Starting phenix.real_space_refine on Fri Dec 8 03:15:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/12_2023/8wx2_37898.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/12_2023/8wx2_37898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/12_2023/8wx2_37898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/12_2023/8wx2_37898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/12_2023/8wx2_37898.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/12_2023/8wx2_37898.pdb" } resolution = 3.44 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= 0.047 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 36 5.16 5 C 4528 2.51 5 N 1110 2.21 5 O 1126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 45": "OE1" <-> "OE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 486": "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: 6800 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3400 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 3400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3400 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 4.08, per 1000 atoms: 0.60 Number of scatterers: 6800 At special positions: 0 Unit cell: (128.65, 88.81, 81.34, 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 36 16.00 O 1126 8.00 N 1110 7.00 C 4528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 526 " - pdb=" SG CYS B 536 " 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: 2.83 Conformation dependent library (CDL) restraints added in 1.3 seconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 30 through 63 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.913A pdb=" N GLN A 71 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 98 removed outlier: 3.555A pdb=" N VAL A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 100 through 123 removed outlier: 3.601A pdb=" N VAL A 104 " --> pdb=" O ARG A 100 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 123 through 131 removed outlier: 3.730A pdb=" N ARG A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 191 Processing helix chain 'A' and resid 191 through 224 removed outlier: 3.774A pdb=" N ILE A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 247 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 304 through 322 removed outlier: 3.700A pdb=" N PHE A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Proline residue: A 318 - end of helix Processing helix chain 'A' and resid 322 through 343 removed outlier: 3.826A pdb=" N TYR A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 393 removed outlier: 3.811A pdb=" N LEU A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.537A pdb=" N LEU A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 439 removed outlier: 3.643A pdb=" N TYR A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 491 through 517 removed outlier: 3.765A pdb=" N MET A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 537 through 564 removed outlier: 3.541A pdb=" N GLU A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 63 Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.913A pdb=" N GLN B 71 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 98 removed outlier: 3.555A pdb=" N VAL B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 100 through 123 removed outlier: 3.602A pdb=" N VAL B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 123 through 131 removed outlier: 3.730A pdb=" N ARG B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 191 Processing helix chain 'B' and resid 191 through 224 removed outlier: 3.774A pdb=" N ILE B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 247 Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 304 through 322 removed outlier: 3.700A pdb=" N PHE B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 315 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Proline residue: B 318 - end of helix Processing helix chain 'B' and resid 322 through 343 removed outlier: 3.827A pdb=" N TYR B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 393 removed outlier: 3.811A pdb=" N LEU B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 387 " --> pdb=" O VAL B 383 " (cutoff:3.500A) Proline residue: B 388 - end of helix Processing helix chain 'B' and resid 393 through 401 removed outlier: 3.537A pdb=" N LEU B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 439 removed outlier: 3.644A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 460 Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 491 through 517 removed outlier: 3.764A pdb=" N MET B 496 " --> pdb=" O GLN B 492 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 537 through 564 removed outlier: 3.540A pdb=" N GLU B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1566 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: 1.85 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.47: 1782 1.47 - 1.59: 3062 1.59 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6982 Sorted by residual: bond pdb=" C ALA A 487 " pdb=" N PRO A 488 " ideal model delta sigma weight residual 1.334 1.369 -0.036 2.34e-02 1.83e+03 2.31e+00 bond pdb=" C ALA B 487 " pdb=" N PRO B 488 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.17e+00 bond pdb=" C LEU B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.99e-01 bond pdb=" C LEU A 519 " pdb=" N PRO A 520 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.36e-01 bond pdb=" CA THR B 248 " pdb=" C THR B 248 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.63e-01 ... (remaining 6977 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.05: 238 107.05 - 113.78: 3853 113.78 - 120.52: 2991 120.52 - 127.26: 2344 127.26 - 133.99: 96 Bond angle restraints: 9522 Sorted by residual: angle pdb=" N PRO A 351 " pdb=" CA PRO A 351 " pdb=" CB PRO A 351 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" N PRO B 351 " pdb=" CA PRO B 351 " pdb=" CB PRO B 351 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.53e+01 angle pdb=" N ALA A 487 " pdb=" CA ALA A 487 " pdb=" C ALA A 487 " ideal model delta sigma weight residual 109.81 117.65 -7.84 2.21e+00 2.05e-01 1.26e+01 angle pdb=" N ALA B 487 " pdb=" CA ALA B 487 " pdb=" C ALA B 487 " ideal model delta sigma weight residual 109.81 117.60 -7.79 2.21e+00 2.05e-01 1.24e+01 angle pdb=" N ARG B 74 " pdb=" CA ARG B 74 " pdb=" CB ARG B 74 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 ... (remaining 9517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.95: 3528 14.95 - 29.91: 338 29.91 - 44.86: 128 44.86 - 59.81: 38 59.81 - 74.77: 4 Dihedral angle restraints: 4036 sinusoidal: 1510 harmonic: 2526 Sorted by residual: dihedral pdb=" CA ALA B 487 " pdb=" C ALA B 487 " pdb=" N PRO B 488 " pdb=" CA PRO B 488 " ideal model delta harmonic sigma weight residual -180.00 -135.20 -44.80 0 5.00e+00 4.00e-02 8.03e+01 dihedral pdb=" CA ALA A 487 " pdb=" C ALA A 487 " pdb=" N PRO A 488 " pdb=" CA PRO A 488 " ideal model delta harmonic sigma weight residual -180.00 -135.27 -44.73 0 5.00e+00 4.00e-02 8.00e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 157 " pdb=" CB CYS B 157 " ideal model delta sinusoidal sigma weight residual -86.00 -28.54 -57.46 1 1.00e+01 1.00e-02 4.44e+01 ... (remaining 4033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 917 0.049 - 0.098: 166 0.098 - 0.147: 25 0.147 - 0.196: 0 0.196 - 0.245: 2 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA PRO B 351 " pdb=" N PRO B 351 " pdb=" C PRO B 351 " pdb=" CB PRO B 351 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO A 351 " pdb=" N PRO A 351 " pdb=" C PRO A 351 " pdb=" CB PRO A 351 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PRO B 488 " pdb=" N PRO B 488 " pdb=" C PRO B 488 " pdb=" CB PRO B 488 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1107 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 487 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO A 488 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 488 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 488 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 487 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO B 488 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 488 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 488 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 118 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO B 119 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.026 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 184 2.72 - 3.26: 7458 3.26 - 3.81: 11484 3.81 - 4.35: 13588 4.35 - 4.90: 22303 Nonbonded interactions: 55017 Sorted by model distance: nonbonded pdb=" N ASN A 66 " pdb=" OD1 ASN A 66 " model vdw 2.171 2.520 nonbonded pdb=" N ASN B 66 " pdb=" OD1 ASN B 66 " model vdw 2.171 2.520 nonbonded pdb=" O PHE B 65 " pdb=" N THR B 68 " model vdw 2.206 2.520 nonbonded pdb=" O PHE A 65 " pdb=" N THR A 68 " model vdw 2.206 2.520 nonbonded pdb=" O VAL B 514 " pdb=" OG SER B 518 " model vdw 2.329 2.440 ... (remaining 55012 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 5.350 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.160 Find NCS groups from input model: 0.330 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 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 : 0.002 0.036 6982 Z= 0.146 Angle : 0.646 7.841 9522 Z= 0.357 Chirality : 0.038 0.245 1110 Planarity : 0.005 0.074 1172 Dihedral : 14.514 74.766 2400 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.51 % Favored : 93.02 % Rotamer: Outliers : 1.99 % Allowed : 14.25 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.26), residues: 860 helix: -0.96 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -3.01 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 67 HIS 0.001 0.000 HIS B 434 PHE 0.011 0.001 PHE A 65 TYR 0.013 0.001 TYR B 59 ARG 0.001 0.000 ARG B 489 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 169 average time/residue: 0.1790 time to fit residues: 40.3343 Evaluate side-chains 115 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0623 time to fit residues: 1.9287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 0.0970 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6982 Z= 0.236 Angle : 0.764 10.549 9522 Z= 0.370 Chirality : 0.042 0.153 1110 Planarity : 0.006 0.074 1172 Dihedral : 5.245 45.685 940 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.85 % Allowed : 18.95 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -0.65 (0.28), residues: 860 helix: 0.23 (0.19), residues: 704 sheet: None (None), residues: 0 loop : -3.17 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 558 HIS 0.007 0.002 HIS B 434 PHE 0.024 0.002 PHE A 244 TYR 0.023 0.002 TYR A 59 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 129 average time/residue: 0.1558 time to fit residues: 28.1403 Evaluate side-chains 115 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0661 time to fit residues: 2.5394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 22 optimal weight: 0.0770 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS A 439 ASN B 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6982 Z= 0.197 Angle : 0.732 11.624 9522 Z= 0.350 Chirality : 0.041 0.151 1110 Planarity : 0.006 0.077 1172 Dihedral : 5.205 46.795 940 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.86 % Favored : 93.02 % Rotamer: Outliers : 1.99 % Allowed : 21.37 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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 (0.29), residues: 860 helix: 0.69 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -2.48 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.005 0.001 HIS B 434 PHE 0.020 0.001 PHE A 244 TYR 0.013 0.001 TYR A 59 ARG 0.003 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 109 average time/residue: 0.1694 time to fit residues: 25.6400 Evaluate side-chains 97 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0798 time to fit residues: 1.6969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6982 Z= 0.240 Angle : 0.747 12.227 9522 Z= 0.360 Chirality : 0.043 0.205 1110 Planarity : 0.006 0.078 1172 Dihedral : 5.176 46.199 940 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.42 % Allowed : 22.08 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.14 (0.29), residues: 860 helix: 0.74 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -3.16 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 558 HIS 0.004 0.001 HIS A 434 PHE 0.022 0.002 PHE A 244 TYR 0.011 0.001 TYR B 484 ARG 0.007 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 122 average time/residue: 0.1814 time to fit residues: 29.9657 Evaluate side-chains 109 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0762 time to fit residues: 2.4710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6982 Z= 0.279 Angle : 0.784 12.125 9522 Z= 0.377 Chirality : 0.044 0.174 1110 Planarity : 0.006 0.100 1172 Dihedral : 5.455 47.817 940 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.21 % Favored : 92.67 % Rotamer: Outliers : 3.42 % Allowed : 22.65 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.24 % 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: 0.14 (0.29), residues: 860 helix: 0.79 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -3.83 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.002 0.001 HIS A 437 PHE 0.022 0.002 PHE A 244 TYR 0.014 0.002 TYR B 484 ARG 0.010 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 122 average time/residue: 0.1613 time to fit residues: 27.4763 Evaluate side-chains 101 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0744 time to fit residues: 1.9703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN B 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6982 Z= 0.221 Angle : 0.792 13.053 9522 Z= 0.372 Chirality : 0.044 0.252 1110 Planarity : 0.006 0.098 1172 Dihedral : 5.353 45.534 940 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.28 % Allowed : 24.93 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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 (0.30), residues: 860 helix: 0.94 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -3.76 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.002 0.000 HIS A 437 PHE 0.035 0.001 PHE B 198 TYR 0.014 0.001 TYR B 484 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 109 average time/residue: 0.1690 time to fit residues: 25.7274 Evaluate side-chains 102 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0724 time to fit residues: 2.4505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6982 Z= 0.208 Angle : 0.769 13.416 9522 Z= 0.364 Chirality : 0.043 0.224 1110 Planarity : 0.006 0.097 1172 Dihedral : 5.364 47.983 940 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.00 % Allowed : 26.35 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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 (0.30), residues: 860 helix: 1.06 (0.20), residues: 732 sheet: None (None), residues: 0 loop : -3.67 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.003 0.000 HIS A 437 PHE 0.023 0.001 PHE A 310 TYR 0.028 0.001 TYR B 484 ARG 0.005 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 102 average time/residue: 0.1581 time to fit residues: 22.9654 Evaluate side-chains 90 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0620 time to fit residues: 1.2235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6982 Z= 0.219 Angle : 0.821 13.568 9522 Z= 0.383 Chirality : 0.046 0.321 1110 Planarity : 0.006 0.091 1172 Dihedral : 5.295 43.998 940 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.28 % Allowed : 27.49 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.74 (0.30), residues: 860 helix: 1.16 (0.20), residues: 726 sheet: None (None), residues: 0 loop : -3.17 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.003 0.000 HIS A 437 PHE 0.044 0.001 PHE B 198 TYR 0.011 0.001 TYR B 484 ARG 0.004 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 99 average time/residue: 0.1615 time to fit residues: 22.8797 Evaluate side-chains 92 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0785 time to fit residues: 1.6009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.0980 chunk 81 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6982 Z= 0.212 Angle : 0.800 13.721 9522 Z= 0.377 Chirality : 0.046 0.342 1110 Planarity : 0.006 0.093 1172 Dihedral : 5.318 47.127 940 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.00 % Allowed : 27.35 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.72 (0.30), residues: 860 helix: 1.18 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.18 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 558 HIS 0.003 0.000 HIS A 437 PHE 0.027 0.001 PHE A 310 TYR 0.017 0.001 TYR A 111 ARG 0.005 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 102 average time/residue: 0.1682 time to fit residues: 23.9412 Evaluate side-chains 90 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0677 time to fit residues: 1.1661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6982 Z= 0.226 Angle : 0.827 13.496 9522 Z= 0.388 Chirality : 0.046 0.339 1110 Planarity : 0.006 0.090 1172 Dihedral : 5.268 43.340 940 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.28 % Allowed : 28.49 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.66 (0.30), residues: 860 helix: 1.18 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.45 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.003 0.000 HIS A 437 PHE 0.038 0.001 PHE B 202 TYR 0.009 0.001 TYR B 59 ARG 0.004 0.000 ARG B 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 93 average time/residue: 0.1577 time to fit residues: 20.7985 Evaluate side-chains 87 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0962 time to fit residues: 1.0783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.158799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.135896 restraints weight = 16948.377| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.94 r_work: 0.4083 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6982 Z= 0.232 Angle : 0.828 13.213 9522 Z= 0.389 Chirality : 0.047 0.367 1110 Planarity : 0.006 0.091 1172 Dihedral : 5.281 45.799 940 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.14 % Allowed : 29.34 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.62 (0.30), residues: 860 helix: 1.15 (0.20), residues: 724 sheet: None (None), residues: 0 loop : -3.60 (0.48), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.003 0.000 HIS A 437 PHE 0.027 0.001 PHE A 310 TYR 0.013 0.001 TYR B 484 ARG 0.004 0.000 ARG A 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1633.06 seconds wall clock time: 30 minutes 17.88 seconds (1817.88 seconds total)