Starting phenix.real_space_refine on Thu Mar 14 15:59:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/03_2024/8fel_29032.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/03_2024/8fel_29032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/03_2024/8fel_29032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/03_2024/8fel_29032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/03_2024/8fel_29032.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/03_2024/8fel_29032.pdb" } resolution = 4.64 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= 0.002 sd= 0.078 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 51 5.16 5 C 5820 2.51 5 N 1509 2.21 5 O 1821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 432": "OE1" <-> "OE2" 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: 9201 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3067 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain breaks: 2 Chain: "B" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3067 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain breaks: 2 Chain: "C" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3067 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain breaks: 2 Time building chain proxies: 4.96, per 1000 atoms: 0.54 Number of scatterers: 9201 At special positions: 0 Unit cell: (93.96, 91.8, 172.8, 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 51 16.00 O 1821 8.00 N 1509 7.00 C 5820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.03 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: 3.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 15 sheets defined 41.8% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 142 through 177 removed outlier: 3.854A pdb=" N GLN A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 210 removed outlier: 3.554A pdb=" N PHE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.613A pdb=" N GLN A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 233 through 241 removed outlier: 4.046A pdb=" N MET A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 255 removed outlier: 3.633A pdb=" N LEU A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 removed outlier: 3.787A pdb=" N ILE A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 477 removed outlier: 3.603A pdb=" N GLU A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 142 through 177 removed outlier: 3.855A pdb=" N GLN B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 171 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 210 removed outlier: 3.554A pdb=" N PHE B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.613A pdb=" N GLN B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 233 through 241 removed outlier: 4.045A pdb=" N MET B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.635A pdb=" N LEU B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.789A pdb=" N ILE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 477 removed outlier: 3.601A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 471 " --> pdb=" O ASP B 467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 472 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 142 through 177 removed outlier: 3.855A pdb=" N GLN C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 210 removed outlier: 3.553A pdb=" N PHE C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.613A pdb=" N GLN C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 233 through 241 removed outlier: 4.046A pdb=" N MET C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 255 removed outlier: 3.634A pdb=" N LEU C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 353 removed outlier: 3.789A pdb=" N ILE C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 477 removed outlier: 3.602A pdb=" N GLU C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS C 471 " --> pdb=" O ASP C 467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 472 " --> pdb=" O TYR C 468 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 281 through 282 removed outlier: 5.940A pdb=" N ASN A 40 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N CYS A 335 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS A 42 " --> pdb=" O CYS A 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 264 removed outlier: 7.107A pdb=" N ALA A 272 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 290 removed outlier: 3.852A pdb=" N GLN A 289 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 311 " --> pdb=" O GLN A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.693A pdb=" N ALA A 372 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 281 through 282 removed outlier: 5.940A pdb=" N ASN B 40 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N CYS B 335 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS B 42 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 264 removed outlier: 7.107A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 288 through 290 removed outlier: 3.852A pdb=" N GLN B 289 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 311 " --> pdb=" O GLN B 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AB1, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.692A pdb=" N ALA B 372 " --> pdb=" O TYR B 379 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 281 through 282 removed outlier: 5.940A pdb=" N ASN C 40 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N CYS C 335 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS C 42 " --> pdb=" O CYS C 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 261 through 264 removed outlier: 7.107A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 288 through 290 removed outlier: 3.853A pdb=" N GLN C 289 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 311 " --> pdb=" O GLN C 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 296 through 298 Processing sheet with id=AB6, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.693A pdb=" N ALA C 372 " --> pdb=" O TYR C 379 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1071 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: 2.48 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3033 1.34 - 1.46: 1803 1.46 - 1.58: 4410 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9318 Sorted by residual: bond pdb=" C ILE A 179 " pdb=" N PRO A 180 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.76e-01 bond pdb=" C ILE C 179 " pdb=" N PRO C 180 " ideal model delta sigma weight residual 1.334 1.354 -0.021 2.34e-02 1.83e+03 7.68e-01 bond pdb=" C ILE B 179 " pdb=" N PRO B 180 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.67e-01 bond pdb=" N GLY B 36 " pdb=" CA GLY B 36 " ideal model delta sigma weight residual 1.445 1.451 -0.007 8.30e-03 1.45e+04 6.90e-01 bond pdb=" N GLY C 36 " pdb=" CA GLY C 36 " ideal model delta sigma weight residual 1.445 1.451 -0.007 8.30e-03 1.45e+04 6.54e-01 ... (remaining 9313 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.44: 195 107.44 - 114.07: 5534 114.07 - 120.69: 3698 120.69 - 127.32: 3188 127.32 - 133.95: 39 Bond angle restraints: 12654 Sorted by residual: angle pdb=" CA TYR B 468 " pdb=" CB TYR B 468 " pdb=" CG TYR B 468 " ideal model delta sigma weight residual 113.90 118.53 -4.63 1.80e+00 3.09e-01 6.63e+00 angle pdb=" CA TYR C 468 " pdb=" CB TYR C 468 " pdb=" CG TYR C 468 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.59e+00 angle pdb=" CA TYR A 468 " pdb=" CB TYR A 468 " pdb=" CG TYR A 468 " ideal model delta sigma weight residual 113.90 118.48 -4.58 1.80e+00 3.09e-01 6.48e+00 angle pdb=" C PRO C 84 " pdb=" N VAL C 85 " pdb=" CA VAL C 85 " ideal model delta sigma weight residual 121.97 126.32 -4.35 1.80e+00 3.09e-01 5.84e+00 angle pdb=" C PRO A 84 " pdb=" N VAL A 85 " pdb=" CA VAL A 85 " ideal model delta sigma weight residual 121.97 126.30 -4.33 1.80e+00 3.09e-01 5.79e+00 ... (remaining 12649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5124 17.77 - 35.54: 429 35.54 - 53.31: 165 53.31 - 71.08: 15 71.08 - 88.85: 6 Dihedral angle restraints: 5739 sinusoidal: 2271 harmonic: 3468 Sorted by residual: dihedral pdb=" CB CYS B 326 " pdb=" SG CYS B 326 " pdb=" SG CYS B 335 " pdb=" CB CYS B 335 " ideal model delta sinusoidal sigma weight residual 93.00 123.72 -30.72 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" CB CYS C 326 " pdb=" SG CYS C 326 " pdb=" SG CYS C 335 " pdb=" CB CYS C 335 " ideal model delta sinusoidal sigma weight residual 93.00 123.70 -30.70 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" CB CYS A 326 " pdb=" SG CYS A 326 " pdb=" SG CYS A 335 " pdb=" CB CYS A 335 " ideal model delta sinusoidal sigma weight residual 93.00 123.67 -30.67 1 1.00e+01 1.00e-02 1.34e+01 ... (remaining 5736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 968 0.024 - 0.048: 307 0.048 - 0.072: 123 0.072 - 0.096: 66 0.096 - 0.120: 78 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA ILE C 57 " pdb=" N ILE C 57 " pdb=" C ILE C 57 " pdb=" CB ILE C 57 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE B 57 " pdb=" N ILE B 57 " pdb=" C ILE B 57 " pdb=" CB ILE B 57 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE C 321 " pdb=" N ILE C 321 " pdb=" C ILE C 321 " pdb=" CB ILE C 321 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 1539 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 468 " -0.007 2.00e-02 2.50e+03 6.63e-03 8.78e-01 pdb=" CG TYR C 468 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 468 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 468 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 468 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 468 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 468 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 468 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 468 " -0.007 2.00e-02 2.50e+03 6.61e-03 8.73e-01 pdb=" CG TYR A 468 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 468 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 468 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 468 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 468 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 468 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 468 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 468 " -0.007 2.00e-02 2.50e+03 6.50e-03 8.46e-01 pdb=" CG TYR B 468 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 468 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 468 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 468 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 468 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 468 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 468 " -0.000 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 433 2.73 - 3.27: 9487 3.27 - 3.82: 14639 3.82 - 4.36: 16541 4.36 - 4.90: 26898 Nonbonded interactions: 67998 Sorted by model distance: nonbonded pdb=" NH1 ARG B 388 " pdb=" O THR B 392 " model vdw 2.191 2.520 nonbonded pdb=" NH1 ARG C 388 " pdb=" O THR C 392 " model vdw 2.192 2.520 nonbonded pdb=" NH1 ARG A 388 " pdb=" O THR A 392 " model vdw 2.192 2.520 nonbonded pdb=" O SER B 186 " pdb=" OG1 THR B 189 " model vdw 2.206 2.440 nonbonded pdb=" O SER A 186 " pdb=" OG1 THR A 189 " model vdw 2.206 2.440 ... (remaining 67993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. 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: 1.910 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: 9.920 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.060 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3825 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 : 0.001 0.021 9318 Z= 0.079 Angle : 0.349 4.845 12654 Z= 0.194 Chirality : 0.039 0.120 1542 Planarity : 0.002 0.020 1617 Dihedral : 14.882 88.852 3462 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.98 % Allowed : 17.28 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1173 helix: 1.32 (0.24), residues: 414 sheet: -0.98 (0.54), residues: 87 loop : -1.02 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 303 HIS 0.000 0.000 HIS B 253 PHE 0.002 0.000 PHE A 230 TYR 0.016 0.001 TYR C 468 ARG 0.001 0.000 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.388 Fit side-chains REVERT: A 168 ASP cc_start: 0.8283 (t0) cc_final: 0.8005 (m-30) REVERT: A 273 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.4942 (pt) outliers start: 7 outliers final: 1 residues processed: 30 average time/residue: 0.1315 time to fit residues: 5.2099 Evaluate side-chains 13 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 11 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.4980 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN A 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4255 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9318 Z= 0.144 Angle : 0.554 7.021 12654 Z= 0.286 Chirality : 0.042 0.180 1542 Planarity : 0.003 0.018 1617 Dihedral : 3.564 14.992 1269 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1173 helix: 2.01 (0.24), residues: 447 sheet: -0.99 (0.52), residues: 87 loop : -0.99 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.001 0.001 HIS B 253 PHE 0.012 0.001 PHE A 230 TYR 0.007 0.001 TYR A 270 ARG 0.002 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.368 Fit side-chains REVERT: A 142 MET cc_start: 0.1687 (mmp) cc_final: 0.1212 (tpt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1070 time to fit residues: 2.5391 Evaluate side-chains 9 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.0020 chunk 32 optimal weight: 0.0270 chunk 88 optimal weight: 0.0170 chunk 72 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 85 optimal weight: 0.3980 overall best weight: 0.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4252 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9318 Z= 0.108 Angle : 0.473 7.495 12654 Z= 0.243 Chirality : 0.041 0.143 1542 Planarity : 0.002 0.013 1617 Dihedral : 3.297 14.564 1269 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 0.33 (0.25), residues: 1173 helix: 2.13 (0.24), residues: 444 sheet: -0.92 (0.52), residues: 87 loop : -1.04 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.001 0.001 HIS C 253 PHE 0.012 0.001 PHE A 230 TYR 0.012 0.001 TYR A 468 ARG 0.001 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.334 Fit side-chains REVERT: A 142 MET cc_start: 0.1710 (mmp) cc_final: 0.1455 (tpt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0883 time to fit residues: 2.3571 Evaluate side-chains 10 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 chunk 113 optimal weight: 0.0870 chunk 101 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4379 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9318 Z= 0.097 Angle : 0.448 7.168 12654 Z= 0.228 Chirality : 0.040 0.129 1542 Planarity : 0.002 0.014 1617 Dihedral : 3.207 13.027 1269 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1173 helix: 2.24 (0.24), residues: 444 sheet: -0.92 (0.52), residues: 87 loop : -0.99 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.001 HIS A 253 PHE 0.010 0.001 PHE B 230 TYR 0.012 0.001 TYR B 468 ARG 0.001 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.367 Fit side-chains REVERT: A 142 MET cc_start: 0.1363 (mmp) cc_final: 0.1157 (tpt) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1045 time to fit residues: 2.2461 Evaluate side-chains 9 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 0.0980 chunk 96 optimal weight: 0.0670 chunk 78 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 0.0470 chunk 101 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4346 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9318 Z= 0.106 Angle : 0.447 6.920 12654 Z= 0.227 Chirality : 0.040 0.124 1542 Planarity : 0.002 0.016 1617 Dihedral : 3.259 14.964 1269 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1173 helix: 2.28 (0.24), residues: 447 sheet: -0.92 (0.53), residues: 87 loop : -0.99 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 303 HIS 0.001 0.001 HIS C 253 PHE 0.010 0.001 PHE A 230 TYR 0.014 0.001 TYR C 468 ARG 0.001 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.390 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1144 time to fit residues: 2.1432 Evaluate side-chains 9 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 0.0040 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 109 optimal weight: 0.0030 overall best weight: 0.6204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4506 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9318 Z= 0.124 Angle : 0.445 5.800 12654 Z= 0.228 Chirality : 0.040 0.119 1542 Planarity : 0.002 0.017 1617 Dihedral : 3.208 13.527 1269 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1173 helix: 2.49 (0.24), residues: 444 sheet: -0.96 (0.53), residues: 87 loop : -0.98 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.000 0.000 HIS A 253 PHE 0.009 0.001 PHE B 230 TYR 0.013 0.001 TYR B 468 ARG 0.001 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.332 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1047 time to fit residues: 2.2979 Evaluate side-chains 9 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 0.0470 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 0.0980 chunk 112 optimal weight: 0.0170 chunk 70 optimal weight: 0.0040 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4350 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9318 Z= 0.097 Angle : 0.460 6.232 12654 Z= 0.234 Chirality : 0.041 0.132 1542 Planarity : 0.002 0.019 1617 Dihedral : 3.195 14.336 1269 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: 0.47 (0.25), residues: 1173 helix: 2.27 (0.24), residues: 447 sheet: -0.90 (0.54), residues: 87 loop : -0.99 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 303 HIS 0.001 0.001 HIS A 253 PHE 0.011 0.001 PHE A 475 TYR 0.008 0.001 TYR B 468 ARG 0.001 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.340 Fit side-chains REVERT: B 471 LYS cc_start: 0.6785 (tptp) cc_final: 0.5950 (mtmt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1197 time to fit residues: 2.8488 Evaluate side-chains 11 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 0.0870 chunk 71 optimal weight: 0.0270 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4723 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9318 Z= 0.175 Angle : 0.519 5.248 12654 Z= 0.271 Chirality : 0.042 0.149 1542 Planarity : 0.002 0.019 1617 Dihedral : 3.780 17.805 1269 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.91 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 0.33 (0.25), residues: 1173 helix: 2.17 (0.24), residues: 450 sheet: -1.10 (0.49), residues: 99 loop : -1.07 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.006 0.004 HIS C 253 PHE 0.010 0.001 PHE A 475 TYR 0.009 0.001 TYR A 249 ARG 0.009 0.001 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.380 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1326 time to fit residues: 2.9632 Evaluate side-chains 11 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 0.0060 chunk 32 optimal weight: 0.0270 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4606 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9318 Z= 0.108 Angle : 0.491 5.388 12654 Z= 0.252 Chirality : 0.041 0.132 1542 Planarity : 0.002 0.023 1617 Dihedral : 3.394 16.933 1269 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1173 helix: 2.11 (0.24), residues: 447 sheet: -1.18 (0.47), residues: 99 loop : -1.11 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 303 HIS 0.004 0.003 HIS A 253 PHE 0.011 0.001 PHE B 475 TYR 0.008 0.001 TYR C 468 ARG 0.002 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.372 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1348 time to fit residues: 2.8175 Evaluate side-chains 12 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.0170 chunk 67 optimal weight: 4.9990 chunk 52 optimal weight: 0.0980 chunk 77 optimal weight: 0.0570 chunk 116 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 92 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.0070 overall best weight: 0.0954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4524 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9318 Z= 0.099 Angle : 0.472 5.245 12654 Z= 0.238 Chirality : 0.041 0.141 1542 Planarity : 0.002 0.025 1617 Dihedral : 3.316 15.918 1269 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.24 (0.25), residues: 1173 helix: 2.06 (0.24), residues: 447 sheet: -0.89 (0.51), residues: 84 loop : -1.14 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 303 HIS 0.003 0.002 HIS C 253 PHE 0.015 0.001 PHE A 475 TYR 0.009 0.001 TYR A 468 ARG 0.001 0.000 ARG B 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.345 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1734 time to fit residues: 3.3236 Evaluate side-chains 12 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0980 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.0370 chunk 38 optimal weight: 0.0270 chunk 95 optimal weight: 0.1980 chunk 11 optimal weight: 0.0470 chunk 17 optimal weight: 0.1980 chunk 81 optimal weight: 0.2980 overall best weight: 0.0552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.084184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.079435 restraints weight = 25157.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.079931 restraints weight = 28258.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.080129 restraints weight = 23994.824| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4533 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.022 9318 Z= 0.095 Angle : 0.452 4.951 12654 Z= 0.226 Chirality : 0.040 0.125 1542 Planarity : 0.002 0.021 1617 Dihedral : 3.144 14.727 1269 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1173 helix: 1.52 (0.24), residues: 447 sheet: -1.43 (0.46), residues: 84 loop : -1.44 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 303 HIS 0.003 0.002 HIS C 253 PHE 0.015 0.001 PHE B 475 TYR 0.010 0.001 TYR B 468 ARG 0.001 0.000 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1529.04 seconds wall clock time: 28 minutes 24.25 seconds (1704.25 seconds total)