Starting phenix.real_space_refine on Fri Mar 15 09:46:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssx_25416/03_2024/7ssx_25416.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssx_25416/03_2024/7ssx_25416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssx_25416/03_2024/7ssx_25416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssx_25416/03_2024/7ssx_25416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssx_25416/03_2024/7ssx_25416.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssx_25416/03_2024/7ssx_25416.pdb" } resolution = 2.89 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= 0.005 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 44 5.16 5 C 7428 2.51 5 N 1868 2.21 5 O 1940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C ARG 205": "NH1" <-> "NH2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D ARG 209": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 364": "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: 11283 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2820 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 2 Chain: "B" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2820 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 2 Chain: "C" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2820 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 2 Chain: "D" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2820 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.87, per 1000 atoms: 0.52 Number of scatterers: 11283 At special positions: 0 Unit cell: (109.056, 109.908, 115.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 44 16.00 O 1940 8.00 N 1868 7.00 C 7428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 4.19 Conformation dependent library (CDL) restraints added in 1.6 seconds 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 71.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.553A pdb=" N PHE A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.531A pdb=" N ARG A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 256 removed outlier: 3.905A pdb=" N ARG A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 316 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.520A pdb=" N THR A 322 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 361 through 370 Processing helix chain 'A' and resid 371 through 372 No H-bonds generated for 'chain 'A' and resid 371 through 372' Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.629A pdb=" N LYS A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.845A pdb=" N GLN A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.632A pdb=" N PHE A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 434 through 444 Processing helix chain 'A' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.925A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.554A pdb=" N PHE B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.530A pdb=" N ARG B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 256 removed outlier: 3.905A pdb=" N ARG B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.519A pdb=" N THR B 322 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'B' and resid 371 through 372 No H-bonds generated for 'chain 'B' and resid 371 through 372' Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.630A pdb=" N LYS B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 removed outlier: 3.845A pdb=" N GLN B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 421 removed outlier: 3.632A pdb=" N PHE B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 434 through 444 Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.925A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.553A pdb=" N PHE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.531A pdb=" N ARG C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 256 removed outlier: 3.904A pdb=" N ARG C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 316 Processing helix chain 'C' and resid 319 through 323 removed outlier: 3.519A pdb=" N THR C 322 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Proline residue: C 338 - end of helix Processing helix chain 'C' and resid 361 through 370 Processing helix chain 'C' and resid 371 through 372 No H-bonds generated for 'chain 'C' and resid 371 through 372' Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.629A pdb=" N LYS C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 394 removed outlier: 3.844A pdb=" N GLN C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 421 removed outlier: 3.631A pdb=" N PHE C 418 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 433 No H-bonds generated for 'chain 'C' and resid 431 through 433' Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.924A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.553A pdb=" N PHE D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 190 through 202 Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.531A pdb=" N ARG D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 256 removed outlier: 3.905A pdb=" N ARG D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 316 Processing helix chain 'D' and resid 319 through 323 removed outlier: 3.520A pdb=" N THR D 322 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 348 removed outlier: 3.629A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Proline residue: D 338 - end of helix Processing helix chain 'D' and resid 361 through 370 Processing helix chain 'D' and resid 371 through 372 No H-bonds generated for 'chain 'D' and resid 371 through 372' Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.629A pdb=" N LYS D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 394 removed outlier: 3.844A pdb=" N GLN D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 421 removed outlier: 3.632A pdb=" N PHE D 418 " --> pdb=" O SER D 414 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 434 through 444 Processing helix chain 'D' and resid 454 through 474 removed outlier: 3.976A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.925A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 Processing sheet with id=AA2, first strand: chain 'B' and resid 113 through 118 Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 118 Processing sheet with id=AA4, first strand: chain 'D' and resid 113 through 118 688 hydrogen bonds defined for protein. 2004 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: 3.06 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1766 1.32 - 1.44: 3266 1.44 - 1.56: 6468 1.56 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 11568 Sorted by residual: bond pdb=" CA GLY B 446 " pdb=" C GLY B 446 " ideal model delta sigma weight residual 1.513 1.468 0.045 1.06e-02 8.90e+03 1.77e+01 bond pdb=" CA GLY D 446 " pdb=" C GLY D 446 " ideal model delta sigma weight residual 1.513 1.468 0.044 1.06e-02 8.90e+03 1.74e+01 bond pdb=" CA GLY A 446 " pdb=" C GLY A 446 " ideal model delta sigma weight residual 1.513 1.469 0.044 1.06e-02 8.90e+03 1.70e+01 bond pdb=" CA GLY C 446 " pdb=" C GLY C 446 " ideal model delta sigma weight residual 1.513 1.469 0.043 1.06e-02 8.90e+03 1.67e+01 bond pdb=" N LEU C 211 " pdb=" CA LEU C 211 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.41e+01 ... (remaining 11563 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.41: 374 106.41 - 113.42: 5860 113.42 - 120.43: 5533 120.43 - 127.44: 3829 127.44 - 134.45: 80 Bond angle restraints: 15676 Sorted by residual: angle pdb=" N VAL B 445 " pdb=" CA VAL B 445 " pdb=" C VAL B 445 " ideal model delta sigma weight residual 110.62 101.10 9.52 1.02e+00 9.61e-01 8.72e+01 angle pdb=" N VAL C 445 " pdb=" CA VAL C 445 " pdb=" C VAL C 445 " ideal model delta sigma weight residual 110.62 101.13 9.49 1.02e+00 9.61e-01 8.65e+01 angle pdb=" N VAL A 445 " pdb=" CA VAL A 445 " pdb=" C VAL A 445 " ideal model delta sigma weight residual 110.62 101.14 9.48 1.02e+00 9.61e-01 8.64e+01 angle pdb=" N VAL D 445 " pdb=" CA VAL D 445 " pdb=" C VAL D 445 " ideal model delta sigma weight residual 110.62 101.14 9.48 1.02e+00 9.61e-01 8.64e+01 angle pdb=" C TYR B 447 " pdb=" CA TYR B 447 " pdb=" CB TYR B 447 " ideal model delta sigma weight residual 110.96 101.20 9.76 1.54e+00 4.22e-01 4.02e+01 ... (remaining 15671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 5739 11.91 - 23.82: 789 23.82 - 35.73: 232 35.73 - 47.64: 60 47.64 - 59.55: 20 Dihedral angle restraints: 6840 sinusoidal: 2820 harmonic: 4020 Sorted by residual: dihedral pdb=" C THR C 444 " pdb=" N THR C 444 " pdb=" CA THR C 444 " pdb=" CB THR C 444 " ideal model delta harmonic sigma weight residual -122.00 -138.31 16.31 0 2.50e+00 1.60e-01 4.26e+01 dihedral pdb=" C THR B 444 " pdb=" N THR B 444 " pdb=" CA THR B 444 " pdb=" CB THR B 444 " ideal model delta harmonic sigma weight residual -122.00 -138.30 16.30 0 2.50e+00 1.60e-01 4.25e+01 dihedral pdb=" C THR A 444 " pdb=" N THR A 444 " pdb=" CA THR A 444 " pdb=" CB THR A 444 " ideal model delta harmonic sigma weight residual -122.00 -138.29 16.29 0 2.50e+00 1.60e-01 4.25e+01 ... (remaining 6837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1420 0.116 - 0.232: 302 0.232 - 0.348: 26 0.348 - 0.463: 4 0.463 - 0.579: 4 Chirality restraints: 1756 Sorted by residual: chirality pdb=" CA THR C 444 " pdb=" N THR C 444 " pdb=" C THR C 444 " pdb=" CB THR C 444 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CA THR A 444 " pdb=" N THR A 444 " pdb=" C THR A 444 " pdb=" CB THR A 444 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" CA THR B 444 " pdb=" N THR B 444 " pdb=" C THR B 444 " pdb=" CB THR B 444 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 1753 not shown) Planarity restraints: 1984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 134 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" C LYS B 134 " 0.054 2.00e-02 2.50e+03 pdb=" O LYS B 134 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG B 135 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 134 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.83e+00 pdb=" C LYS D 134 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS D 134 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG D 135 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 134 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.77e+00 pdb=" C LYS A 134 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS A 134 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 135 " 0.018 2.00e-02 2.50e+03 ... (remaining 1981 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 3399 2.83 - 3.41: 11705 3.41 - 3.98: 20721 3.98 - 4.56: 29283 4.56 - 5.14: 41863 Nonbonded interactions: 106971 Sorted by model distance: nonbonded pdb=" NH1 ARG A 105 " pdb=" OE2 GLU B 146 " model vdw 2.251 2.520 nonbonded pdb=" O VAL C 409 " pdb=" OG SER C 413 " model vdw 2.286 2.440 nonbonded pdb=" O VAL D 409 " pdb=" OG SER D 413 " model vdw 2.286 2.440 nonbonded pdb=" O VAL A 409 " pdb=" OG SER A 413 " model vdw 2.287 2.440 nonbonded pdb=" O VAL B 409 " pdb=" OG SER B 413 " model vdw 2.287 2.440 ... (remaining 106966 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' and resid 103 through 491) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.420 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.860 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.060 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 : 0.012 0.079 11568 Z= 0.776 Angle : 1.375 9.762 15676 Z= 0.963 Chirality : 0.096 0.579 1756 Planarity : 0.008 0.075 1984 Dihedral : 12.346 59.552 4240 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.61 % Allowed : 3.58 % Favored : 93.81 % Cbeta Deviations : 0.92 % 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: -1.17 (0.21), residues: 1360 helix: -0.48 (0.16), residues: 916 sheet: 0.57 (0.74), residues: 48 loop : -1.35 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 305 HIS 0.003 0.001 HIS B 451 PHE 0.022 0.002 PHE C 251 TYR 0.014 0.002 TYR B 487 ARG 0.004 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 261 time to evaluate : 1.178 Fit side-chains REVERT: A 374 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7652 (mt) outliers start: 32 outliers final: 5 residues processed: 288 average time/residue: 1.1832 time to fit residues: 367.0942 Evaluate side-chains 163 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain D residue 374 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 145 ASN B 124 GLN B 145 ASN C 124 GLN C 145 ASN D 124 GLN D 145 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11568 Z= 0.198 Angle : 0.606 7.849 15676 Z= 0.322 Chirality : 0.042 0.123 1756 Planarity : 0.007 0.064 1984 Dihedral : 4.517 35.644 1548 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.44 % Allowed : 13.44 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1360 helix: 1.46 (0.17), residues: 896 sheet: 1.73 (0.70), residues: 40 loop : -0.53 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 221 HIS 0.001 0.000 HIS C 451 PHE 0.022 0.002 PHE D 140 TYR 0.012 0.002 TYR D 139 ARG 0.008 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.295 Fit side-chains REVERT: A 135 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.6044 (ttp80) outliers start: 30 outliers final: 14 residues processed: 188 average time/residue: 0.8447 time to fit residues: 176.9401 Evaluate side-chains 151 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11568 Z= 0.368 Angle : 0.683 6.929 15676 Z= 0.365 Chirality : 0.047 0.157 1756 Planarity : 0.007 0.066 1984 Dihedral : 4.812 44.740 1544 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.32 % Allowed : 13.52 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.23), residues: 1360 helix: 1.62 (0.17), residues: 900 sheet: 1.57 (0.73), residues: 40 loop : -0.48 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 437 HIS 0.005 0.001 HIS C 451 PHE 0.027 0.002 PHE A 140 TYR 0.014 0.002 TYR C 139 ARG 0.004 0.000 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 158 time to evaluate : 1.420 Fit side-chains REVERT: A 450 MET cc_start: 0.5031 (OUTLIER) cc_final: 0.4711 (tmt) REVERT: B 138 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6712 (ptp90) REVERT: B 157 ASP cc_start: 0.6899 (p0) cc_final: 0.6660 (p0) REVERT: C 138 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6671 (ptp90) REVERT: C 157 ASP cc_start: 0.6891 (p0) cc_final: 0.6657 (p0) REVERT: D 138 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6668 (ptp90) outliers start: 53 outliers final: 33 residues processed: 196 average time/residue: 0.6664 time to fit residues: 149.4863 Evaluate side-chains 182 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 chunk 131 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11568 Z= 0.166 Angle : 0.535 7.485 15676 Z= 0.281 Chirality : 0.040 0.155 1756 Planarity : 0.006 0.064 1984 Dihedral : 4.376 42.138 1544 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.58 % Allowed : 14.41 % Favored : 82.00 % 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: 2.14 (0.24), residues: 1360 helix: 2.19 (0.18), residues: 896 sheet: 1.79 (0.78), residues: 40 loop : -0.31 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 221 HIS 0.001 0.000 HIS C 451 PHE 0.024 0.001 PHE D 186 TYR 0.010 0.001 TYR D 139 ARG 0.004 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 152 time to evaluate : 1.111 Fit side-chains REVERT: A 450 MET cc_start: 0.4784 (OUTLIER) cc_final: 0.4544 (mpt) REVERT: B 157 ASP cc_start: 0.6448 (p0) cc_final: 0.6214 (p0) REVERT: C 157 ASP cc_start: 0.6397 (p0) cc_final: 0.6172 (p0) outliers start: 44 outliers final: 25 residues processed: 181 average time/residue: 0.5599 time to fit residues: 118.5837 Evaluate side-chains 171 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11568 Z= 0.256 Angle : 0.583 6.312 15676 Z= 0.309 Chirality : 0.042 0.131 1756 Planarity : 0.006 0.065 1984 Dihedral : 4.464 43.838 1544 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.66 % Allowed : 16.21 % Favored : 80.13 % 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: 2.05 (0.24), residues: 1360 helix: 2.17 (0.18), residues: 896 sheet: 1.88 (0.82), residues: 40 loop : -0.47 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 437 HIS 0.003 0.001 HIS C 451 PHE 0.024 0.002 PHE A 140 TYR 0.011 0.002 TYR C 487 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 147 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: A 450 MET cc_start: 0.4871 (OUTLIER) cc_final: 0.4616 (tmt) REVERT: D 225 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6803 (tm-30) outliers start: 45 outliers final: 31 residues processed: 182 average time/residue: 0.6870 time to fit residues: 142.6721 Evaluate side-chains 178 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11568 Z= 0.271 Angle : 0.592 6.746 15676 Z= 0.314 Chirality : 0.042 0.129 1756 Planarity : 0.006 0.065 1984 Dihedral : 4.579 46.971 1544 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.66 % Allowed : 17.18 % Favored : 79.15 % 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: 1.99 (0.24), residues: 1360 helix: 2.10 (0.18), residues: 900 sheet: 1.93 (0.86), residues: 40 loop : -0.46 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 437 HIS 0.004 0.001 HIS D 451 PHE 0.025 0.002 PHE D 186 TYR 0.011 0.002 TYR B 187 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: A 450 MET cc_start: 0.4926 (OUTLIER) cc_final: 0.4650 (tmt) outliers start: 45 outliers final: 32 residues processed: 170 average time/residue: 0.6782 time to fit residues: 131.8793 Evaluate side-chains 173 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11568 Z= 0.173 Angle : 0.522 7.562 15676 Z= 0.274 Chirality : 0.039 0.123 1756 Planarity : 0.005 0.064 1984 Dihedral : 4.308 44.808 1544 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.18 % Allowed : 17.83 % Favored : 78.99 % 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: 2.37 (0.24), residues: 1360 helix: 2.42 (0.18), residues: 896 sheet: 2.09 (0.88), residues: 40 loop : -0.36 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 221 HIS 0.001 0.000 HIS A 451 PHE 0.026 0.001 PHE C 186 TYR 0.009 0.001 TYR D 139 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: B 225 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: C 225 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: D 225 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6834 (tm-30) outliers start: 39 outliers final: 20 residues processed: 178 average time/residue: 0.6751 time to fit residues: 137.0580 Evaluate side-chains 168 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 0.0050 chunk 89 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.0010 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11568 Z= 0.152 Angle : 0.503 8.261 15676 Z= 0.261 Chirality : 0.038 0.123 1756 Planarity : 0.005 0.064 1984 Dihedral : 4.015 40.044 1544 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.52 % Allowed : 18.73 % Favored : 78.75 % 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: 2.48 (0.24), residues: 1360 helix: 2.57 (0.18), residues: 900 sheet: 2.19 (0.89), residues: 40 loop : -0.54 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 221 HIS 0.001 0.000 HIS C 451 PHE 0.025 0.001 PHE D 140 TYR 0.007 0.001 TYR B 487 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.287 Fit side-chains REVERT: C 119 LEU cc_start: 0.7563 (mt) cc_final: 0.7187 (mt) REVERT: D 119 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7265 (mt) outliers start: 31 outliers final: 16 residues processed: 171 average time/residue: 0.6857 time to fit residues: 133.9397 Evaluate side-chains 162 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 129 optimal weight: 5.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN B 164 GLN C 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11568 Z= 0.365 Angle : 0.649 9.462 15676 Z= 0.341 Chirality : 0.045 0.136 1756 Planarity : 0.006 0.063 1984 Dihedral : 3.848 14.029 1536 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.52 % Allowed : 18.81 % Favored : 78.66 % 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: 1.89 (0.24), residues: 1360 helix: 2.08 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -0.40 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 437 HIS 0.004 0.001 HIS A 451 PHE 0.025 0.002 PHE B 186 TYR 0.014 0.002 TYR A 187 ARG 0.003 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: B 157 ASP cc_start: 0.6895 (p0) cc_final: 0.6649 (p0) REVERT: C 157 ASP cc_start: 0.6868 (p0) cc_final: 0.6600 (p0) REVERT: D 225 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6897 (tm-30) outliers start: 31 outliers final: 19 residues processed: 158 average time/residue: 0.7167 time to fit residues: 128.8904 Evaluate side-chains 151 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 107 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11568 Z= 0.188 Angle : 0.562 10.355 15676 Z= 0.292 Chirality : 0.040 0.123 1756 Planarity : 0.005 0.063 1984 Dihedral : 3.682 14.791 1536 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.63 % Allowed : 20.20 % Favored : 78.18 % 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: 2.13 (0.24), residues: 1360 helix: 2.35 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -0.52 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 221 HIS 0.001 0.000 HIS B 451 PHE 0.024 0.001 PHE D 186 TYR 0.009 0.001 TYR C 487 ARG 0.003 0.000 ARG A 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.272 Fit side-chains REVERT: A 170 ARG cc_start: 0.7223 (mmt-90) cc_final: 0.6949 (mmt-90) outliers start: 20 outliers final: 15 residues processed: 152 average time/residue: 0.7515 time to fit residues: 129.4533 Evaluate side-chains 149 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN B 164 GLN C 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.204256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.148589 restraints weight = 11566.640| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.87 r_work: 0.3030 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11568 Z= 0.311 Angle : 0.631 10.000 15676 Z= 0.330 Chirality : 0.044 0.126 1756 Planarity : 0.006 0.062 1984 Dihedral : 3.832 14.602 1536 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.95 % Allowed : 19.87 % Favored : 78.18 % 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: 1.90 (0.24), residues: 1360 helix: 2.12 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -0.46 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 437 HIS 0.003 0.001 HIS B 451 PHE 0.028 0.002 PHE A 140 TYR 0.012 0.002 TYR C 187 ARG 0.002 0.000 ARG C 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3552.25 seconds wall clock time: 63 minutes 27.66 seconds (3807.66 seconds total)