 0.003 PHE F 491 TYR 0.017 0.002 TYR B 293 ARG 0.006 0.001 ARG D 277 *********************** 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 277 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8791 (mt) cc_final: 0.8559 (mt) REVERT: A 147 ILE cc_start: 0.8582 (mm) cc_final: 0.8298 (mm) REVERT: A 150 THR cc_start: 0.7625 (p) cc_final: 0.7340 (m) REVERT: B 322 TYR cc_start: 0.7329 (t80) cc_final: 0.5875 (t80) REVERT: B 412 GLU cc_start: 0.7701 (tp30) cc_final: 0.7309 (tp30) REVERT: B 463 MET cc_start: 0.7040 (ttt) cc_final: 0.6542 (ttt) REVERT: B 487 MET cc_start: 0.5611 (tmm) cc_final: 0.3433 (mmm) REVERT: B 493 LEU cc_start: 0.6533 (tp) cc_final: 0.6262 (tp) REVERT: B 551 ASP cc_start: 0.7126 (m-30) cc_final: 0.6487 (t70) REVERT: B 567 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6203 (mm-30) REVERT: C 193 ASN cc_start: 0.9017 (m-40) cc_final: 0.8263 (m-40) REVERT: C 200 ASN cc_start: 0.7697 (t0) cc_final: 0.7449 (t0) REVERT: D 322 TYR cc_start: 0.7068 (t80) cc_final: 0.5389 (t80) REVERT: D 551 ASP cc_start: 0.7060 (m-30) cc_final: 0.6675 (t70) REVERT: F 305 MET cc_start: 0.3092 (mpp) cc_final: 0.2550 (mtm) REVERT: F 430 TYR cc_start: 0.8817 (m-80) cc_final: 0.8467 (m-80) REVERT: F 551 ASP cc_start: 0.6856 (m-30) cc_final: 0.6300 (t70) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1784 time to fit residues: 71.8176 Evaluate side-chains 222 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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: 6.9990 chunk 116 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 102 optimal weight: 0.0270 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- 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** ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS F 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9978 Z= 0.175 Angle : 0.639 7.836 13548 Z= 0.332 Chirality : 0.048 0.343 1647 Planarity : 0.004 0.035 1716 Dihedral : 5.668 27.075 1377 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.23), residues: 1281 helix: 1.04 (0.30), residues: 315 sheet: -1.57 (0.43), residues: 117 loop : -1.64 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 423 HIS 0.005 0.001 HIS A 138 PHE 0.008 0.002 PHE B 526 TYR 0.011 0.001 TYR B 293 ARG 0.006 0.000 ARG D 277 *********************** 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 277 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.8586 (mm) cc_final: 0.8295 (mm) REVERT: A 150 THR cc_start: 0.7617 (p) cc_final: 0.7371 (m) REVERT: A 204 THR cc_start: 0.7710 (p) cc_final: 0.7313 (p) REVERT: B 314 LEU cc_start: 0.9215 (mt) cc_final: 0.9004 (mt) REVERT: B 322 TYR cc_start: 0.7041 (t80) cc_final: 0.5777 (t80) REVERT: B 412 GLU cc_start: 0.7760 (tp30) cc_final: 0.7347 (tp30) REVERT: B 463 MET cc_start: 0.6701 (ttt) cc_final: 0.6476 (ttt) REVERT: B 487 MET cc_start: 0.5605 (tmm) cc_final: 0.3378 (mmm) REVERT: B 493 LEU cc_start: 0.6550 (tp) cc_final: 0.6276 (tp) REVERT: B 551 ASP cc_start: 0.7001 (m-30) cc_final: 0.6387 (t70) REVERT: B 567 GLU cc_start: 0.6577 (mm-30) cc_final: 0.6099 (mm-30) REVERT: C 193 ASN cc_start: 0.8934 (m-40) cc_final: 0.8333 (m-40) REVERT: D 250 HIS cc_start: 0.6529 (t70) cc_final: 0.6308 (t70) REVERT: D 371 ILE cc_start: 0.8579 (mm) cc_final: 0.8194 (mp) REVERT: D 493 LEU cc_start: 0.6076 (tp) cc_final: 0.5826 (tp) REVERT: D 510 TYR cc_start: 0.7280 (t80) cc_final: 0.6828 (t80) REVERT: D 543 GLN cc_start: 0.7456 (tt0) cc_final: 0.6863 (tp-100) REVERT: D 551 ASP cc_start: 0.6988 (m-30) cc_final: 0.6232 (t70) REVERT: E 142 LEU cc_start: 0.8771 (mt) cc_final: 0.8554 (mt) REVERT: F 430 TYR cc_start: 0.8739 (m-80) cc_final: 0.8405 (m-80) REVERT: F 463 MET cc_start: 0.6953 (ttm) cc_final: 0.6078 (ttm) REVERT: F 468 GLN cc_start: 0.8454 (mm110) cc_final: 0.7432 (mm-40) REVERT: F 487 MET cc_start: 0.6328 (tmm) cc_final: 0.4151 (mmm) REVERT: F 551 ASP cc_start: 0.6900 (m-30) cc_final: 0.5983 (t70) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1873 time to fit residues: 76.8680 Evaluate side-chains 229 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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: 6.9990 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 106 optimal weight: 0.3980 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 200 ASN F 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9978 Z= 0.205 Angle : 0.658 7.903 13548 Z= 0.343 Chirality : 0.048 0.329 1647 Planarity : 0.004 0.035 1716 Dihedral : 5.771 24.145 1377 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.23), residues: 1281 helix: 0.95 (0.30), residues: 315 sheet: -1.59 (0.43), residues: 117 loop : -1.64 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 423 HIS 0.004 0.001 HIS A 138 PHE 0.013 0.002 PHE D 526 TYR 0.022 0.002 TYR F 322 ARG 0.005 0.001 ARG D 277 ********************** 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 270 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.8591 (mm) cc_final: 0.8338 (mm) REVERT: A 150 THR cc_start: 0.7647 (p) cc_final: 0.7367 (m) REVERT: A 204 THR cc_start: 0.7712 (p) cc_final: 0.7352 (p) REVERT: B 412 GLU cc_start: 0.7685 (tp30) cc_final: 0.7329 (tp30) REVERT: B 463 MET cc_start: 0.6741 (ttt) cc_final: 0.6517 (ttt) REVERT: B 487 MET cc_start: 0.5631 (tmm) cc_final: 0.3514 (mmm) REVERT: B 493 LEU cc_start: 0.6644 (tp) cc_final: 0.6362 (tp) REVERT: B 551 ASP cc_start: 0.7036 (m-30) cc_final: 0.6400 (t70) REVERT: B 567 GLU cc_start: 0.6403 (mm-30) cc_final: 0.6045 (mm-30) REVERT: C 193 ASN cc_start: 0.9001 (m-40) cc_final: 0.8339 (m-40) REVERT: D 250 HIS cc_start: 0.6492 (t70) cc_final: 0.6268 (t70) REVERT: D 487 MET cc_start: 0.6084 (tmm) cc_final: 0.3952 (mmm) REVERT: D 493 LEU cc_start: 0.6098 (tp) cc_final: 0.5848 (tp) REVERT: D 510 TYR cc_start: 0.6993 (t80) cc_final: 0.6705 (t80) REVERT: D 543 GLN cc_start: 0.7520 (tt0) cc_final: 0.6945 (tp-100) REVERT: D 551 ASP cc_start: 0.7066 (m-30) cc_final: 0.6313 (t70) REVERT: D 567 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6295 (mm-30) REVERT: E 142 LEU cc_start: 0.8788 (mt) cc_final: 0.8580 (mt) REVERT: F 429 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7447 (tpt90) REVERT: F 430 TYR cc_start: 0.8831 (m-80) cc_final: 0.8575 (m-80) REVERT: F 463 MET cc_start: 0.6866 (ttm) cc_final: 0.6254 (ttm) REVERT: F 468 GLN cc_start: 0.8451 (mm110) cc_final: 0.7359 (mm-40) REVERT: F 487 MET cc_start: 0.6203 (tmm) cc_final: 0.4019 (mmm) REVERT: F 551 ASP cc_start: 0.6912 (m-30) cc_final: 0.5987 (t70) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1806 time to fit residues: 70.9089 Evaluate side-chains 228 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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: 5.9990 chunk 14 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- 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 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.159878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.137196 restraints weight = 20012.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.140403 restraints weight = 13337.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.142750 restraints weight = 9853.240| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.5433 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= 0.197 Angle : 0.646 7.847 13548 Z= 0.335 Chirality : 0.048 0.347 1647 Planarity : 0.004 0.037 1716 Dihedral : 5.728 23.832 1377 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.23), residues: 1281 helix: 1.40 (0.30), residues: 297 sheet: -1.54 (0.43), residues: 117 loop : -1.61 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 423 HIS 0.004 0.001 HIS A 138 PHE 0.018 0.002 PHE B 491 TYR 0.013 0.001 TYR D 424 ARG 0.005 0.000 ARG D 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.98 seconds wall clock time: 39 minutes 38.06 seconds (2378.06 seconds total)