Starting phenix.real_space_refine on Fri Dec 8 21:39:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/12_2023/8fel_29032.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/12_2023/8fel_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_29032/12_2023/8fel_29032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/12_2023/8fel_29032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/12_2023/8fel_29032.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/12_2023/8fel_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-1.21rc1-5172/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: 5.31, per 1000 atoms: 0.58 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: 3.53 Conformation dependent library (CDL) restraints added in 2.1 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: 0.98 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: 3.76 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.980 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.070 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:3.100 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.530 ------------------------------------------------------------------------------- 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 : 0.409 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 30 average time/residue: 0.1374 time to fit residues: 5.4647 Evaluate side-chains 11 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0319 time to fit residues: 0.5516 ------------------------------------------------------------------------------- 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: 1.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 0.0370 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: 0.5258 ------------------------------------------------------------------------------- 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: 0.4189 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9318 Z= 0.140 Angle : 0.536 6.925 12654 Z= 0.278 Chirality : 0.042 0.181 1542 Planarity : 0.003 0.018 1617 Dihedral : 3.459 14.926 1269 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1173 helix: 2.03 (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 0.004 0.001 TRP C 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 B 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 : 0.356 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1407 time to fit residues: 3.0628 Evaluate side-chains 11 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4563 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 0.1980 chunk 88 optimal weight: 0.0270 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 85 optimal weight: 0.0970 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4245 moved from start: 0.2717 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= 0.107 Angle : 0.475 6.673 12654 Z= 0.246 Chirality : 0.041 0.146 1542 Planarity : 0.002 0.015 1617 Dihedral : 3.237 13.995 1269 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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: 0.36 (0.25), residues: 1173 helix: 2.13 (0.24), residues: 447 sheet: -0.84 (0.53), residues: 87 loop : -1.03 (0.25), residues: 639 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 0.011 0.001 PHE B 230 TYR 0.012 0.001 TYR B 468 ARG 0.001 0.000 ARG C 388 *********************** 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 : 0.446 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1367 time to fit residues: 3.3731 Evaluate side-chains 11 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4936 ------------------------------------------------------------------------------- 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: 3.9990 chunk 80 optimal weight: 0.0040 chunk 55 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 0.0870 chunk 101 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.2368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4288 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9318 Z= 0.105 Angle : 0.459 6.603 12654 Z= 0.235 Chirality : 0.041 0.134 1542 Planarity : 0.002 0.014 1617 Dihedral : 3.242 13.502 1269 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: 0.39 (0.25), residues: 1173 helix: 2.23 (0.24), residues: 447 sheet: -0.88 (0.53), residues: 87 loop : -1.07 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.001 HIS C 253 PHE 0.010 0.001 PHE B 230 TYR 0.013 0.001 TYR B 468 ARG 0.001 0.000 ARG A 232 *********************** 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 16 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.366 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1327 time to fit residues: 3.0832 Evaluate side-chains 11 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5068 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 0.0270 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 0.1980 chunk 96 optimal weight: 0.0070 chunk 78 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 0.0970 chunk 101 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.1054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4287 moved from start: 0.3110 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= 0.096 Angle : 0.453 7.027 12654 Z= 0.230 Chirality : 0.040 0.129 1542 Planarity : 0.002 0.015 1617 Dihedral : 3.093 12.752 1269 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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: 0.43 (0.25), residues: 1173 helix: 2.23 (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 0.001 0.000 TRP C 303 HIS 0.002 0.001 HIS B 253 PHE 0.010 0.001 PHE B 230 TYR 0.014 0.001 TYR C 468 ARG 0.001 0.000 ARG C 309 *********************** 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 13 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.481 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1675 time to fit residues: 3.3139 Evaluate side-chains 11 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4681 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.4507 moved from start: 0.3719 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= 0.120 Angle : 0.484 6.348 12654 Z= 0.249 Chirality : 0.041 0.127 1542 Planarity : 0.003 0.031 1617 Dihedral : 3.365 14.950 1269 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: 0.54 (0.25), residues: 1173 helix: 2.47 (0.24), residues: 447 sheet: -1.09 (0.52), residues: 87 loop : -1.03 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 303 HIS 0.001 0.001 HIS C 253 PHE 0.010 0.001 PHE B 230 TYR 0.012 0.001 TYR B 468 ARG 0.003 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 : 0.386 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1086 time to fit residues: 2.4036 Evaluate side-chains 9 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4976 ------------------------------------------------------------------------------- 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: 5.9990 chunk 64 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 112 optimal weight: 0.1980 chunk 70 optimal weight: 0.0980 chunk 68 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.4686 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9318 Z= 0.170 Angle : 0.529 7.112 12654 Z= 0.281 Chirality : 0.042 0.177 1542 Planarity : 0.003 0.019 1617 Dihedral : 3.671 16.379 1269 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1173 helix: 2.40 (0.25), residues: 450 sheet: -1.31 (0.46), residues: 99 loop : -0.98 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.001 HIS B 253 PHE 0.024 0.002 PHE B 475 TYR 0.008 0.001 TYR B 270 ARG 0.002 0.000 ARG C 258 *********************** 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 17 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.339 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1525 time to fit residues: 3.5565 Evaluate side-chains 12 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4663 ------------------------------------------------------------------------------- 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: 0.0980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 0.0870 chunk 102 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.4576 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9318 Z= 0.109 Angle : 0.491 5.515 12654 Z= 0.250 Chirality : 0.041 0.137 1542 Planarity : 0.002 0.022 1617 Dihedral : 3.384 13.106 1269 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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: 0.30 (0.25), residues: 1173 helix: 2.10 (0.24), residues: 447 sheet: -1.28 (0.47), residues: 99 loop : -1.00 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 303 HIS 0.003 0.002 HIS B 253 PHE 0.018 0.001 PHE B 475 TYR 0.008 0.001 TYR C 270 ARG 0.002 0.000 ARG A 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 16 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.387 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1237 time to fit residues: 2.9574 Evaluate side-chains 12 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4978 ------------------------------------------------------------------------------- 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: 0.0980 chunk 105 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 69 optimal weight: 0.0370 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.4589 moved from start: 0.4954 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= 0.110 Angle : 0.496 5.015 12654 Z= 0.256 Chirality : 0.042 0.124 1542 Planarity : 0.002 0.023 1617 Dihedral : 3.340 14.292 1269 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: 0.18 (0.25), residues: 1173 helix: 2.02 (0.24), residues: 447 sheet: -1.38 (0.46), residues: 99 loop : -1.08 (0.26), residues: 627 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 0.013 0.001 PHE B 475 TYR 0.008 0.001 TYR C 468 ARG 0.002 0.000 ARG A 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 17 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.370 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1312 time to fit residues: 3.2157 Evaluate side-chains 15 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5047 ------------------------------------------------------------------------------- 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: 0.0040 chunk 67 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 77 optimal weight: 0.4980 chunk 116 optimal weight: 0.0870 chunk 107 optimal weight: 0.0980 chunk 92 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.0170 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4456 moved from start: 0.4928 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= 0.105 Angle : 0.477 5.060 12654 Z= 0.243 Chirality : 0.041 0.122 1542 Planarity : 0.002 0.026 1617 Dihedral : 3.174 13.710 1269 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: 0.15 (0.25), residues: 1173 helix: 1.92 (0.24), residues: 447 sheet: -1.22 (0.48), residues: 84 loop : -1.08 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 303 HIS 0.003 0.002 HIS C 253 PHE 0.013 0.001 PHE C 475 TYR 0.010 0.001 TYR C 468 ARG 0.001 0.000 ARG C 388 ********************** REFINEMENT MACRO_CYCLE 10 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 17 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.416 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1441 time to fit residues: 3.5872 Evaluate side-chains 13 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5206 ------------------------------------------------------------------------------- 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: 0.2980 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 0.0670 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.0770 chunk 38 optimal weight: 0.0470 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.1774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.083675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.078787 restraints weight = 24817.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.079418 restraints weight = 29928.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.080135 restraints weight = 19736.033| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4610 moved from start: 0.4974 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= 0.100 Angle : 0.472 4.825 12654 Z= 0.241 Chirality : 0.041 0.129 1542 Planarity : 0.002 0.025 1617 Dihedral : 3.221 13.850 1269 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.75 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: 0.13 (0.25), residues: 1173 helix: 1.97 (0.24), residues: 447 sheet: -1.26 (0.49), residues: 84 loop : -1.14 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 303 HIS 0.003 0.002 HIS C 253 PHE 0.009 0.001 PHE B 475 TYR 0.010 0.001 TYR A 468 ARG 0.001 0.000 ARG A 309 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1581.99 seconds wall clock time: 29 minutes 36.38 seconds (1776.38 seconds total)